Starting phenix.real_space_refine on Wed Feb 4 01:23:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzg_47329/02_2026/9dzg_47329.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzg_47329/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dzg_47329/02_2026/9dzg_47329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzg_47329/02_2026/9dzg_47329.map" model { file = "/net/cci-nas-00/data/ceres_data/9dzg_47329/02_2026/9dzg_47329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzg_47329/02_2026/9dzg_47329.cif" } 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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 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: 1.64, per 1000 atoms: 0.20 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: 0.57 Conformation dependent library (CDL) restraints added in 309.5 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: 0.19 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: 1.21 Time building geometry restraints manager: 0.72 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: 0.910 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 covalent geometry : bond 0.00289 ( 8333) covalent geometry : angle 0.59599 (11401) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.51493 ( 12) hydrogen bonds : bond 0.19332 ( 278) hydrogen bonds : angle 7.18891 ( 759) link_BETA1-4 : bond 0.00519 ( 5) link_BETA1-4 : angle 2.09688 ( 15) link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 5.54526 ( 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 : 0.268 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: 0.0756 time to fit residues: 10.5737 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 : 0.211 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.125511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.099590 restraints weight = 9404.023| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.95 r_work: 0.2849 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8348 Z= 0.127 Angle : 0.585 9.050 11440 Z= 0.287 Chirality : 0.043 0.255 1300 Planarity : 0.004 0.047 1451 Dihedral : 8.268 60.038 1364 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.35 % Allowed : 12.26 % Favored : 86.39 % 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: -1.84 (0.25), residues: 1073 helix: -1.08 (0.29), residues: 318 sheet: -1.02 (0.30), residues: 302 loop : -1.28 (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 0.012 0.001 PHE B 219 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8333) covalent geometry : angle 0.58073 (11401) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.70722 ( 12) hydrogen bonds : bond 0.04091 ( 278) hydrogen bonds : angle 5.06922 ( 759) link_BETA1-4 : bond 0.00566 ( 5) link_BETA1-4 : angle 1.88478 ( 15) link_NAG-ASN : bond 0.00385 ( 4) link_NAG-ASN : angle 1.07451 ( 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 104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.219 Fit side-chains REVERT: A 252 GLN cc_start: 0.7645 (tm-30) cc_final: 0.6938 (tp40) REVERT: B 323 ASP cc_start: 0.7848 (m-30) cc_final: 0.7560 (m-30) REVERT: B 371 ASP cc_start: 0.8036 (m-30) cc_final: 0.7324 (m-30) REVERT: B 389 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6133 (mtm180) REVERT: L 55 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7614 (tp40) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.0699 time to fit residues: 9.7953 Evaluate side-chains 95 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3287 r_free = 0.3287 target = 0.123474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097372 restraints weight = 9423.464| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.02 r_work: 0.2813 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8348 Z= 0.151 Angle : 0.574 9.680 11440 Z= 0.282 Chirality : 0.044 0.273 1300 Planarity : 0.004 0.050 1451 Dihedral : 7.184 58.242 1364 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.75 % Allowed : 13.34 % Favored : 84.91 % 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: -1.69 (0.25), residues: 1073 helix: -0.80 (0.29), residues: 312 sheet: -0.94 (0.30), residues: 301 loop : -1.31 (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 B 290 PHE 0.015 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 covalent geometry : bond 0.00375 ( 8333) covalent geometry : angle 0.56968 (11401) SS BOND : bond 0.00299 ( 6) SS BOND : angle 0.78864 ( 12) hydrogen bonds : bond 0.03971 ( 278) hydrogen bonds : angle 4.80983 ( 759) link_BETA1-4 : bond 0.00452 ( 5) link_BETA1-4 : angle 1.90394 ( 15) link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 0.99377 ( 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 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.326 Fit side-chains REVERT: A 252 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7000 (tp40) REVERT: B 274 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 371 ASP cc_start: 0.8164 (m-30) cc_final: 0.7824 (m-30) REVERT: B 389 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6235 (mtm180) REVERT: L 55 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7232 (tt0) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.0851 time to fit residues: 11.6976 Evaluate side-chains 98 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3299 r_free = 0.3299 target = 0.124606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.098751 restraints weight = 9557.856| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.98 r_work: 0.2815 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1257 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= 0.125 Angle : 0.546 9.742 11440 Z= 0.269 Chirality : 0.042 0.266 1300 Planarity : 0.004 0.048 1451 Dihedral : 6.443 57.796 1364 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.16 % Allowed : 14.15 % Favored : 83.69 % 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: -1.58 (0.25), residues: 1073 helix: -0.63 (0.30), residues: 312 sheet: -0.89 (0.30), residues: 301 loop : -1.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.010 0.001 TYR B 290 PHE 0.013 0.001 PHE A 136 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8333) covalent geometry : angle 0.54227 (11401) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.68524 ( 12) hydrogen bonds : bond 0.03354 ( 278) hydrogen bonds : angle 4.56744 ( 759) link_BETA1-4 : bond 0.00465 ( 5) link_BETA1-4 : angle 1.81992 ( 15) link_NAG-ASN : bond 0.00344 ( 4) link_NAG-ASN : angle 0.80539 ( 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 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.246 Fit side-chains REVERT: A 252 GLN cc_start: 0.7681 (tm-30) cc_final: 0.6976 (tp40) REVERT: A 389 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7338 (ppt170) REVERT: B 274 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7489 (t80) REVERT: B 323 ASP cc_start: 0.7803 (m-30) cc_final: 0.7568 (m-30) REVERT: B 389 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6202 (mtm180) REVERT: L 55 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7190 (tt0) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.0735 time to fit residues: 10.0710 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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 H residue 91 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3286 r_free = 0.3286 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098886 restraints weight = 9443.844| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.97 r_work: 0.2876 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1409 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= 0.115 Angle : 0.532 9.791 11440 Z= 0.261 Chirality : 0.042 0.260 1300 Planarity : 0.004 0.046 1451 Dihedral : 6.229 58.320 1364 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.16 % Allowed : 15.50 % 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: -1.49 (0.25), residues: 1073 helix: -0.50 (0.30), residues: 312 sheet: -0.83 (0.30), residues: 301 loop : -1.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.009 0.001 TYR B 290 PHE 0.012 0.001 PHE A 136 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8333) covalent geometry : angle 0.52783 (11401) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.68827 ( 12) hydrogen bonds : bond 0.03184 ( 278) hydrogen bonds : angle 4.45617 ( 759) link_BETA1-4 : bond 0.00465 ( 5) link_BETA1-4 : angle 1.89808 ( 15) link_NAG-ASN : bond 0.00321 ( 4) link_NAG-ASN : angle 0.76297 ( 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 104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.210 Fit side-chains REVERT: A 252 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7042 (tp40) REVERT: A 389 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7453 (ppt170) REVERT: B 274 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7494 (t80) REVERT: B 323 ASP cc_start: 0.7882 (m-30) cc_final: 0.7626 (m-30) REVERT: B 389 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6421 (mtm180) REVERT: L 55 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7232 (tt0) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.0713 time to fit residues: 9.9893 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 0.0020 chunk 39 optimal weight: 0.5980 chunk 96 optimal weight: 0.0020 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3344 r_free = 0.3344 target = 0.128227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101965 restraints weight = 9253.728| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.07 r_work: 0.2882 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8348 Z= 0.082 Angle : 0.486 9.619 11440 Z= 0.237 Chirality : 0.040 0.249 1300 Planarity : 0.004 0.043 1451 Dihedral : 5.742 56.810 1364 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.43 % Allowed : 15.63 % Favored : 81.94 % 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: -1.19 (0.25), residues: 1073 helix: -0.15 (0.30), residues: 312 sheet: -0.70 (0.30), residues: 301 loop : -1.18 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.008 0.001 TYR B 290 PHE 0.008 0.001 PHE B 172 TRP 0.007 0.001 TRP A 379 HIS 0.004 0.000 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8333) covalent geometry : angle 0.48255 (11401) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.58509 ( 12) hydrogen bonds : bond 0.02498 ( 278) hydrogen bonds : angle 4.24281 ( 759) link_BETA1-4 : bond 0.00518 ( 5) link_BETA1-4 : angle 1.58691 ( 15) link_NAG-ASN : bond 0.00380 ( 4) link_NAG-ASN : angle 0.58850 ( 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 104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.186 Fit side-chains REVERT: A 252 GLN cc_start: 0.7661 (tm-30) cc_final: 0.6917 (tp40) REVERT: A 389 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7468 (ppt170) REVERT: B 274 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7448 (t80) REVERT: B 323 ASP cc_start: 0.7889 (m-30) cc_final: 0.7604 (m-30) REVERT: B 389 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6334 (mtm180) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.0848 time to fit residues: 11.7584 Evaluate side-chains 92 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 364 LEU 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 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3312 r_free = 0.3312 target = 0.125658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099498 restraints weight = 9452.701| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.09 r_work: 0.2842 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8348 Z= 0.124 Angle : 0.530 9.820 11440 Z= 0.257 Chirality : 0.042 0.261 1300 Planarity : 0.004 0.044 1451 Dihedral : 5.844 58.035 1364 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -1.15 (0.25), residues: 1073 helix: -0.10 (0.29), residues: 312 sheet: -0.68 (0.30), residues: 301 loop : -1.15 (0.27), residues: 460 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 0.013 0.001 PHE A 136 TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8333) covalent geometry : angle 0.52569 (11401) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.70380 ( 12) hydrogen bonds : bond 0.03037 ( 278) hydrogen bonds : angle 4.22163 ( 759) link_BETA1-4 : bond 0.00421 ( 5) link_BETA1-4 : angle 1.72180 ( 15) link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 0.82024 ( 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 99 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.248 Fit side-chains REVERT: A 252 GLN cc_start: 0.7698 (tm-30) cc_final: 0.6944 (tp40) REVERT: A 389 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7465 (ppt170) REVERT: B 105 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 274 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 323 ASP cc_start: 0.7937 (m-30) cc_final: 0.7670 (m-30) REVERT: B 389 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6365 (mtm180) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.0682 time to fit residues: 9.5013 Evaluate side-chains 93 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 364 LEU 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 H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3300 r_free = 0.3300 target = 0.124730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098315 restraints weight = 9378.188| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.08 r_work: 0.2813 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8348 Z= 0.132 Angle : 0.541 9.839 11440 Z= 0.263 Chirality : 0.042 0.266 1300 Planarity : 0.004 0.046 1451 Dihedral : 5.876 57.983 1364 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.43 % Allowed : 16.71 % Favored : 80.86 % 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: -1.16 (0.25), residues: 1073 helix: -0.05 (0.29), residues: 312 sheet: -0.74 (0.30), residues: 303 loop : -1.16 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.010 0.001 TYR H 80 PHE 0.015 0.001 PHE A 136 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8333) covalent geometry : angle 0.53720 (11401) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.71427 ( 12) hydrogen bonds : bond 0.03201 ( 278) hydrogen bonds : angle 4.23685 ( 759) link_BETA1-4 : bond 0.00434 ( 5) link_BETA1-4 : angle 1.73691 ( 15) link_NAG-ASN : bond 0.00317 ( 4) link_NAG-ASN : angle 0.88871 ( 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 98 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.270 Fit side-chains REVERT: A 252 GLN cc_start: 0.7708 (tm-30) cc_final: 0.6960 (tp40) REVERT: A 344 ASP cc_start: 0.7144 (m-30) cc_final: 0.6766 (m-30) REVERT: A 389 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7407 (ppt170) REVERT: B 274 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 323 ASP cc_start: 0.7968 (m-30) cc_final: 0.7712 (m-30) REVERT: B 389 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6348 (mtm180) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.0715 time to fit residues: 9.6721 Evaluate side-chains 96 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 374 THR 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 H residue 112 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3285 r_free = 0.3285 target = 0.123816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098516 restraints weight = 9405.776| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.98 r_work: 0.2874 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8348 Z= 0.135 Angle : 0.547 9.851 11440 Z= 0.265 Chirality : 0.042 0.267 1300 Planarity : 0.004 0.046 1451 Dihedral : 5.878 58.146 1364 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.56 % Allowed : 16.58 % Favored : 80.86 % 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: -1.15 (0.25), residues: 1073 helix: -0.04 (0.29), residues: 312 sheet: -0.73 (0.30), residues: 304 loop : -1.18 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.010 0.001 TYR L 49 PHE 0.014 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 covalent geometry : bond 0.00339 ( 8333) covalent geometry : angle 0.54286 (11401) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.73879 ( 12) hydrogen bonds : bond 0.03237 ( 278) hydrogen bonds : angle 4.25339 ( 759) link_BETA1-4 : bond 0.00427 ( 5) link_BETA1-4 : angle 1.75301 ( 15) link_NAG-ASN : bond 0.00323 ( 4) link_NAG-ASN : angle 0.91545 ( 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 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.175 Fit side-chains REVERT: A 252 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7139 (tp40) REVERT: A 389 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7497 (ppt170) REVERT: B 274 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7418 (t80) REVERT: B 323 ASP cc_start: 0.8033 (m-30) cc_final: 0.7779 (m-30) REVERT: B 389 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6432 (mtm180) outliers start: 19 outliers final: 16 residues processed: 100 average time/residue: 0.0614 time to fit residues: 8.5966 Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 314 VAL 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 112 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 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 91 THR Chi-restraints excluded: chain H residue 112 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU 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: 0.0980 chunk 41 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 19 optimal weight: 0.0170 chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3322 r_free = 0.3322 target = 0.126674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.100485 restraints weight = 9392.275| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.11 r_work: 0.2857 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8348 Z= 0.087 Angle : 0.500 9.679 11440 Z= 0.242 Chirality : 0.041 0.251 1300 Planarity : 0.004 0.071 1451 Dihedral : 5.552 56.864 1364 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.29 % Allowed : 16.85 % Favored : 80.86 % 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: -0.94 (0.25), residues: 1073 helix: 0.23 (0.30), residues: 312 sheet: -0.67 (0.30), residues: 304 loop : -1.07 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.008 0.001 TYR B 290 PHE 0.007 0.001 PHE B 172 TRP 0.007 0.001 TRP A 379 HIS 0.003 0.000 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8333) covalent geometry : angle 0.49657 (11401) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.57113 ( 12) hydrogen bonds : bond 0.02657 ( 278) hydrogen bonds : angle 4.14423 ( 759) link_BETA1-4 : bond 0.00481 ( 5) link_BETA1-4 : angle 1.59292 ( 15) link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 0.72260 ( 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 99 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.301 Fit side-chains REVERT: A 252 GLN cc_start: 0.7658 (tm-30) cc_final: 0.6924 (tp40) REVERT: A 271 ARG cc_start: 0.7530 (ttt-90) cc_final: 0.7062 (ttt-90) REVERT: A 344 ASP cc_start: 0.7104 (m-30) cc_final: 0.6824 (m-30) REVERT: A 389 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7256 (ppt170) REVERT: B 274 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7452 (t80) REVERT: B 323 ASP cc_start: 0.7856 (m-30) cc_final: 0.7624 (m-30) REVERT: B 389 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6276 (mtm180) outliers start: 17 outliers final: 11 residues processed: 98 average time/residue: 0.0912 time to fit residues: 12.3043 Evaluate side-chains 92 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 314 VAL 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 112 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 364 LEU 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 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3286 r_free = 0.3286 target = 0.123854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.097324 restraints weight = 9438.306| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.09 r_work: 0.2806 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8348 Z= 0.143 Angle : 0.556 9.878 11440 Z= 0.268 Chirality : 0.043 0.266 1300 Planarity : 0.004 0.046 1451 Dihedral : 5.781 58.272 1364 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.02 % Allowed : 17.52 % Favored : 80.46 % 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: -1.02 (0.25), residues: 1073 helix: 0.16 (0.30), residues: 312 sheet: -0.68 (0.30), residues: 304 loop : -1.15 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.011 0.001 TYR L 49 PHE 0.017 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 covalent geometry : bond 0.00360 ( 8333) covalent geometry : angle 0.55210 (11401) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.78316 ( 12) hydrogen bonds : bond 0.03271 ( 278) hydrogen bonds : angle 4.21649 ( 759) link_BETA1-4 : bond 0.00416 ( 5) link_BETA1-4 : angle 1.75249 ( 15) link_NAG-ASN : bond 0.00308 ( 4) link_NAG-ASN : angle 0.94990 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.05 seconds wall clock time: 31 minutes 56.77 seconds (1916.77 seconds total)