Starting phenix.real_space_refine on Sat Aug 23 09:33:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yix_33865/08_2025/7yix_33865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yix_33865/08_2025/7yix_33865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yix_33865/08_2025/7yix_33865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yix_33865/08_2025/7yix_33865.map" model { file = "/net/cci-nas-00/data/ceres_data/7yix_33865/08_2025/7yix_33865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yix_33865/08_2025/7yix_33865.cif" } resolution = 2.96 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= 0.142 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 Mg 2 5.21 5 S 54 5.16 5 C 6928 2.51 5 N 1914 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11080 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3738 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain: "B" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3738 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain: "C" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1708 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1720 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 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: "G" 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: "H" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 1, ' MG': 1, ' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 1, ' MG': 1, ' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.03, per 1000 atoms: 0.27 Number of scatterers: 11080 At special positions: 0 Unit cell: (143, 84.7, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 54 16.00 Mg 2 11.99 O 2176 8.00 N 1914 7.00 C 6928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 497 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 251 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 251 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 601 " - " ASN A 140 " " NAG A 602 " - " ASN A 303 " " NAG B 601 " - " ASN B 140 " " NAG B 602 " - " ASN B 303 " " NAG E 1 " - " ASN A 271 " " NAG F 1 " - " ASN A 430 " " NAG G 1 " - " ASN B 271 " " NAG H 1 " - " ASN B 430 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 583.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 454 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 341 " pdb=" ZN A 606 " pdb="ZN ZN A 606 " - pdb=" NE2 HIS A 379 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 341 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 454 " pdb=" ZN B 606 " pdb="ZN ZN B 606 " - pdb=" ND1 HIS B 379 " 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 26.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 25 through 43 removed outlier: 3.908A pdb=" N TRP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.889A pdb=" N HIS A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.839A pdb=" N THR A 141 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.754A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 343 removed outlier: 4.278A pdb=" N HIS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 removed outlier: 3.862A pdb=" N ALA A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 365 " --> pdb=" O GLN A 361 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.082A pdb=" N LEU A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 471' Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.587A pdb=" N VAL A 483 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 25 through 43 removed outlier: 4.050A pdb=" N TRP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.573A pdb=" N THR B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.792A pdb=" N THR B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.864A pdb=" N THR B 141 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 142 " --> pdb=" O CYS B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.599A pdb=" N TRP B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.580A pdb=" N MET B 192 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.525A pdb=" N GLN B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.798A pdb=" N TYR B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 226 " --> pdb=" O ARG B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.559A pdb=" N LYS B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 277 through 278 No H-bonds generated for 'chain 'B' and resid 277 through 278' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.756A pdb=" N VAL B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.195A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 342 " --> pdb=" O HIS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 366 removed outlier: 3.717A pdb=" N ALA B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 467 through 471 removed outlier: 4.037A pdb=" N LEU B 470 " --> pdb=" O MET B 467 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 467 through 471' Processing helix chain 'B' and resid 478 through 488 removed outlier: 4.373A pdb=" N HIS B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 483 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.648A pdb=" N TYR C 59 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 4.228A pdb=" N PHE C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.612A pdb=" N TYR D 59 " --> pdb=" O PHE D 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.640A pdb=" N ILE A 218 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 217 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 221 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 167 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 54 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL A 331 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET A 56 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY A 333 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 58 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 377 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 460 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS A 475 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 97 " --> pdb=" O HIS A 475 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 removed outlier: 4.123A pdb=" N SER A 380 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 385 removed outlier: 7.319A pdb=" N SER A 445 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY A 416 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 447 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.674A pdb=" N GLU A 427 " --> pdb=" O VAL A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.614A pdb=" N ILE B 218 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY B 221 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 167 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 377 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA B 460 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 94 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N HIS B 475 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 97 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 383 through 385 Processing sheet with id=AA7, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.873A pdb=" N GLU B 427 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 33 Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.743A pdb=" N ILE C 61 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP C 77 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP C 63 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.639A pdb=" N TYR C 137 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.824A pdb=" N ASP C 233 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.879A pdb=" N VAL C 174 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 196 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR C 212 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP C 198 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.879A pdb=" N VAL C 174 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR C 260 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 33 Processing sheet with id=AB7, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.692A pdb=" N GLU D 37 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE D 61 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP D 77 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP D 63 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.692A pdb=" N GLU D 37 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.208A pdb=" N ASP D 233 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 230 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 216 through 217 removed outlier: 6.631A pdb=" N TRP D 198 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR D 212 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU D 196 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 260 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 removed outlier: 6.631A pdb=" N TRP D 198 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR D 212 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU D 196 " --> pdb=" O TYR D 212 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1044 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: 1.96 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3646 1.34 - 1.46: 2639 1.46 - 1.58: 4945 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11320 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 11315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15083 1.64 - 3.28: 252 3.28 - 4.92: 19 4.92 - 6.56: 3 6.56 - 8.20: 1 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N GLU A 351 " pdb=" CA GLU A 351 " pdb=" CB GLU A 351 " ideal model delta sigma weight residual 110.28 114.61 -4.33 1.55e+00 4.16e-01 7.80e+00 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 124.50 -8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" C VAL A 447 " pdb=" CA VAL A 447 " pdb=" CB VAL A 447 " ideal model delta sigma weight residual 110.13 112.40 -2.27 9.70e-01 1.06e+00 5.47e+00 angle pdb=" C HIS A 350 " pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta sigma weight residual 120.31 116.96 3.35 1.52e+00 4.33e-01 4.85e+00 angle pdb=" C LEU A 18 " pdb=" N VAL A 19 " pdb=" CA VAL A 19 " ideal model delta sigma weight residual 122.13 126.12 -3.99 1.85e+00 2.92e-01 4.66e+00 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6247 17.84 - 35.69: 489 35.69 - 53.53: 96 53.53 - 71.37: 18 71.37 - 89.22: 14 Dihedral angle restraints: 6864 sinusoidal: 2826 harmonic: 4038 Sorted by residual: dihedral pdb=" CB CYS B 489 " pdb=" SG CYS B 489 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual -86.00 -168.64 82.64 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 489 " pdb=" SG CYS A 489 " pdb=" SG CYS A 497 " pdb=" CB CYS A 497 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS A 139 " pdb=" SG CYS A 139 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual -86.00 -143.29 57.29 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1515 0.068 - 0.136: 190 0.136 - 0.204: 4 0.204 - 0.271: 0 0.271 - 0.339: 1 Chirality restraints: 1710 Sorted by residual: chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 303 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA GLU A 351 " pdb=" N GLU A 351 " pdb=" C GLU A 351 " pdb=" CB GLU A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB VAL A 19 " pdb=" CA VAL A 19 " pdb=" CG1 VAL A 19 " pdb=" CG2 VAL A 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1707 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 77 " -0.016 2.00e-02 2.50e+03 1.48e-02 5.47e+00 pdb=" CG TRP C 77 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 77 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 77 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 77 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 77 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 77 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 77 " 0.015 2.00e-02 2.50e+03 1.29e-02 4.14e+00 pdb=" CG TRP D 77 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 77 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 77 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 80 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO B 81 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.026 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 69 2.58 - 3.16: 8446 3.16 - 3.74: 15812 3.74 - 4.32: 22740 4.32 - 4.90: 40197 Nonbonded interactions: 87264 Sorted by model distance: nonbonded pdb=" OD2 ASP B 337 " pdb="ZN ZN B 604 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP B 60 " pdb="ZN ZN B 606 " model vdw 2.088 2.230 nonbonded pdb=" OD1 ASP A 378 " pdb="ZN ZN A 606 " model vdw 2.119 2.230 nonbonded pdb=" OD2 ASP B 60 " pdb="MG MG B 603 " model vdw 2.147 2.170 nonbonded pdb=" OD2 ASP A 60 " pdb="MG MG A 603 " model vdw 2.155 2.170 ... (remaining 87259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 28 through 146 or resid 164 through 269)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.610 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 0.032 11346 Z= 0.141 Angle : 0.522 8.203 15410 Z= 0.274 Chirality : 0.044 0.339 1710 Planarity : 0.003 0.047 1980 Dihedral : 13.438 89.215 4276 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.34 (0.22), residues: 1404 helix: 0.54 (0.32), residues: 280 sheet: 0.61 (0.28), residues: 322 loop : -0.86 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.011 0.001 TYR A 117 PHE 0.012 0.001 PHE A 383 TRP 0.040 0.002 TRP C 77 HIS 0.007 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00312 (11320) covalent geometry : angle 0.51450 (15358) SS BOND : bond 0.00338 ( 8) SS BOND : angle 1.01512 ( 16) hydrogen bonds : bond 0.15440 ( 372) hydrogen bonds : angle 5.89478 ( 1044) metal coordination : bond 0.00131 ( 6) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 0.83615 ( 12) link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 2.11379 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 195 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6580 (pt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.6647 time to fit residues: 102.0563 Evaluate side-chains 117 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 300 ASN B 282 ASN ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118504 restraints weight = 12042.601| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.27 r_work: 0.3425 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11346 Z= 0.207 Angle : 0.582 6.153 15410 Z= 0.307 Chirality : 0.046 0.289 1710 Planarity : 0.004 0.049 1980 Dihedral : 6.172 57.416 1784 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.88 % Allowed : 8.65 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.58 (0.21), residues: 1404 helix: 0.18 (0.31), residues: 290 sheet: 0.59 (0.28), residues: 323 loop : -1.03 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 224 TYR 0.015 0.002 TYR B 206 PHE 0.020 0.002 PHE A 383 TRP 0.032 0.002 TRP C 77 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00515 (11320) covalent geometry : angle 0.57565 (15358) SS BOND : bond 0.00376 ( 8) SS BOND : angle 0.84971 ( 16) hydrogen bonds : bond 0.05414 ( 372) hydrogen bonds : angle 4.85863 ( 1044) metal coordination : bond 0.00294 ( 6) link_BETA1-4 : bond 0.00293 ( 4) link_BETA1-4 : angle 1.05663 ( 12) link_NAG-ASN : bond 0.00117 ( 8) link_NAG-ASN : angle 2.05933 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7248 (mtm180) REVERT: A 199 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6421 (mt0) REVERT: A 214 ASP cc_start: 0.8380 (p0) cc_final: 0.8149 (p0) REVERT: A 240 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7169 (mp0) REVERT: A 433 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: C 267 LEU cc_start: 0.8225 (tt) cc_final: 0.8022 (tt) REVERT: D 140 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7620 (pt0) outliers start: 22 outliers final: 8 residues processed: 122 average time/residue: 0.6464 time to fit residues: 85.0073 Evaluate side-chains 121 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120456 restraints weight = 12052.586| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.21 r_work: 0.3453 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11346 Z= 0.136 Angle : 0.516 6.634 15410 Z= 0.272 Chirality : 0.044 0.291 1710 Planarity : 0.004 0.048 1980 Dihedral : 5.761 56.037 1784 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.40 % Allowed : 10.27 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.51 (0.22), residues: 1404 helix: 0.32 (0.31), residues: 290 sheet: 0.68 (0.29), residues: 308 loop : -1.01 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 224 TYR 0.013 0.001 TYR B 206 PHE 0.013 0.002 PHE A 383 TRP 0.024 0.002 TRP C 77 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00331 (11320) covalent geometry : angle 0.51039 (15358) SS BOND : bond 0.00276 ( 8) SS BOND : angle 0.61634 ( 16) hydrogen bonds : bond 0.04287 ( 372) hydrogen bonds : angle 4.59220 ( 1044) metal coordination : bond 0.00186 ( 6) link_BETA1-4 : bond 0.00306 ( 4) link_BETA1-4 : angle 1.01244 ( 12) link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 1.92604 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: A 214 ASP cc_start: 0.8276 (p0) cc_final: 0.7875 (p0) REVERT: A 240 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7154 (mp0) REVERT: A 351 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 433 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7602 (mmt) REVERT: D 70 GLN cc_start: 0.6359 (mp10) cc_final: 0.6159 (mp10) REVERT: D 140 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7616 (pt0) outliers start: 28 outliers final: 15 residues processed: 121 average time/residue: 0.6629 time to fit residues: 86.2695 Evaluate side-chains 126 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 87 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121415 restraints weight = 12214.074| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.38 r_work: 0.3453 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11346 Z= 0.110 Angle : 0.487 7.164 15410 Z= 0.255 Chirality : 0.043 0.279 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.458 55.575 1784 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.48 % Allowed : 11.56 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.40 (0.22), residues: 1404 helix: 0.51 (0.31), residues: 290 sheet: 0.64 (0.29), residues: 310 loop : -0.94 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 224 TYR 0.012 0.001 TYR A 117 PHE 0.010 0.001 PHE A 94 TRP 0.021 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00263 (11320) covalent geometry : angle 0.48108 (15358) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.53658 ( 16) hydrogen bonds : bond 0.03710 ( 372) hydrogen bonds : angle 4.39121 ( 1044) metal coordination : bond 0.00141 ( 6) link_BETA1-4 : bond 0.00301 ( 4) link_BETA1-4 : angle 0.94846 ( 12) link_NAG-ASN : bond 0.00228 ( 8) link_NAG-ASN : angle 1.84457 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7260 (mtm180) REVERT: A 199 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6170 (mt0) REVERT: A 214 ASP cc_start: 0.8177 (p0) cc_final: 0.7821 (p0) REVERT: A 404 ASP cc_start: 0.7014 (p0) cc_final: 0.6802 (p0) REVERT: A 433 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7603 (mmt) REVERT: B 219 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7185 (mmt) REVERT: B 404 ASP cc_start: 0.6924 (m-30) cc_final: 0.6638 (m-30) REVERT: C 70 GLN cc_start: 0.6469 (mp10) cc_final: 0.6211 (mp10) REVERT: D 140 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7631 (pt0) outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 0.6693 time to fit residues: 86.9684 Evaluate side-chains 123 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 0.0050 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118272 restraints weight = 12020.128| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.26 r_work: 0.3421 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11346 Z= 0.178 Angle : 0.561 8.627 15410 Z= 0.291 Chirality : 0.045 0.293 1710 Planarity : 0.004 0.049 1980 Dihedral : 5.587 57.773 1784 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.17 % Allowed : 12.41 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.59 (0.21), residues: 1404 helix: 0.33 (0.31), residues: 288 sheet: 0.45 (0.28), residues: 320 loop : -1.03 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.017 0.002 TYR B 206 PHE 0.017 0.002 PHE A 383 TRP 0.024 0.002 TRP C 77 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00444 (11320) covalent geometry : angle 0.55367 (15358) SS BOND : bond 0.00374 ( 8) SS BOND : angle 0.83575 ( 16) hydrogen bonds : bond 0.04864 ( 372) hydrogen bonds : angle 4.60805 ( 1044) metal coordination : bond 0.00239 ( 6) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 1.11549 ( 12) link_NAG-ASN : bond 0.00220 ( 8) link_NAG-ASN : angle 2.13755 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8339 (ttm) REVERT: A 192 MET cc_start: 0.8497 (mtp) cc_final: 0.8099 (mtp) REVERT: A 199 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6020 (mt0) REVERT: A 214 ASP cc_start: 0.8124 (p0) cc_final: 0.7723 (p0) REVERT: A 240 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7131 (mp0) REVERT: A 351 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: A 433 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7645 (mmt) REVERT: B 240 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7052 (mp0) REVERT: D 70 GLN cc_start: 0.6263 (mp10) cc_final: 0.5918 (mp10) REVERT: D 140 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7691 (pt0) outliers start: 37 outliers final: 16 residues processed: 123 average time/residue: 0.6389 time to fit residues: 84.6622 Evaluate side-chains 123 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 454 HIS D 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122433 restraints weight = 12206.775| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.40 r_work: 0.3461 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 11346 Z= 0.110 Angle : 0.476 9.149 15410 Z= 0.248 Chirality : 0.042 0.276 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.265 54.758 1784 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 14.04 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.36 (0.22), residues: 1404 helix: 0.67 (0.32), residues: 290 sheet: 0.37 (0.28), residues: 328 loop : -0.85 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 224 TYR 0.015 0.001 TYR A 117 PHE 0.010 0.001 PHE A 94 TRP 0.016 0.001 TRP C 77 HIS 0.003 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00217 (11320) covalent geometry : angle 0.47007 (15358) SS BOND : bond 0.00201 ( 8) SS BOND : angle 0.46315 ( 16) hydrogen bonds : bond 0.03316 ( 372) hydrogen bonds : angle 4.32882 ( 1044) metal coordination : bond 0.07684 ( 6) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 0.96571 ( 12) link_NAG-ASN : bond 0.00262 ( 8) link_NAG-ASN : angle 1.85954 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: A 192 MET cc_start: 0.8425 (mtp) cc_final: 0.8177 (mtm) REVERT: A 214 ASP cc_start: 0.8032 (p0) cc_final: 0.7726 (p0) REVERT: A 240 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7032 (mp0) REVERT: A 433 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7630 (mmt) REVERT: B 404 ASP cc_start: 0.6939 (m-30) cc_final: 0.6669 (m-30) REVERT: C 70 GLN cc_start: 0.6213 (mp10) cc_final: 0.5965 (mp10) REVERT: D 70 GLN cc_start: 0.6143 (mp10) cc_final: 0.5866 (mp10) outliers start: 32 outliers final: 16 residues processed: 130 average time/residue: 0.6365 time to fit residues: 89.1777 Evaluate side-chains 128 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122196 restraints weight = 12015.710| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.22 r_work: 0.3473 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11346 Z= 0.106 Angle : 0.485 8.869 15410 Z= 0.251 Chirality : 0.042 0.267 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.201 55.277 1784 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.57 % Allowed : 14.47 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.32 (0.22), residues: 1404 helix: 0.68 (0.31), residues: 290 sheet: 0.38 (0.28), residues: 328 loop : -0.81 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.012 0.001 TYR B 206 PHE 0.010 0.001 PHE A 268 TRP 0.019 0.001 TRP C 77 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00256 (11320) covalent geometry : angle 0.47853 (15358) SS BOND : bond 0.00239 ( 8) SS BOND : angle 0.55566 ( 16) hydrogen bonds : bond 0.03521 ( 372) hydrogen bonds : angle 4.32364 ( 1044) metal coordination : bond 0.00175 ( 6) link_BETA1-4 : bond 0.00312 ( 4) link_BETA1-4 : angle 1.00170 ( 12) link_NAG-ASN : bond 0.00235 ( 8) link_NAG-ASN : angle 1.90186 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.476 Fit side-chains REVERT: A 62 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8564 (ttp) REVERT: A 214 ASP cc_start: 0.7952 (p0) cc_final: 0.7717 (p0) REVERT: A 433 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7621 (mmt) REVERT: B 240 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6793 (mp0) REVERT: B 404 ASP cc_start: 0.6942 (m-30) cc_final: 0.6687 (m-30) REVERT: C 70 GLN cc_start: 0.6237 (mp10) cc_final: 0.5946 (mp10) REVERT: D 70 GLN cc_start: 0.6358 (mp10) cc_final: 0.5864 (mp10) outliers start: 30 outliers final: 17 residues processed: 128 average time/residue: 0.6424 time to fit residues: 88.6172 Evaluate side-chains 129 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122808 restraints weight = 12032.433| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.32 r_work: 0.3474 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11346 Z= 0.107 Angle : 0.493 8.842 15410 Z= 0.254 Chirality : 0.043 0.262 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.166 55.134 1784 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.31 % Allowed : 14.98 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.30 (0.22), residues: 1404 helix: 0.73 (0.32), residues: 290 sheet: 0.39 (0.28), residues: 328 loop : -0.81 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.012 0.001 TYR B 206 PHE 0.010 0.001 PHE A 268 TRP 0.018 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00258 (11320) covalent geometry : angle 0.48380 (15358) SS BOND : bond 0.00304 ( 8) SS BOND : angle 1.73868 ( 16) hydrogen bonds : bond 0.03476 ( 372) hydrogen bonds : angle 4.31326 ( 1044) metal coordination : bond 0.00136 ( 6) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.00464 ( 12) link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 1.90348 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.500 Fit side-chains REVERT: A 214 ASP cc_start: 0.7933 (p0) cc_final: 0.7698 (p0) REVERT: A 240 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6864 (mp0) REVERT: A 433 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7598 (mmt) REVERT: B 240 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6936 (mp0) REVERT: B 404 ASP cc_start: 0.6954 (m-30) cc_final: 0.6700 (m-30) REVERT: C 70 GLN cc_start: 0.6238 (mp10) cc_final: 0.5993 (mp10) REVERT: D 70 GLN cc_start: 0.6363 (mp10) cc_final: 0.5910 (mp10) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.6337 time to fit residues: 87.3458 Evaluate side-chains 132 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 chunk 16 optimal weight: 0.9980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125862 restraints weight = 11997.804| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.41 r_work: 0.3503 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11346 Z= 0.079 Angle : 0.466 9.430 15410 Z= 0.240 Chirality : 0.041 0.244 1710 Planarity : 0.003 0.046 1980 Dihedral : 4.974 54.224 1784 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 15.33 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.11 (0.22), residues: 1404 helix: 0.95 (0.32), residues: 290 sheet: 0.46 (0.29), residues: 328 loop : -0.68 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.017 0.001 TYR B 117 PHE 0.009 0.001 PHE A 94 TRP 0.017 0.001 TRP C 77 HIS 0.002 0.000 HIS B 496 Details of bonding type rmsd covalent geometry : bond 0.00179 (11320) covalent geometry : angle 0.45687 (15358) SS BOND : bond 0.00168 ( 8) SS BOND : angle 1.78398 ( 16) hydrogen bonds : bond 0.02733 ( 372) hydrogen bonds : angle 4.13167 ( 1044) metal coordination : bond 0.00063 ( 6) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 0.92396 ( 12) link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 1.75642 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.432 Fit side-chains REVERT: A 195 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6253 (pt0) REVERT: A 214 ASP cc_start: 0.7875 (p0) cc_final: 0.7648 (p0) REVERT: A 240 GLU cc_start: 0.7635 (tm-30) cc_final: 0.6731 (mp0) REVERT: A 433 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7570 (mmt) REVERT: B 138 ARG cc_start: 0.7236 (mtp85) cc_final: 0.6829 (ttm-80) REVERT: B 404 ASP cc_start: 0.7021 (m-30) cc_final: 0.6740 (m-30) REVERT: C 70 GLN cc_start: 0.6181 (mp10) cc_final: 0.5952 (mp10) REVERT: C 96 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7231 (p) REVERT: D 70 GLN cc_start: 0.6282 (mp10) cc_final: 0.5814 (mp10) outliers start: 22 outliers final: 12 residues processed: 138 average time/residue: 0.6354 time to fit residues: 94.6872 Evaluate side-chains 130 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 11 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 6 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125056 restraints weight = 12082.724| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.34 r_work: 0.3496 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11346 Z= 0.096 Angle : 0.488 9.850 15410 Z= 0.251 Chirality : 0.042 0.238 1710 Planarity : 0.003 0.046 1980 Dihedral : 4.978 54.487 1784 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.54 % Allowed : 16.27 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.14 (0.22), residues: 1404 helix: 0.88 (0.32), residues: 290 sheet: 0.47 (0.29), residues: 328 loop : -0.69 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.013 0.001 TYR B 117 PHE 0.009 0.001 PHE A 94 TRP 0.019 0.001 TRP C 77 HIS 0.009 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00228 (11320) covalent geometry : angle 0.47881 (15358) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.95849 ( 16) hydrogen bonds : bond 0.03106 ( 372) hydrogen bonds : angle 4.15530 ( 1044) metal coordination : bond 0.00217 ( 6) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 0.97205 ( 12) link_NAG-ASN : bond 0.00231 ( 8) link_NAG-ASN : angle 1.83957 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6770 (mp0) REVERT: A 433 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7580 (mmt) REVERT: B 138 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6857 (ttm-80) REVERT: B 240 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6749 (mp0) REVERT: B 404 ASP cc_start: 0.7032 (m-30) cc_final: 0.6753 (m-30) REVERT: C 96 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7280 (p) REVERT: D 70 GLN cc_start: 0.6317 (mp10) cc_final: 0.5846 (mp10) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.6784 time to fit residues: 90.6910 Evaluate side-chains 125 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123130 restraints weight = 11984.370| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.21 r_work: 0.3483 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11346 Z= 0.120 Angle : 0.521 9.971 15410 Z= 0.268 Chirality : 0.043 0.242 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.064 55.280 1784 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.80 % Allowed : 16.01 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.22 (0.22), residues: 1404 helix: 0.78 (0.32), residues: 290 sheet: 0.44 (0.29), residues: 328 loop : -0.75 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.011 0.001 TYR B 206 PHE 0.011 0.001 PHE A 268 TRP 0.021 0.001 TRP C 77 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00293 (11320) covalent geometry : angle 0.51169 (15358) SS BOND : bond 0.00252 ( 8) SS BOND : angle 1.97123 ( 16) hydrogen bonds : bond 0.03555 ( 372) hydrogen bonds : angle 4.26438 ( 1044) metal coordination : bond 0.00165 ( 6) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 1.01783 ( 12) link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 1.92361 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3860.99 seconds wall clock time: 66 minutes 45.71 seconds (4005.71 seconds total)