Starting phenix.real_space_refine on Thu Sep 18 10:21:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrp_60401/09_2025/8zrp_60401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrp_60401/09_2025/8zrp_60401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrp_60401/09_2025/8zrp_60401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrp_60401/09_2025/8zrp_60401.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrp_60401/09_2025/8zrp_60401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrp_60401/09_2025/8zrp_60401.cif" } resolution = 3.32 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= -0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10501 2.51 5 N 2521 2.21 5 O 2924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16042 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3160 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3104 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3197 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3115 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 1 Chain: "E" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3125 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'NCT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'NCT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.34, per 1000 atoms: 0.27 Number of scatterers: 16042 At special positions: 0 Unit cell: (94.35, 98.6, 170.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2924 8.00 N 2521 7.00 C 10501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 167 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN A 171 " " NAG G 1 " - " ASN B 138 " " NAG H 1 " - " ASN B 166 " " NAG I 1 " - " ASN C 171 " " NAG J 1 " - " ASN D 138 " " NAG K 1 " - " ASN D 166 " " NAG L 1 " - " ASN E 138 " " NAG M 1 " - " ASN E 166 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 635.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 40.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 removed outlier: 4.674A pdb=" N HIS A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.695A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 270 through 291 removed outlier: 3.613A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 329 removed outlier: 3.654A pdb=" N PHE A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.932A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 651 through 706 removed outlier: 3.500A pdb=" N TRP A 679 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.387A pdb=" N VAL B 253 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 254 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 283 removed outlier: 3.557A pdb=" N SER B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 321 removed outlier: 3.671A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.536A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 574 removed outlier: 3.802A pdb=" N PHE B 559 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 42 Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.522A pdb=" N LYS C 114 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 115 " --> pdb=" O ALA C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 115' Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.992A pdb=" N ILE C 245 " --> pdb=" O MET C 241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 246' Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.780A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.673A pdb=" N VAL C 261 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 291 Processing helix chain 'C' and resid 305 through 326 removed outlier: 3.613A pdb=" N VAL C 319 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.778A pdb=" N VAL C 344 " --> pdb=" O TRP C 340 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 removed outlier: 4.052A pdb=" N VAL C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 348 through 353' Processing helix chain 'C' and resid 651 through 706 removed outlier: 3.630A pdb=" N VAL C 675 " --> pdb=" O GLU C 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 702 " --> pdb=" O CYS C 698 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 703 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY C 704 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 705 " --> pdb=" O GLY C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 159 through 162 Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.698A pdb=" N ASN D 238 " --> pdb=" O PHE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 248 Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.704A pdb=" N LEU D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 256 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.791A pdb=" N LYS D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 321 removed outlier: 3.652A pdb=" N MET D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 339 through 345 removed outlier: 3.841A pdb=" N THR D 343 " --> pdb=" O HIS D 339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 575 removed outlier: 3.896A pdb=" N TRP D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 549 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 551 " --> pdb=" O ASP D 547 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 552 " --> pdb=" O TRP D 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 553 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.524A pdb=" N LEU E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 35 " --> pdb=" O MET E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.867A pdb=" N ILE E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN E 238 " --> pdb=" O PHE E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 238' Processing helix chain 'E' and resid 239 through 250 removed outlier: 3.857A pdb=" N CYS E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 262 through 285 removed outlier: 4.428A pdb=" N LEU E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 321 removed outlier: 3.664A pdb=" N TYR E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET E 300 " --> pdb=" O GLY E 296 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 338 Processing helix chain 'E' and resid 340 through 345 removed outlier: 4.242A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 571 removed outlier: 3.743A pdb=" N PHE E 559 " --> pdb=" O VAL E 555 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 560 " --> pdb=" O ASP E 556 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP E 561 " --> pdb=" O ARG E 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 148 removed outlier: 7.162A pdb=" N ASN A 83 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 91 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR A 60 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 187 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 61 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.267A pdb=" N SER A 178 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR A 228 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR A 235 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.267A pdb=" N SER A 178 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR A 228 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.766A pdb=" N ALA B 147 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 74 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER B 67 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR B 76 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B 78 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 57 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 117 removed outlier: 5.281A pdb=" N SER B 173 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL B 220 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE B 227 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 117 removed outlier: 5.281A pdb=" N SER B 173 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL B 220 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 148 removed outlier: 3.502A pdb=" N TRP C 90 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 61 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 74 removed outlier: 7.942A pdb=" N THR C 68 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N TRP C 85 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU C 70 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN C 83 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN C 72 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 122 removed outlier: 4.649A pdb=" N SER C 178 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR C 228 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 58 Processing sheet with id=AB7, first strand: chain 'D' and resid 61 through 68 removed outlier: 7.644A pdb=" N ALA D 63 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N TRP D 80 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU D 65 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN D 78 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 79 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 147 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 102 through 106 Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 117 removed outlier: 4.974A pdb=" N SER D 173 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL D 220 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.732A pdb=" N VAL E 135 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER E 140 " --> pdb=" O ARG E 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.732A pdb=" N VAL E 135 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER E 140 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE E 74 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER E 67 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR E 76 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU E 65 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN E 78 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.575A pdb=" N ILE E 228 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 222 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER E 173 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL E 220 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE E 227 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.575A pdb=" N ILE E 228 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 222 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER E 173 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL E 220 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 221 " --> pdb=" O THR E 211 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2091 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: 2.62 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4033 1.33 - 1.45: 3147 1.45 - 1.57: 9126 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 16458 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" N GLU E 180 " pdb=" CA GLU E 180 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.06e-02 8.90e+03 9.97e+00 bond pdb=" N VAL C 659 " pdb=" CA VAL C 659 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 9.04e+00 bond pdb=" N TYR E 176 " pdb=" CA TYR E 176 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.64e+00 bond pdb=" N MET E 553 " pdb=" CA MET E 553 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.95e+00 ... (remaining 16453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 21725 1.51 - 3.03: 571 3.03 - 4.54: 106 4.54 - 6.05: 41 6.05 - 7.57: 13 Bond angle restraints: 22456 Sorted by residual: angle pdb=" N LEU E 290 " pdb=" CA LEU E 290 " pdb=" C LEU E 290 " ideal model delta sigma weight residual 114.62 109.88 4.74 1.14e+00 7.69e-01 1.73e+01 angle pdb=" N MET A 355 " pdb=" CA MET A 355 " pdb=" C MET A 355 " ideal model delta sigma weight residual 113.12 108.31 4.81 1.25e+00 6.40e-01 1.48e+01 angle pdb=" N LEU A 656 " pdb=" CA LEU A 656 " pdb=" C LEU A 656 " ideal model delta sigma weight residual 111.07 107.43 3.64 1.07e+00 8.73e-01 1.16e+01 angle pdb=" CA LEU A 354 " pdb=" C LEU A 354 " pdb=" O LEU A 354 " ideal model delta sigma weight residual 122.27 118.34 3.93 1.16e+00 7.43e-01 1.15e+01 angle pdb=" N LEU C 656 " pdb=" CA LEU C 656 " pdb=" C LEU C 656 " ideal model delta sigma weight residual 111.14 107.49 3.65 1.08e+00 8.57e-01 1.14e+01 ... (remaining 22451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.78: 8852 22.78 - 45.56: 941 45.56 - 68.34: 134 68.34 - 91.11: 97 91.11 - 113.89: 66 Dihedral angle restraints: 10090 sinusoidal: 4359 harmonic: 5731 Sorted by residual: dihedral pdb=" CB CYS D 153 " pdb=" SG CYS D 153 " pdb=" SG CYS D 167 " pdb=" CB CYS D 167 " ideal model delta sinusoidal sigma weight residual 93.00 22.67 70.33 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" SG CYS B 167 " pdb=" CB CYS B 167 " ideal model delta sinusoidal sigma weight residual 93.00 27.76 65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CD ARG A 356 " pdb=" NE ARG A 356 " pdb=" CZ ARG A 356 " pdb=" NH1 ARG A 356 " ideal model delta sinusoidal sigma weight residual 0.00 -60.57 60.57 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 10087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2316 0.064 - 0.129: 344 0.129 - 0.193: 23 0.193 - 0.258: 2 0.258 - 0.322: 10 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 166 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 171 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2692 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 356 " -0.957 9.50e-02 1.11e+02 4.29e-01 1.11e+02 pdb=" NE ARG A 356 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 356 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 356 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 356 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 109 " -0.698 9.50e-02 1.11e+02 3.13e-01 5.97e+01 pdb=" NE ARG A 109 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 109 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 109 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 210 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.49e+01 pdb=" NE ARG E 210 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG E 210 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 210 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 210 " -0.015 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 158 2.66 - 3.22: 13997 3.22 - 3.78: 23110 3.78 - 4.34: 30211 4.34 - 4.90: 52549 Nonbonded interactions: 120025 Sorted by model distance: nonbonded pdb=" O SER C 281 " pdb=" CD2 PHE C 285 " model vdw 2.096 3.340 nonbonded pdb=" OD1 ASP D 122 " pdb=" OG1 THR D 124 " model vdw 2.104 3.040 nonbonded pdb=" OD2 ASP B 33 " pdb=" OH TYR B 97 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU D 527 " pdb=" OG SER E 529 " model vdw 2.220 3.040 nonbonded pdb=" O HIS C 39 " pdb=" OG SER C 43 " model vdw 2.244 3.040 ... (remaining 120020 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 'C' and (resid 32 through 356 or resid 650 through 707 or resid 801)) } ncs_group { reference = (chain 'B' and resid 25 through 574) selection = (chain 'D' and resid 25 through 574) selection = (chain 'E' and (resid 25 through 350 or resid 520 through 574)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 6.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.860 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.066 16487 Z= 0.208 Angle : 0.638 10.063 22538 Z= 0.333 Chirality : 0.048 0.322 2695 Planarity : 0.012 0.429 2716 Dihedral : 22.059 113.892 6335 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 0.89 % Allowed : 27.60 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1899 helix: 1.87 (0.21), residues: 685 sheet: -0.76 (0.27), residues: 379 loop : -2.27 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.019 0.001 TYR E 88 PHE 0.028 0.001 PHE A 256 TRP 0.009 0.001 TRP E 332 HIS 0.003 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00363 (16458) covalent geometry : angle 0.61772 (22456) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.45392 ( 10) hydrogen bonds : bond 0.21591 ( 687) hydrogen bonds : angle 6.56058 ( 2091) link_BETA1-4 : bond 0.01006 ( 16) link_BETA1-4 : angle 2.82229 ( 48) link_NAG-ASN : bond 0.00444 ( 8) link_NAG-ASN : angle 3.04601 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: C 141 LYS cc_start: 0.7468 (mttt) cc_final: 0.7133 (ttpt) outliers start: 16 outliers final: 5 residues processed: 231 average time/residue: 0.1297 time to fit residues: 44.6716 Evaluate side-chains 214 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 180 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122460 restraints weight = 21843.292| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.01 r_work: 0.3287 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16487 Z= 0.129 Angle : 0.624 11.080 22538 Z= 0.292 Chirality : 0.046 0.310 2695 Planarity : 0.004 0.056 2716 Dihedral : 17.076 95.979 2594 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.63 % Rotamer: Outliers : 3.51 % Allowed : 25.65 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1899 helix: 2.27 (0.20), residues: 699 sheet: -0.71 (0.27), residues: 379 loop : -2.24 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.007 0.001 TYR B 224 PHE 0.016 0.001 PHE C 313 TRP 0.011 0.001 TRP E 85 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00279 (16458) covalent geometry : angle 0.59600 (22456) SS BOND : bond 0.00251 ( 5) SS BOND : angle 0.55223 ( 10) hydrogen bonds : bond 0.06473 ( 687) hydrogen bonds : angle 4.68054 ( 2091) link_BETA1-4 : bond 0.00879 ( 16) link_BETA1-4 : angle 3.61426 ( 48) link_NAG-ASN : bond 0.00499 ( 8) link_NAG-ASN : angle 2.60844 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 670 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8076 (t0) REVERT: C 141 LYS cc_start: 0.7651 (mttt) cc_final: 0.7229 (ttpt) REVERT: C 687 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: D 144 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8462 (tt) REVERT: E 525 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6708 (tt) outliers start: 63 outliers final: 33 residues processed: 262 average time/residue: 0.1192 time to fit residues: 47.8156 Evaluate side-chains 240 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 255 TYR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 568 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 182 optimal weight: 0.3980 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121154 restraints weight = 22162.725| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.06 r_work: 0.3264 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.142 Angle : 0.629 12.728 22538 Z= 0.290 Chirality : 0.046 0.315 2695 Planarity : 0.004 0.059 2716 Dihedral : 13.563 84.852 2590 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 5.12 % Allowed : 25.04 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.20), residues: 1899 helix: 2.35 (0.20), residues: 704 sheet: -0.67 (0.27), residues: 372 loop : -2.28 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 339 TYR 0.012 0.001 TYR A 142 PHE 0.017 0.001 PHE C 313 TRP 0.010 0.001 TRP E 85 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00330 (16458) covalent geometry : angle 0.59603 (22456) SS BOND : bond 0.00336 ( 5) SS BOND : angle 0.65020 ( 10) hydrogen bonds : bond 0.06421 ( 687) hydrogen bonds : angle 4.40026 ( 2091) link_BETA1-4 : bond 0.00895 ( 16) link_BETA1-4 : angle 3.96193 ( 48) link_NAG-ASN : bond 0.00409 ( 8) link_NAG-ASN : angle 2.82503 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 214 time to evaluate : 0.625 Fit side-chains REVERT: A 64 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: A 185 GLU cc_start: 0.8345 (mp0) cc_final: 0.8056 (mp0) REVERT: A 279 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8104 (tp) REVERT: C 141 LYS cc_start: 0.7777 (mttt) cc_final: 0.7237 (ttpt) REVERT: C 687 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: D 144 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8567 (tt) REVERT: E 525 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6724 (tt) outliers start: 92 outliers final: 59 residues processed: 283 average time/residue: 0.1184 time to fit residues: 50.9658 Evaluate side-chains 266 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 202 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 93 optimal weight: 0.0010 chunk 164 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 19 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 41 ASN B 52 GLN C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124399 restraints weight = 21888.988| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.06 r_work: 0.3307 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16487 Z= 0.107 Angle : 0.579 8.591 22538 Z= 0.267 Chirality : 0.045 0.323 2695 Planarity : 0.004 0.059 2716 Dihedral : 11.606 85.555 2587 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 3.90 % Allowed : 26.49 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.20), residues: 1899 helix: 2.64 (0.20), residues: 701 sheet: -0.50 (0.27), residues: 380 loop : -2.18 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.009 0.001 TYR A 142 PHE 0.017 0.001 PHE C 313 TRP 0.010 0.001 TRP C 90 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00230 (16458) covalent geometry : angle 0.54509 (22456) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.57634 ( 10) hydrogen bonds : bond 0.05163 ( 687) hydrogen bonds : angle 4.02850 ( 2091) link_BETA1-4 : bond 0.00938 ( 16) link_BETA1-4 : angle 3.79575 ( 48) link_NAG-ASN : bond 0.00482 ( 8) link_NAG-ASN : angle 2.72770 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.566 Fit side-chains REVERT: A 64 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: A 185 GLU cc_start: 0.8343 (mp0) cc_final: 0.8058 (mp0) REVERT: C 210 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7259 (t70) REVERT: C 241 MET cc_start: 0.7414 (tpp) cc_final: 0.6989 (tpp) REVERT: C 687 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: D 59 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7650 (tp40) REVERT: D 144 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8451 (tt) REVERT: E 525 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6600 (tt) outliers start: 70 outliers final: 42 residues processed: 272 average time/residue: 0.1241 time to fit residues: 51.4526 Evaluate side-chains 252 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 153 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS D 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122782 restraints weight = 21881.224| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.07 r_work: 0.3287 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16487 Z= 0.122 Angle : 0.589 8.156 22538 Z= 0.273 Chirality : 0.045 0.332 2695 Planarity : 0.004 0.060 2716 Dihedral : 10.995 79.415 2587 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.84 % Rotamer: Outliers : 4.51 % Allowed : 25.65 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1899 helix: 2.61 (0.20), residues: 701 sheet: -0.53 (0.27), residues: 378 loop : -2.18 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.009 0.001 TYR A 142 PHE 0.014 0.001 PHE C 313 TRP 0.009 0.001 TRP E 85 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00280 (16458) covalent geometry : angle 0.55813 (22456) SS BOND : bond 0.00299 ( 5) SS BOND : angle 0.65732 ( 10) hydrogen bonds : bond 0.05451 ( 687) hydrogen bonds : angle 4.02656 ( 2091) link_BETA1-4 : bond 0.00887 ( 16) link_BETA1-4 : angle 3.70584 ( 48) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 2.68714 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 212 time to evaluate : 0.494 Fit side-chains REVERT: A 64 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: C 80 MET cc_start: 0.8793 (ttp) cc_final: 0.8575 (ttm) REVERT: C 210 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7247 (t70) REVERT: C 241 MET cc_start: 0.7435 (tpp) cc_final: 0.7025 (tpp) REVERT: C 687 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: D 59 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7709 (tp40) REVERT: D 144 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8508 (tt) REVERT: D 165 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8139 (mp-120) REVERT: E 525 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6643 (tt) outliers start: 81 outliers final: 52 residues processed: 275 average time/residue: 0.1229 time to fit residues: 51.6664 Evaluate side-chains 261 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 152 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122387 restraints weight = 21995.456| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.07 r_work: 0.3285 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16487 Z= 0.125 Angle : 0.595 8.137 22538 Z= 0.274 Chirality : 0.045 0.339 2695 Planarity : 0.004 0.059 2716 Dihedral : 10.387 73.018 2587 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 5.01 % Allowed : 25.99 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1899 helix: 2.58 (0.20), residues: 701 sheet: -0.55 (0.27), residues: 386 loop : -2.16 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.010 0.001 TYR A 142 PHE 0.015 0.001 PHE C 313 TRP 0.011 0.001 TRP B 174 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00290 (16458) covalent geometry : angle 0.56297 (22456) SS BOND : bond 0.00309 ( 5) SS BOND : angle 0.61958 ( 10) hydrogen bonds : bond 0.05547 ( 687) hydrogen bonds : angle 4.01627 ( 2091) link_BETA1-4 : bond 0.00890 ( 16) link_BETA1-4 : angle 3.70603 ( 48) link_NAG-ASN : bond 0.00342 ( 8) link_NAG-ASN : angle 2.81596 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 0.616 Fit side-chains REVERT: A 64 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: B 144 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8960 (tt) REVERT: C 80 MET cc_start: 0.8821 (ttp) cc_final: 0.8617 (ttm) REVERT: C 209 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8455 (pt) REVERT: C 210 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7237 (t70) REVERT: C 241 MET cc_start: 0.7429 (tpp) cc_final: 0.7028 (tpp) REVERT: C 687 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: D 59 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7710 (tp40) REVERT: D 144 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8524 (tt) REVERT: E 75 MET cc_start: 0.7233 (ttm) cc_final: 0.7025 (ttp) REVERT: E 525 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6685 (tt) outliers start: 90 outliers final: 66 residues processed: 279 average time/residue: 0.1118 time to fit residues: 47.9162 Evaluate side-chains 277 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 203 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 175 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 41 ASN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121424 restraints weight = 21961.540| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.04 r_work: 0.3264 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.133 Angle : 0.605 8.624 22538 Z= 0.280 Chirality : 0.045 0.362 2695 Planarity : 0.004 0.059 2716 Dihedral : 9.408 63.653 2587 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.58 % Rotamer: Outliers : 5.01 % Allowed : 25.77 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.20), residues: 1899 helix: 2.53 (0.20), residues: 701 sheet: -0.55 (0.27), residues: 387 loop : -2.14 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 39 TYR 0.010 0.001 TYR A 142 PHE 0.015 0.001 PHE C 313 TRP 0.011 0.001 TRP B 174 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00311 (16458) covalent geometry : angle 0.57342 (22456) SS BOND : bond 0.00314 ( 5) SS BOND : angle 0.60170 ( 10) hydrogen bonds : bond 0.05789 ( 687) hydrogen bonds : angle 4.03777 ( 2091) link_BETA1-4 : bond 0.00932 ( 16) link_BETA1-4 : angle 3.74468 ( 48) link_NAG-ASN : bond 0.00339 ( 8) link_NAG-ASN : angle 2.72036 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 206 time to evaluate : 0.635 Fit side-chains REVERT: A 64 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: B 144 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8979 (tt) REVERT: C 80 MET cc_start: 0.8845 (ttp) cc_final: 0.8636 (ttm) REVERT: C 209 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8452 (pt) REVERT: C 687 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: D 59 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7766 (tp40) REVERT: D 144 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8551 (tt) REVERT: E 75 MET cc_start: 0.7216 (ttm) cc_final: 0.7003 (ttp) REVERT: E 525 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6722 (tt) outliers start: 90 outliers final: 67 residues processed: 270 average time/residue: 0.1175 time to fit residues: 48.1481 Evaluate side-chains 274 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 200 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 173 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 41 ASN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123873 restraints weight = 21970.601| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.98 r_work: 0.3293 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.113 Angle : 0.589 8.713 22538 Z= 0.271 Chirality : 0.044 0.353 2695 Planarity : 0.004 0.058 2716 Dihedral : 8.879 61.860 2587 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.16 % Favored : 93.73 % Rotamer: Outliers : 4.40 % Allowed : 26.60 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.20), residues: 1899 helix: 2.65 (0.20), residues: 701 sheet: -0.47 (0.27), residues: 388 loop : -2.09 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.009 0.001 TYR A 142 PHE 0.015 0.001 PHE C 313 TRP 0.010 0.001 TRP C 90 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00252 (16458) covalent geometry : angle 0.55678 (22456) SS BOND : bond 0.00272 ( 5) SS BOND : angle 0.57043 ( 10) hydrogen bonds : bond 0.05348 ( 687) hydrogen bonds : angle 3.91982 ( 2091) link_BETA1-4 : bond 0.00962 ( 16) link_BETA1-4 : angle 3.74126 ( 48) link_NAG-ASN : bond 0.00349 ( 8) link_NAG-ASN : angle 2.72538 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 206 time to evaluate : 0.527 Fit side-chains REVERT: A 64 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 185 GLU cc_start: 0.8247 (mp0) cc_final: 0.7779 (mp0) REVERT: B 144 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8867 (tt) REVERT: C 209 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8488 (pt) REVERT: C 241 MET cc_start: 0.7499 (tpp) cc_final: 0.7282 (tpt) REVERT: C 687 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: D 59 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7599 (tp40) REVERT: D 144 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8442 (tt) REVERT: E 525 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6884 (tt) outliers start: 79 outliers final: 64 residues processed: 266 average time/residue: 0.1134 time to fit residues: 46.1994 Evaluate side-chains 272 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 8 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124514 restraints weight = 21901.102| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.03 r_work: 0.3292 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16487 Z= 0.108 Angle : 0.583 9.453 22538 Z= 0.268 Chirality : 0.044 0.354 2695 Planarity : 0.004 0.058 2716 Dihedral : 8.422 60.054 2587 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.21 % Favored : 93.73 % Rotamer: Outliers : 4.17 % Allowed : 26.32 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1899 helix: 2.72 (0.20), residues: 701 sheet: -0.44 (0.27), residues: 388 loop : -2.05 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 39 TYR 0.013 0.001 TYR A 102 PHE 0.015 0.001 PHE C 313 TRP 0.010 0.001 TRP C 90 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00235 (16458) covalent geometry : angle 0.55067 (22456) SS BOND : bond 0.00226 ( 5) SS BOND : angle 0.55804 ( 10) hydrogen bonds : bond 0.05054 ( 687) hydrogen bonds : angle 3.82112 ( 2091) link_BETA1-4 : bond 0.00987 ( 16) link_BETA1-4 : angle 3.72295 ( 48) link_NAG-ASN : bond 0.00352 ( 8) link_NAG-ASN : angle 2.70211 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 208 time to evaluate : 0.476 Fit side-chains REVERT: A 64 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: A 185 GLU cc_start: 0.8213 (mp0) cc_final: 0.7740 (mp0) REVERT: B 41 ASN cc_start: 0.8007 (t0) cc_final: 0.7800 (t0) REVERT: B 144 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8831 (tt) REVERT: C 687 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: D 59 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7604 (tp40) REVERT: D 144 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8407 (tt) REVERT: D 276 PHE cc_start: 0.7048 (m-10) cc_final: 0.6810 (m-80) REVERT: E 525 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6919 (tt) outliers start: 75 outliers final: 62 residues processed: 268 average time/residue: 0.1164 time to fit residues: 47.4231 Evaluate side-chains 271 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124068 restraints weight = 21931.498| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.00 r_work: 0.3292 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.114 Angle : 0.588 9.805 22538 Z= 0.271 Chirality : 0.044 0.367 2695 Planarity : 0.004 0.058 2716 Dihedral : 7.806 57.537 2587 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 4.06 % Allowed : 26.88 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.20), residues: 1899 helix: 2.69 (0.20), residues: 702 sheet: -0.48 (0.27), residues: 389 loop : -2.05 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 39 TYR 0.009 0.001 TYR A 142 PHE 0.018 0.001 PHE A 256 TRP 0.010 0.001 TRP B 174 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00258 (16458) covalent geometry : angle 0.55512 (22456) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.59092 ( 10) hydrogen bonds : bond 0.05140 ( 687) hydrogen bonds : angle 3.81862 ( 2091) link_BETA1-4 : bond 0.01013 ( 16) link_BETA1-4 : angle 3.76206 ( 48) link_NAG-ASN : bond 0.00323 ( 8) link_NAG-ASN : angle 2.75198 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 202 time to evaluate : 0.617 Fit side-chains REVERT: A 64 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: A 185 GLU cc_start: 0.8250 (mp0) cc_final: 0.7799 (mp0) REVERT: B 144 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8835 (tt) REVERT: C 209 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8510 (pt) REVERT: C 687 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: D 59 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: D 144 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8432 (tt) REVERT: D 276 PHE cc_start: 0.7024 (m-10) cc_final: 0.6785 (m-80) REVERT: E 525 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6932 (tt) outliers start: 73 outliers final: 61 residues processed: 262 average time/residue: 0.1156 time to fit residues: 46.5882 Evaluate side-chains 267 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 199 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 149 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124153 restraints weight = 21802.154| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.01 r_work: 0.3284 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 16487 Z= 0.170 Angle : 0.802 59.034 22538 Z= 0.426 Chirality : 0.051 1.349 2695 Planarity : 0.004 0.058 2716 Dihedral : 7.853 57.543 2587 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.58 % Rotamer: Outliers : 4.01 % Allowed : 26.93 % Favored : 69.06 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.20), residues: 1899 helix: 2.69 (0.20), residues: 702 sheet: -0.48 (0.27), residues: 389 loop : -2.05 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 39 TYR 0.008 0.001 TYR A 142 PHE 0.015 0.001 PHE C 313 TRP 0.009 0.001 TRP C 90 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00346 (16458) covalent geometry : angle 0.77915 (22456) SS BOND : bond 0.00274 ( 5) SS BOND : angle 0.60218 ( 10) hydrogen bonds : bond 0.05163 ( 687) hydrogen bonds : angle 3.81956 ( 2091) link_BETA1-4 : bond 0.00995 ( 16) link_BETA1-4 : angle 3.76917 ( 48) link_NAG-ASN : bond 0.00322 ( 8) link_NAG-ASN : angle 2.75277 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4022.98 seconds wall clock time: 69 minutes 32.84 seconds (4172.84 seconds total)