Starting phenix.real_space_refine on Fri Jul 3 00:38:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_33865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_33865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_33865.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_33865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_33865.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_33865.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2026/7yix_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-dev-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.35, per 1000 atoms: 0.21 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: 0.68 Conformation dependent library (CDL) restraints added in 264.3 milliseconds 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: 0.37 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: 1.80 Time building geometry restraints manager: 0.96 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: 6025 17.84 - 35.69: 482 35.69 - 53.53: 77 53.53 - 71.37: 14 71.37 - 89.22: 14 Dihedral angle restraints: 6612 sinusoidal: 2574 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 6609 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 13.363 89.215 4024 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 are 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/Z covalent geometry : bond 0.00312 / 0.14 (11320) covalent geometry : angle 0.51450 / 0.27 (15358) SS BOND : bond 0.00338 / 0.16 ( 8) SS BOND : angle 1.01512 / 0.49 ( 16) hydrogen bonds : bond 0.15440 / 9.35 ( 372) hydrogen bonds : angle 5.89478 / 4.24 ( 1044) metal coordination : bond 0.00131 / 0.07 ( 6) link_BETA1-4 : bond 0.00362 / 0.18 ( 4) link_BETA1-4 : angle 0.83615 / 0.43 ( 12) link_NAG-ASN : bond 0.00209 / 0.07 ( 8) link_NAG-ASN : angle 2.11379 / 1.21 ( 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 : 0.400 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: 0.5698 time to fit residues: 87.6640 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 : 0.375 ------------------------------------------------------------------------------- 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... 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 = 0.3965 r_free = 0.3965 target = 0.153395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118823 restraints weight = 12157.753| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.29 r_work: 0.3427 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11346 Z= 0.206 Angle : 0.588 6.203 15410 Z= 0.310 Chirality : 0.046 0.283 1710 Planarity : 0.004 0.049 1980 Dihedral : 4.429 22.824 1532 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.97 % Allowed : 8.82 % Favored : 89.21 % 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 are not related in a simple way. whole: -0.59 (0.21), residues: 1404 helix: 0.16 (0.31), residues: 290 sheet: 0.69 (0.29), residues: 317 loop : -1.07 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 224 TYR 0.016 0.002 TYR B 206 PHE 0.020 0.002 PHE A 383 TRP 0.033 0.002 TRP C 77 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (11320) covalent geometry : angle 0.58184 / 0.31 (15358) SS BOND : bond 0.00394 / 0.20 ( 8) SS BOND : angle 0.85441 / 0.41 ( 16) hydrogen bonds : bond 0.05433 / 3.42 ( 372) hydrogen bonds : angle 4.83836 / 3.44 ( 1044) metal coordination : bond 0.00318 / 0.17 ( 6) link_BETA1-4 : bond 0.00143 / 0.07 ( 4) link_BETA1-4 : angle 1.10457 / 0.57 ( 12) link_NAG-ASN : bond 0.00115 / 0.05 ( 8) link_NAG-ASN : angle 2.09965 / 1.18 ( 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: 23 poor density : 114 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7291 (mtm180) REVERT: A 199 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6398 (mt0) REVERT: A 214 ASP cc_start: 0.8418 (p0) cc_final: 0.8170 (p0) REVERT: A 240 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7181 (mp0) REVERT: A 433 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7673 (mmt) REVERT: B 56 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8300 (ttm) REVERT: B 209 MET cc_start: 0.7648 (mmt) cc_final: 0.7446 (mmt) REVERT: D 140 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7649 (pt0) outliers start: 23 outliers final: 7 residues processed: 121 average time/residue: 0.5661 time to fit residues: 73.8751 Evaluate side-chains 119 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 56 MET 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: 0.6980 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3957 r_free = 0.3957 target = 0.152693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119008 restraints weight = 12073.471| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.27 r_work: 0.3432 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11346 Z= 0.159 Angle : 0.539 6.660 15410 Z= 0.283 Chirality : 0.044 0.289 1710 Planarity : 0.004 0.049 1980 Dihedral : 4.342 22.449 1532 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.57 % Allowed : 10.45 % Favored : 86.99 % 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 are not related in a simple way. whole: -0.59 (0.21), residues: 1404 helix: 0.22 (0.31), residues: 290 sheet: 0.66 (0.29), residues: 308 loop : -1.07 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 224 TYR 0.015 0.001 TYR B 206 PHE 0.015 0.002 PHE A 383 TRP 0.026 0.002 TRP C 77 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (11320) covalent geometry : angle 0.53243 / 0.28 (15358) SS BOND : bond 0.00307 / 0.16 ( 8) SS BOND : angle 0.69474 / 0.33 ( 16) hydrogen bonds : bond 0.04663 / 2.97 ( 372) hydrogen bonds : angle 4.67214 / 3.32 ( 1044) metal coordination : bond 0.00218 / 0.11 ( 6) link_BETA1-4 : bond 0.00232 / 0.12 ( 4) link_BETA1-4 : angle 1.03354 / 0.53 ( 12) link_NAG-ASN : bond 0.00188 / 0.07 ( 8) link_NAG-ASN : angle 2.01517 / 1.15 ( 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: 30 poor density : 109 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6285 (mt0) REVERT: A 214 ASP cc_start: 0.8203 (p0) cc_final: 0.7965 (p0) REVERT: A 240 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7187 (mp0) REVERT: A 351 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 433 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7645 (mmt) REVERT: D 140 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7660 (pt0) outliers start: 30 outliers final: 13 residues processed: 120 average time/residue: 0.6066 time to fit residues: 78.3321 Evaluate side-chains 122 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 234 VAL 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 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL 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: 0.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3987 r_free = 0.3987 target = 0.155644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121059 restraints weight = 12215.482| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.32 r_work: 0.3452 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11346 Z= 0.123 Angle : 0.505 7.629 15410 Z= 0.264 Chirality : 0.043 0.276 1710 Planarity : 0.004 0.048 1980 Dihedral : 4.182 21.452 1532 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.91 % Allowed : 12.24 % Favored : 84.85 % 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 are not related in a simple way. whole: -0.49 (0.22), residues: 1404 helix: 0.41 (0.31), residues: 290 sheet: 0.60 (0.29), residues: 310 loop : -0.99 (0.21), residues: 804 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 0.011 0.001 PHE A 383 TRP 0.021 0.002 TRP C 77 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (11320) covalent geometry : angle 0.49932 / 0.26 (15358) SS BOND : bond 0.00256 / 0.13 ( 8) SS BOND : angle 0.58978 / 0.28 ( 16) hydrogen bonds : bond 0.03937 / 2.53 ( 372) hydrogen bonds : angle 4.46728 / 3.17 ( 1044) metal coordination : bond 0.00166 / 0.09 ( 6) link_BETA1-4 : bond 0.00293 / 0.15 ( 4) link_BETA1-4 : angle 0.97008 / 0.49 ( 12) link_NAG-ASN : bond 0.00216 / 0.07 ( 8) link_NAG-ASN : angle 1.89483 / 1.09 ( 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 144 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7265 (mtm180) REVERT: A 199 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6239 (mt0) REVERT: A 351 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: A 404 ASP cc_start: 0.7144 (p0) cc_final: 0.6939 (p0) REVERT: A 433 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7628 (mmt) REVERT: B 240 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7035 (mp0) REVERT: B 404 ASP cc_start: 0.6959 (m-30) cc_final: 0.6713 (m-30) REVERT: C 70 GLN cc_start: 0.6612 (mp10) cc_final: 0.6292 (mp10) REVERT: D 70 GLN cc_start: 0.6240 (mp10) cc_final: 0.5986 (mp10) REVERT: D 140 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: D 169 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7318 (tt0) outliers start: 34 outliers final: 15 residues processed: 126 average time/residue: 0.5795 time to fit residues: 78.9196 Evaluate side-chains 125 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 35 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 108 MET 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 140 GLN Chi-restraints excluded: chain D residue 169 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: 4.9990 chunk 108 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3771 r_free = 0.3771 target = 0.148301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114877 restraints weight = 12342.357| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.24 r_work: 0.3308 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11346 Z= 0.215 Angle : 0.593 7.945 15410 Z= 0.308 Chirality : 0.047 0.307 1710 Planarity : 0.004 0.050 1980 Dihedral : 4.474 22.711 1532 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.25 % Allowed : 13.18 % Favored : 83.56 % 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 are not related in a simple way. whole: -0.74 (0.21), residues: 1404 helix: 0.16 (0.31), residues: 288 sheet: 0.51 (0.28), residues: 314 loop : -1.17 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.018 0.002 TYR B 206 PHE 0.019 0.002 PHE A 383 TRP 0.025 0.002 TRP C 77 HIS 0.005 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.21 (11320) covalent geometry : angle 0.58539 / 0.31 (15358) SS BOND : bond 0.00408 / 0.21 ( 8) SS BOND : angle 0.90346 / 0.45 ( 16) hydrogen bonds : bond 0.05294 / 3.39 ( 372) hydrogen bonds : angle 4.71583 / 3.35 ( 1044) metal coordination : bond 0.00304 / 0.16 ( 6) link_BETA1-4 : bond 0.00287 / 0.14 ( 4) link_BETA1-4 : angle 1.18228 / 0.60 ( 12) link_NAG-ASN : bond 0.00223 / 0.10 ( 8) link_NAG-ASN : angle 2.25106 / 1.29 ( 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: 38 poor density : 104 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8388 (ttm) REVERT: A 199 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6075 (mt0) REVERT: A 240 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7066 (mp0) REVERT: A 433 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7529 (mmt) REVERT: C 70 GLN cc_start: 0.6430 (mp10) cc_final: 0.6104 (mp10) REVERT: C 224 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7453 (mtm110) REVERT: D 140 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7698 (pt0) outliers start: 38 outliers final: 18 residues processed: 125 average time/residue: 0.6016 time to fit residues: 80.9054 Evaluate side-chains 124 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 151 LEU 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 35 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 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 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: 0.6980 chunk 77 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 0.0470 chunk 35 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3992 r_free = 0.3992 target = 0.156193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121675 restraints weight = 12195.261| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.32 r_work: 0.3460 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.203 11346 Z= 0.115 Angle : 0.491 8.960 15410 Z= 0.256 Chirality : 0.042 0.285 1710 Planarity : 0.003 0.047 1980 Dihedral : 4.143 20.975 1532 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.40 % Allowed : 14.98 % Favored : 82.62 % 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 are not related in a simple way. whole: -0.49 (0.22), residues: 1404 helix: 0.53 (0.31), residues: 290 sheet: 0.35 (0.28), residues: 328 loop : -0.96 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.015 0.001 TYR A 117 PHE 0.010 0.001 PHE A 94 TRP 0.017 0.001 TRP C 77 HIS 0.003 0.000 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (11320) covalent geometry : angle 0.48496 / 0.25 (15358) SS BOND : bond 0.00208 / 0.11 ( 8) SS BOND : angle 0.50061 / 0.24 ( 16) hydrogen bonds : bond 0.03484 / 2.26 ( 372) hydrogen bonds : angle 4.42558 / 3.14 ( 1044) metal coordination : bond 0.08269 / 4.13 ( 6) link_BETA1-4 : bond 0.00351 / 0.17 ( 4) link_BETA1-4 : angle 0.99179 / 0.50 ( 12) link_NAG-ASN : bond 0.00267 / 0.09 ( 8) link_NAG-ASN : angle 1.93655 / 1.16 ( 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 135 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8784 (ttp) cc_final: 0.8431 (ttp) REVERT: A 240 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7118 (mp0) REVERT: A 351 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: A 433 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7641 (mmt) REVERT: B 240 GLU cc_start: 0.7736 (tm-30) cc_final: 0.6994 (mp0) REVERT: B 404 ASP cc_start: 0.6970 (m-30) cc_final: 0.6731 (m-30) REVERT: B 433 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7733 (mmt) REVERT: C 70 GLN cc_start: 0.6475 (mp10) cc_final: 0.6203 (mp10) outliers start: 28 outliers final: 10 residues processed: 121 average time/residue: 0.6190 time to fit residues: 80.6269 Evaluate side-chains 116 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 125 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.0170 chunk 120 optimal weight: 0.6980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3981 r_free = 0.3981 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121411 restraints weight = 12014.130| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.28 r_work: 0.3459 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1355 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= 0.107 Angle : 0.490 8.519 15410 Z= 0.254 Chirality : 0.043 0.264 1710 Planarity : 0.003 0.047 1980 Dihedral : 4.021 20.278 1532 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.48 % Allowed : 14.81 % 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 are not related in a simple way. whole: -0.44 (0.22), residues: 1404 helix: 0.61 (0.31), residues: 290 sheet: 0.28 (0.28), residues: 332 loop : -0.88 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.013 0.001 TYR A 117 PHE 0.010 0.001 PHE A 383 TRP 0.018 0.001 TRP C 77 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (11320) covalent geometry : angle 0.48342 / 0.25 (15358) SS BOND : bond 0.00249 / 0.13 ( 8) SS BOND : angle 0.56640 / 0.28 ( 16) hydrogen bonds : bond 0.03540 / 2.29 ( 372) hydrogen bonds : angle 4.34878 / 3.08 ( 1044) metal coordination : bond 0.00328 / 0.16 ( 6) link_BETA1-4 : bond 0.00326 / 0.16 ( 4) link_BETA1-4 : angle 0.99534 / 0.51 ( 12) link_NAG-ASN : bond 0.00233 / 0.08 ( 8) link_NAG-ASN : angle 1.93686 / 1.16 ( 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: 29 poor density : 113 time to evaluate : 0.412 Fit side-chains REVERT: A 62 MET cc_start: 0.8847 (ttp) cc_final: 0.8520 (ttp) REVERT: A 192 MET cc_start: 0.8509 (mtp) cc_final: 0.8232 (mtm) REVERT: A 214 ASP cc_start: 0.8313 (p0) cc_final: 0.8042 (p0) REVERT: A 240 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7074 (mp0) REVERT: A 351 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 433 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7597 (mmt) REVERT: B 404 ASP cc_start: 0.6968 (m-30) cc_final: 0.6716 (m-30) REVERT: B 433 MET cc_start: 0.7929 (mmm) cc_final: 0.7682 (mmt) REVERT: C 96 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7245 (p) outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 0.5314 time to fit residues: 74.6653 Evaluate side-chains 130 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3995 r_free = 0.3995 target = 0.156473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121975 restraints weight = 12085.567| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.32 r_work: 0.3459 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1398 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= 0.117 Angle : 0.508 8.269 15410 Z= 0.263 Chirality : 0.043 0.262 1710 Planarity : 0.003 0.047 1980 Dihedral : 4.018 20.070 1532 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.31 % Allowed : 15.41 % Favored : 82.28 % 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 are not related in a simple way. whole: -0.44 (0.22), residues: 1404 helix: 0.62 (0.31), residues: 290 sheet: 0.28 (0.28), residues: 332 loop : -0.88 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.012 0.001 TYR B 206 PHE 0.010 0.001 PHE B 268 TRP 0.018 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (11320) covalent geometry : angle 0.49894 / 0.26 (15358) SS BOND : bond 0.00315 / 0.16 ( 8) SS BOND : angle 1.81384 / 0.91 ( 16) hydrogen bonds : bond 0.03629 / 2.35 ( 372) hydrogen bonds : angle 4.36362 / 3.09 ( 1044) metal coordination : bond 0.00146 / 0.07 ( 6) link_BETA1-4 : bond 0.00321 / 0.16 ( 4) link_BETA1-4 : angle 0.99780 / 0.51 ( 12) link_NAG-ASN : bond 0.00229 / 0.08 ( 8) link_NAG-ASN : angle 1.95608 / 1.17 ( 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 136 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.294 Fit side-chains REVERT: A 62 MET cc_start: 0.8853 (ttp) cc_final: 0.8536 (ttp) REVERT: A 192 MET cc_start: 0.8560 (mtp) cc_final: 0.8342 (mtm) REVERT: A 351 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 433 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7593 (mmt) REVERT: B 56 MET cc_start: 0.8493 (ttt) cc_final: 0.8211 (ttt) REVERT: B 240 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6802 (mp0) REVERT: B 404 ASP cc_start: 0.6976 (m-30) cc_final: 0.6722 (m-30) REVERT: B 427 GLU cc_start: 0.7686 (mp0) cc_final: 0.7309 (mp0) REVERT: B 433 MET cc_start: 0.7912 (mmm) cc_final: 0.7662 (mmt) REVERT: C 70 GLN cc_start: 0.6227 (mp10) cc_final: 0.5905 (mp10) REVERT: C 96 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7257 (p) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.6057 time to fit residues: 80.7991 Evaluate side-chains 129 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 241 LYS 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 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: 0.3980 chunk 47 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4014 r_free = 0.4014 target = 0.158284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123886 restraints weight = 12052.309| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.32 r_work: 0.3484 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1437 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= 0.092 Angle : 0.492 9.853 15410 Z= 0.254 Chirality : 0.042 0.252 1710 Planarity : 0.003 0.046 1980 Dihedral : 3.880 19.040 1532 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 15.67 % 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 are not related in a simple way. whole: -0.27 (0.22), residues: 1404 helix: 0.80 (0.32), residues: 290 sheet: 0.40 (0.28), residues: 328 loop : -0.80 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.015 0.001 TYR A 117 PHE 0.009 0.001 PHE A 94 TRP 0.017 0.001 TRP C 77 HIS 0.003 0.000 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 (11320) covalent geometry : angle 0.48293 / 0.25 (15358) SS BOND : bond 0.00192 / 0.10 ( 8) SS BOND : angle 1.89009 / 1.06 ( 16) hydrogen bonds : bond 0.03117 / 2.04 ( 372) hydrogen bonds : angle 4.23635 / 3.01 ( 1044) metal coordination : bond 0.00089 / 0.05 ( 6) link_BETA1-4 : bond 0.00365 / 0.18 ( 4) link_BETA1-4 : angle 0.95449 / 0.48 ( 12) link_NAG-ASN : bond 0.00254 / 0.09 ( 8) link_NAG-ASN : angle 1.87659 / 1.15 ( 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 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.406 Fit side-chains REVERT: A 62 MET cc_start: 0.8787 (ttp) cc_final: 0.8453 (ttp) REVERT: A 195 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6304 (pt0) REVERT: A 240 GLU cc_start: 0.7740 (tm-30) cc_final: 0.6881 (mp0) REVERT: A 351 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: A 433 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7553 (mmt) REVERT: B 240 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6741 (mp0) REVERT: B 404 ASP cc_start: 0.7018 (m-30) cc_final: 0.6768 (m-30) REVERT: B 427 GLU cc_start: 0.7627 (mp0) cc_final: 0.7243 (mp0) REVERT: B 433 MET cc_start: 0.7952 (mmm) cc_final: 0.7682 (mmt) REVERT: C 70 GLN cc_start: 0.6205 (mp10) cc_final: 0.5856 (mp10) REVERT: C 96 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7205 (p) outliers start: 25 outliers final: 13 residues processed: 132 average time/residue: 0.5266 time to fit residues: 75.1530 Evaluate side-chains 131 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU 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 241 LYS 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 167 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3970 r_free = 0.3970 target = 0.153964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120351 restraints weight = 12067.501| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.29 r_work: 0.3445 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11346 Z= 0.145 Angle : 0.552 13.613 15410 Z= 0.283 Chirality : 0.044 0.258 1710 Planarity : 0.004 0.048 1980 Dihedral : 4.070 19.932 1532 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.71 % Allowed : 16.70 % Favored : 81.59 % 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 are not related in a simple way. whole: -0.50 (0.22), residues: 1404 helix: 0.58 (0.31), residues: 290 sheet: 0.20 (0.28), residues: 332 loop : -0.91 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.013 0.001 TYR B 206 PHE 0.012 0.002 PHE B 268 TRP 0.021 0.002 TRP C 77 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11320) covalent geometry : angle 0.54130 / 0.28 (15358) SS BOND : bond 0.00315 / 0.16 ( 8) SS BOND : angle 2.15539 / 1.21 ( 16) hydrogen bonds : bond 0.04089 / 2.65 ( 372) hydrogen bonds : angle 4.41445 / 3.15 ( 1044) metal coordination : bond 0.00211 / 0.11 ( 6) link_BETA1-4 : bond 0.00316 / 0.16 ( 4) link_BETA1-4 : angle 1.05012 / 0.53 ( 12) link_NAG-ASN : bond 0.00216 / 0.08 ( 8) link_NAG-ASN : angle 2.05148 / 1.22 ( 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 125 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.265 Fit side-chains REVERT: A 62 MET cc_start: 0.8888 (ttp) cc_final: 0.8589 (ttp) REVERT: A 240 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7040 (mp0) REVERT: A 351 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 433 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7606 (mmt) REVERT: B 240 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7060 (mp0) REVERT: B 404 ASP cc_start: 0.6984 (m-30) cc_final: 0.6725 (m-30) REVERT: B 427 GLU cc_start: 0.7672 (mp0) cc_final: 0.7274 (mp0) REVERT: B 433 MET cc_start: 0.8002 (mmm) cc_final: 0.7730 (mmt) REVERT: C 70 GLN cc_start: 0.6276 (mp10) cc_final: 0.5937 (mp10) REVERT: C 96 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7286 (p) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.5599 time to fit residues: 71.5811 Evaluate side-chains 120 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 25 ASP 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 96 THR Chi-restraints excluded: chain C residue 118 THR 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 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3792 r_free = 0.3792 target = 0.150258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117042 restraints weight = 12396.361| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.20 r_work: 0.3331 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11346 Z= 0.178 Angle : 0.584 13.411 15410 Z= 0.300 Chirality : 0.045 0.286 1710 Planarity : 0.004 0.048 1980 Dihedral : 4.299 21.181 1532 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.63 % Allowed : 16.78 % Favored : 81.59 % 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 are not related in a simple way. whole: -0.66 (0.22), residues: 1404 helix: 0.40 (0.31), residues: 290 sheet: 0.17 (0.28), residues: 332 loop : -1.03 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.015 0.002 TYR B 206 PHE 0.013 0.002 PHE B 268 TRP 0.024 0.002 TRP C 77 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (11320) covalent geometry : angle 0.57300 / 0.30 (15358) SS BOND : bond 0.00354 / 0.18 ( 8) SS BOND : angle 2.34808 / 1.33 ( 16) hydrogen bonds : bond 0.04622 / 2.98 ( 372) hydrogen bonds : angle 4.56874 / 3.26 ( 1044) metal coordination : bond 0.00271 / 0.14 ( 6) link_BETA1-4 : bond 0.00266 / 0.13 ( 4) link_BETA1-4 : angle 1.12133 / 0.57 ( 12) link_NAG-ASN : bond 0.00220 / 0.09 ( 8) link_NAG-ASN : angle 2.19429 / 1.30 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.31 seconds wall clock time: 57 minutes 35.83 seconds (3455.83 seconds total)