Starting phenix.real_space_refine on Tue Jul 29 08:44:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yix_33865/07_2025/7yix_33865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yix_33865/07_2025/7yix_33865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2025/7yix_33865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2025/7yix_33865.map" model { file = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2025/7yix_33865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yix_33865/07_2025/7yix_33865.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11080 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3738 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain: "B" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3738 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain: "C" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1708 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1720 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 1, ' MG': 1, ' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 1, ' MG': 1, ' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.97, per 1000 atoms: 0.63 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: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.51 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: 3.41 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3646 1.34 - 1.46: 2639 1.46 - 1.58: 4945 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11320 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 11315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15083 1.64 - 3.28: 252 3.28 - 4.92: 19 4.92 - 6.56: 3 6.56 - 8.20: 1 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N GLU A 351 " pdb=" CA GLU A 351 " pdb=" CB GLU A 351 " ideal model delta sigma weight residual 110.28 114.61 -4.33 1.55e+00 4.16e-01 7.80e+00 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 124.50 -8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" C VAL A 447 " pdb=" CA VAL A 447 " pdb=" CB VAL A 447 " ideal model delta sigma weight residual 110.13 112.40 -2.27 9.70e-01 1.06e+00 5.47e+00 angle pdb=" C HIS A 350 " pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta sigma weight residual 120.31 116.96 3.35 1.52e+00 4.33e-01 4.85e+00 angle pdb=" C LEU A 18 " pdb=" N VAL A 19 " pdb=" CA VAL A 19 " ideal model delta sigma weight residual 122.13 126.12 -3.99 1.85e+00 2.92e-01 4.66e+00 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6247 17.84 - 35.69: 489 35.69 - 53.53: 96 53.53 - 71.37: 18 71.37 - 89.22: 14 Dihedral angle restraints: 6864 sinusoidal: 2826 harmonic: 4038 Sorted by residual: dihedral pdb=" CB CYS B 489 " pdb=" SG CYS B 489 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual -86.00 -168.64 82.64 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 489 " pdb=" SG CYS A 489 " pdb=" SG CYS A 497 " pdb=" CB CYS A 497 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS A 139 " pdb=" SG CYS A 139 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual -86.00 -143.29 57.29 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1515 0.068 - 0.136: 190 0.136 - 0.204: 4 0.204 - 0.271: 0 0.271 - 0.339: 1 Chirality restraints: 1710 Sorted by residual: chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 303 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA GLU A 351 " pdb=" N GLU A 351 " pdb=" C GLU A 351 " pdb=" CB GLU A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB VAL A 19 " pdb=" CA VAL A 19 " pdb=" CG1 VAL A 19 " pdb=" CG2 VAL A 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1707 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 77 " -0.016 2.00e-02 2.50e+03 1.48e-02 5.47e+00 pdb=" CG TRP C 77 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 77 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 77 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 77 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 77 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 77 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 77 " 0.015 2.00e-02 2.50e+03 1.29e-02 4.14e+00 pdb=" CG TRP D 77 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 77 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 77 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 77 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 80 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO B 81 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.026 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 69 2.58 - 3.16: 8446 3.16 - 3.74: 15812 3.74 - 4.32: 22740 4.32 - 4.90: 40197 Nonbonded interactions: 87264 Sorted by model distance: nonbonded pdb=" OD2 ASP B 337 " pdb="ZN ZN B 604 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP B 60 " pdb="ZN ZN B 606 " model vdw 2.088 2.230 nonbonded pdb=" OD1 ASP A 378 " pdb="ZN ZN A 606 " model vdw 2.119 2.230 nonbonded pdb=" OD2 ASP B 60 " pdb="MG MG B 603 " model vdw 2.147 2.170 nonbonded pdb=" OD2 ASP A 60 " pdb="MG MG A 603 " model vdw 2.155 2.170 ... (remaining 87259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 28 through 146 or resid 164 through 269)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.580 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11346 Z= 0.141 Angle : 0.522 8.203 15410 Z= 0.274 Chirality : 0.044 0.339 1710 Planarity : 0.003 0.047 1980 Dihedral : 13.438 89.215 4276 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (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 TRP 0.040 0.002 TRP C 77 HIS 0.007 0.001 HIS A 379 PHE 0.012 0.001 PHE A 383 TYR 0.011 0.001 TYR A 117 ARG 0.003 0.000 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 2.11379 ( 24) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 0.83615 ( 12) hydrogen bonds : bond 0.15440 ( 372) hydrogen bonds : angle 5.89478 ( 1044) metal coordination : bond 0.00131 ( 6) SS BOND : bond 0.00338 ( 8) SS BOND : angle 1.01512 ( 16) covalent geometry : bond 0.00312 (11320) covalent geometry : angle 0.51450 (15358) *********************** 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 : 1.246 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: 1.3977 time to fit residues: 214.9830 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 : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 300 ASN B 282 ASN B 454 HIS D 33 GLN D 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123038 restraints weight = 11964.062| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.16 r_work: 0.3485 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.206 11346 Z= 0.135 Angle : 0.503 5.710 15410 Z= 0.266 Chirality : 0.043 0.263 1710 Planarity : 0.004 0.048 1980 Dihedral : 5.943 55.332 1784 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.54 % Allowed : 7.53 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1404 helix: 0.53 (0.32), residues: 290 sheet: 0.79 (0.28), residues: 318 loop : -0.87 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 77 HIS 0.004 0.001 HIS A 379 PHE 0.012 0.001 PHE A 383 TYR 0.012 0.001 TYR A 206 ARG 0.004 0.000 ARG D 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 8) link_NAG-ASN : angle 1.72311 ( 24) link_BETA1-4 : bond 0.00156 ( 4) link_BETA1-4 : angle 0.97393 ( 12) hydrogen bonds : bond 0.04150 ( 372) hydrogen bonds : angle 4.68182 ( 1044) metal coordination : bond 0.08392 ( 6) SS BOND : bond 0.00254 ( 8) SS BOND : angle 0.57764 ( 16) covalent geometry : bond 0.00282 (11320) covalent geometry : angle 0.49833 (15358) *********************** 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 141 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7212 (mtm180) REVERT: A 199 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6355 (mt0) REVERT: A 214 ASP cc_start: 0.8297 (p0) cc_final: 0.8045 (p0) REVERT: A 240 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7058 (mp0) REVERT: A 433 MET cc_start: 0.8003 (mmm) cc_final: 0.7628 (mmt) REVERT: B 427 GLU cc_start: 0.7559 (mp0) cc_final: 0.7321 (mp0) REVERT: D 140 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7515 (pt0) outliers start: 18 outliers final: 6 residues processed: 129 average time/residue: 1.2380 time to fit residues: 172.8283 Evaluate side-chains 121 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain B residue 195 GLU 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 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 130 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121552 restraints weight = 12012.845| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.17 r_work: 0.3467 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0984 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= 0.129 Angle : 0.507 7.121 15410 Z= 0.265 Chirality : 0.043 0.271 1710 Planarity : 0.004 0.048 1980 Dihedral : 5.618 56.027 1784 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.05 % Allowed : 9.85 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1404 helix: 0.51 (0.31), residues: 290 sheet: 0.85 (0.29), residues: 305 loop : -0.90 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 77 HIS 0.003 0.001 HIS A 341 PHE 0.014 0.002 PHE A 383 TYR 0.013 0.001 TYR B 206 ARG 0.002 0.000 ARG D 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 8) link_NAG-ASN : angle 1.86077 ( 24) link_BETA1-4 : bond 0.00264 ( 4) link_BETA1-4 : angle 0.95698 ( 12) hydrogen bonds : bond 0.04136 ( 372) hydrogen bonds : angle 4.48616 ( 1044) metal coordination : bond 0.00411 ( 6) SS BOND : bond 0.00270 ( 8) SS BOND : angle 0.62135 ( 16) covalent geometry : bond 0.00317 (11320) covalent geometry : angle 0.50152 (15358) *********************** 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 132 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6809 (mmtt) REVERT: A 199 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6233 (mt0) REVERT: A 214 ASP cc_start: 0.8280 (p0) cc_final: 0.7987 (p0) REVERT: A 240 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7147 (mp0) REVERT: A 351 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: A 433 MET cc_start: 0.7958 (mmm) cc_final: 0.7580 (mmt) REVERT: D 140 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7602 (pt0) outliers start: 24 outliers final: 11 residues processed: 118 average time/residue: 1.2595 time to fit residues: 160.7640 Evaluate side-chains 119 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS 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 452 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain 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 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 123 optimal weight: 0.0470 chunk 126 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120307 restraints weight = 12097.052| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.29 r_work: 0.3448 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1147 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= 0.150 Angle : 0.526 7.941 15410 Z= 0.274 Chirality : 0.044 0.281 1710 Planarity : 0.004 0.048 1980 Dihedral : 5.527 56.854 1784 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.74 % Allowed : 11.13 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1404 helix: 0.43 (0.31), residues: 290 sheet: 0.76 (0.29), residues: 306 loop : -0.95 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 77 HIS 0.004 0.001 HIS A 341 PHE 0.015 0.002 PHE A 383 TYR 0.014 0.001 TYR B 206 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 8) link_NAG-ASN : angle 1.97841 ( 24) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 1.01035 ( 12) hydrogen bonds : bond 0.04389 ( 372) hydrogen bonds : angle 4.49831 ( 1044) metal coordination : bond 0.00321 ( 6) SS BOND : bond 0.00305 ( 8) SS BOND : angle 0.69181 ( 16) covalent geometry : bond 0.00373 (11320) covalent geometry : angle 0.51942 (15358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7286 (mtm180) REVERT: A 192 MET cc_start: 0.8469 (mtm) cc_final: 0.7881 (mtp) REVERT: A 199 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6222 (mt0) REVERT: A 351 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 433 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7626 (mmt) REVERT: C 70 GLN cc_start: 0.6580 (mp10) cc_final: 0.6262 (mp10) REVERT: D 70 GLN cc_start: 0.6284 (mp10) cc_final: 0.5979 (mp10) REVERT: D 140 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7631 (pt0) outliers start: 32 outliers final: 14 residues processed: 119 average time/residue: 1.3338 time to fit residues: 171.4632 Evaluate side-chains 123 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 138 ARG 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 166 THR Chi-restraints excluded: chain B residue 195 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 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.152212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117156 restraints weight = 12101.846| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.38 r_work: 0.3400 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11346 Z= 0.208 Angle : 0.579 9.059 15410 Z= 0.302 Chirality : 0.046 0.305 1710 Planarity : 0.004 0.049 1980 Dihedral : 5.674 58.469 1784 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.91 % Allowed : 12.41 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1404 helix: 0.22 (0.31), residues: 288 sheet: 0.54 (0.28), residues: 314 loop : -1.09 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 77 HIS 0.005 0.001 HIS B 340 PHE 0.019 0.002 PHE A 383 TYR 0.017 0.002 TYR B 206 ARG 0.003 0.000 ARG B 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 2.21528 ( 24) link_BETA1-4 : bond 0.00177 ( 4) link_BETA1-4 : angle 1.15396 ( 12) hydrogen bonds : bond 0.05164 ( 372) hydrogen bonds : angle 4.68090 ( 1044) metal coordination : bond 0.00340 ( 6) SS BOND : bond 0.00389 ( 8) SS BOND : angle 0.86196 ( 16) covalent geometry : bond 0.00522 (11320) covalent geometry : angle 0.57139 (15358) *********************** 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 138 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6178 (mt0) REVERT: A 240 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7036 (mp0) REVERT: A 351 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 433 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7658 (mmt) REVERT: B 240 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7171 (mp0) REVERT: C 70 GLN cc_start: 0.6540 (mp10) cc_final: 0.6200 (mp10) REVERT: C 224 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7462 (mtm110) REVERT: D 140 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: D 169 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7463 (tt0) outliers start: 34 outliers final: 16 residues processed: 122 average time/residue: 1.3323 time to fit residues: 175.3689 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 : 1.175 ------------------------------------------------------------------------------- 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 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 195 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 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 169 GLN 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 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 89 GLN D 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121675 restraints weight = 12190.446| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.40 r_work: 0.3452 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11346 Z= 0.101 Angle : 0.485 9.600 15410 Z= 0.252 Chirality : 0.042 0.288 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.328 55.019 1784 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.83 % Allowed : 13.44 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1404 helix: 0.56 (0.31), residues: 290 sheet: 0.36 (0.28), residues: 328 loop : -0.89 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.003 0.000 HIS B 267 PHE 0.010 0.001 PHE A 94 TYR 0.014 0.001 TYR B 117 ARG 0.001 0.000 ARG D 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 8) link_NAG-ASN : angle 1.89685 ( 24) link_BETA1-4 : bond 0.00312 ( 4) link_BETA1-4 : angle 0.98535 ( 12) hydrogen bonds : bond 0.03456 ( 372) hydrogen bonds : angle 4.38430 ( 1044) metal coordination : bond 0.00124 ( 6) SS BOND : bond 0.00207 ( 8) SS BOND : angle 0.47818 ( 16) covalent geometry : bond 0.00238 (11320) covalent geometry : angle 0.47863 (15358) *********************** 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 141 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7008 (mp0) REVERT: A 351 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 433 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7650 (mmt) REVERT: B 404 ASP cc_start: 0.6952 (m-30) cc_final: 0.6682 (m-30) REVERT: C 70 GLN cc_start: 0.6652 (mp10) cc_final: 0.6395 (mp10) REVERT: D 140 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7576 (pm20) outliers start: 33 outliers final: 15 residues processed: 123 average time/residue: 1.6659 time to fit residues: 220.4014 Evaluate side-chains 120 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 166 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain 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 140 GLN 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 41 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.152845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118266 restraints weight = 12311.644| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.32 r_work: 0.3418 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11346 Z= 0.196 Angle : 0.567 9.513 15410 Z= 0.294 Chirality : 0.046 0.301 1710 Planarity : 0.004 0.049 1980 Dihedral : 5.537 57.860 1784 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.83 % Allowed : 13.87 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1404 helix: 0.31 (0.31), residues: 288 sheet: 0.27 (0.28), residues: 328 loop : -1.02 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 77 HIS 0.004 0.001 HIS A 341 PHE 0.016 0.002 PHE A 383 TYR 0.017 0.002 TYR B 206 ARG 0.003 0.000 ARG B 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 8) link_NAG-ASN : angle 2.16315 ( 24) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 1.15969 ( 12) hydrogen bonds : bond 0.04865 ( 372) hydrogen bonds : angle 4.62330 ( 1044) metal coordination : bond 0.00333 ( 6) SS BOND : bond 0.00369 ( 8) SS BOND : angle 0.83831 ( 16) covalent geometry : bond 0.00493 (11320) covalent geometry : angle 0.56013 (15358) *********************** 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 138 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7095 (mp0) REVERT: A 433 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7670 (mmt) REVERT: B 240 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7139 (mp0) REVERT: B 404 ASP cc_start: 0.6997 (m-30) cc_final: 0.6741 (m-30) REVERT: D 140 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7671 (pt0) outliers start: 33 outliers final: 17 residues processed: 124 average time/residue: 1.8022 time to fit residues: 243.3691 Evaluate side-chains 122 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 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 166 THR 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 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122157 restraints weight = 12129.893| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.32 r_work: 0.3463 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11346 Z= 0.101 Angle : 0.490 8.924 15410 Z= 0.254 Chirality : 0.042 0.287 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.283 55.095 1784 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.14 % Allowed : 14.81 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1404 helix: 0.59 (0.31), residues: 290 sheet: 0.35 (0.28), residues: 328 loop : -0.88 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 77 HIS 0.003 0.001 HIS A 341 PHE 0.010 0.001 PHE A 94 TYR 0.015 0.001 TYR B 117 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 8) link_NAG-ASN : angle 1.93694 ( 24) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 1.03003 ( 12) hydrogen bonds : bond 0.03402 ( 372) hydrogen bonds : angle 4.38939 ( 1044) metal coordination : bond 0.00108 ( 6) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.49866 ( 16) covalent geometry : bond 0.00239 (11320) covalent geometry : angle 0.48345 (15358) *********************** 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 132 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.033 Fit side-chains REVERT: A 195 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6340 (pt0) REVERT: A 351 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: A 433 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7621 (mmt) REVERT: B 240 GLU cc_start: 0.7783 (tm-30) cc_final: 0.6998 (mp0) REVERT: B 404 ASP cc_start: 0.6963 (m-30) cc_final: 0.6716 (m-30) REVERT: C 70 GLN cc_start: 0.6450 (mp10) cc_final: 0.6127 (mp10) REVERT: C 96 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7234 (p) REVERT: D 140 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7526 (pm20) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 1.4106 time to fit residues: 187.5904 Evaluate side-chains 123 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS 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 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 0.0070 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4000 r_free = 0.4000 target = 0.156945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122329 restraints weight = 12248.581| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.34 r_work: 0.3462 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11346 Z= 0.107 Angle : 0.504 8.728 15410 Z= 0.260 Chirality : 0.043 0.274 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.226 55.268 1784 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.14 % Allowed : 14.81 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1404 helix: 0.66 (0.31), residues: 290 sheet: 0.37 (0.28), residues: 328 loop : -0.84 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.003 0.001 HIS B 496 PHE 0.010 0.001 PHE A 268 TYR 0.013 0.001 TYR B 117 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 8) link_NAG-ASN : angle 1.92370 ( 24) link_BETA1-4 : bond 0.00345 ( 4) link_BETA1-4 : angle 1.02826 ( 12) hydrogen bonds : bond 0.03475 ( 372) hydrogen bonds : angle 4.33744 ( 1044) metal coordination : bond 0.00122 ( 6) SS BOND : bond 0.00309 ( 8) SS BOND : angle 1.93469 ( 16) covalent geometry : bond 0.00260 (11320) covalent geometry : angle 0.49481 (15358) *********************** 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 133 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.313 Fit side-chains REVERT: A 195 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6344 (pt0) REVERT: A 214 ASP cc_start: 0.8414 (p0) cc_final: 0.8090 (p0) REVERT: A 240 GLU cc_start: 0.7713 (tm-30) cc_final: 0.6858 (mp0) REVERT: A 433 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7589 (mmt) REVERT: B 404 ASP cc_start: 0.7013 (m-30) cc_final: 0.6766 (m-30) REVERT: C 70 GLN cc_start: 0.6416 (mp10) cc_final: 0.6072 (mp10) REVERT: C 96 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7262 (p) REVERT: D 140 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7512 (pm20) outliers start: 25 outliers final: 18 residues processed: 126 average time/residue: 1.2380 time to fit residues: 169.6748 Evaluate side-chains 127 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 134 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4014 r_free = 0.4014 target = 0.158271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123652 restraints weight = 12052.435| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.33 r_work: 0.3481 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11346 Z= 0.097 Angle : 0.498 10.169 15410 Z= 0.257 Chirality : 0.042 0.259 1710 Planarity : 0.003 0.046 1980 Dihedral : 5.116 54.633 1784 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 14.81 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1404 helix: 0.80 (0.32), residues: 290 sheet: 0.42 (0.29), residues: 328 loop : -0.77 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 77 HIS 0.003 0.000 HIS A 341 PHE 0.009 0.001 PHE A 94 TYR 0.015 0.001 TYR B 117 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 1.87275 ( 24) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 0.99924 ( 12) hydrogen bonds : bond 0.03213 ( 372) hydrogen bonds : angle 4.24925 ( 1044) metal coordination : bond 0.00096 ( 6) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.85725 ( 16) covalent geometry : bond 0.00231 (11320) covalent geometry : angle 0.48842 (15358) ********************** 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 141 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.170 Fit side-chains REVERT: A 195 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6329 (pt0) REVERT: A 240 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6825 (mp0) REVERT: A 433 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7557 (mmt) REVERT: B 240 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7056 (mp0) REVERT: B 404 ASP cc_start: 0.7045 (m-30) cc_final: 0.6806 (m-30) REVERT: C 70 GLN cc_start: 0.6428 (mp10) cc_final: 0.6065 (mp10) REVERT: C 96 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7245 (p) outliers start: 25 outliers final: 18 residues processed: 130 average time/residue: 1.1989 time to fit residues: 168.9181 Evaluate side-chains 133 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 167 MET 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 53 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 0.0000 chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 438 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 = 0.4021 r_free = 0.4021 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124284 restraints weight = 12053.489| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.34 r_work: 0.3486 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11346 Z= 0.096 Angle : 0.497 10.436 15410 Z= 0.256 Chirality : 0.042 0.252 1710 Planarity : 0.003 0.047 1980 Dihedral : 5.044 54.578 1784 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.05 % Allowed : 15.41 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1404 helix: 0.85 (0.32), residues: 290 sheet: 0.44 (0.29), residues: 328 loop : -0.74 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.002 0.000 HIS A 341 PHE 0.009 0.001 PHE A 94 TYR 0.014 0.001 TYR B 117 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 8) link_NAG-ASN : angle 1.88393 ( 24) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 0.99076 ( 12) hydrogen bonds : bond 0.03125 ( 372) hydrogen bonds : angle 4.19511 ( 1044) metal coordination : bond 0.00095 ( 6) SS BOND : bond 0.00209 ( 8) SS BOND : angle 1.99619 ( 16) covalent geometry : bond 0.00230 (11320) covalent geometry : angle 0.48759 (15358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8040.16 seconds wall clock time: 143 minutes 29.66 seconds (8609.66 seconds total)