Starting phenix.real_space_refine on Sat May 17 18:49:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrp_60401/05_2025/8zrp_60401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrp_60401/05_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_60401/05_2025/8zrp_60401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrp_60401/05_2025/8zrp_60401.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrp_60401/05_2025/8zrp_60401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrp_60401/05_2025/8zrp_60401.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.48, per 1000 atoms: 0.65 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: 4.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.84 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: 5.30 Time building geometry restraints manager: 4.92 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.050 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.650 ------------------------------------------------------------------------------- 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 : 5.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (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 TRP 0.009 0.001 TRP E 332 HIS 0.003 0.001 HIS E 178 PHE 0.028 0.001 PHE A 256 TYR 0.019 0.001 TYR E 88 ARG 0.003 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 8) link_NAG-ASN : angle 3.04601 ( 24) link_BETA1-4 : bond 0.01006 ( 16) link_BETA1-4 : angle 2.82229 ( 48) hydrogen bonds : bond 0.21591 ( 687) hydrogen bonds : angle 6.56058 ( 2091) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.45392 ( 10) covalent geometry : bond 0.00363 (16458) covalent geometry : angle 0.61772 (22456) *********************** 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 : 1.934 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: 0.2892 time to fit residues: 99.0270 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 : 1.776 ------------------------------------------------------------------------------- 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 160 optimal weight: 0.0870 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.146051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121824 restraints weight = 21936.181| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.01 r_work: 0.3276 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16487 Z= 0.135 Angle : 0.630 10.840 22538 Z= 0.295 Chirality : 0.046 0.312 2695 Planarity : 0.004 0.056 2716 Dihedral : 17.088 95.573 2594 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 3.73 % Allowed : 25.54 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1899 helix: 2.23 (0.20), residues: 699 sheet: -0.74 (0.27), residues: 379 loop : -2.25 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 85 HIS 0.004 0.001 HIS B 320 PHE 0.017 0.001 PHE C 313 TYR 0.008 0.001 TYR B 224 ARG 0.004 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 8) link_NAG-ASN : angle 2.63480 ( 24) link_BETA1-4 : bond 0.00855 ( 16) link_BETA1-4 : angle 3.63472 ( 48) hydrogen bonds : bond 0.06557 ( 687) hydrogen bonds : angle 4.70944 ( 2091) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.55310 ( 10) covalent geometry : bond 0.00299 (16458) covalent geometry : angle 0.60258 (22456) *********************** 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 284 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 670 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7992 (t0) REVERT: C 141 LYS cc_start: 0.7634 (mttt) cc_final: 0.7173 (ttpt) REVERT: C 687 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: D 53 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7613 (mp) REVERT: D 144 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8488 (tt) REVERT: E 525 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6680 (tt) outliers start: 67 outliers final: 36 residues processed: 265 average time/residue: 0.2482 time to fit residues: 100.1407 Evaluate side-chains 246 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 218 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 293 ILE 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 53 LEU 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 288 THR 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 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 281 ILE 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 46 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122083 restraints weight = 21814.021| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.08 r_work: 0.3272 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1208 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= 0.126 Angle : 0.612 12.623 22538 Z= 0.280 Chirality : 0.046 0.308 2695 Planarity : 0.004 0.058 2716 Dihedral : 13.613 85.344 2590 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 4.51 % Allowed : 25.71 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1899 helix: 2.43 (0.20), residues: 704 sheet: -0.62 (0.27), residues: 372 loop : -2.24 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 85 HIS 0.002 0.001 HIS C 216 PHE 0.017 0.001 PHE C 313 TYR 0.011 0.001 TYR B 97 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 8) link_NAG-ASN : angle 2.75053 ( 24) link_BETA1-4 : bond 0.00902 ( 16) link_BETA1-4 : angle 3.94680 ( 48) hydrogen bonds : bond 0.06003 ( 687) hydrogen bonds : angle 4.31297 ( 2091) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.63933 ( 10) covalent geometry : bond 0.00282 (16458) covalent geometry : angle 0.57788 (22456) *********************** 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 304 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 223 time to evaluate : 1.894 Fit side-chains REVERT: A 64 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 185 GLU cc_start: 0.8338 (mp0) cc_final: 0.8025 (mp0) REVERT: A 279 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8072 (tp) REVERT: C 141 LYS cc_start: 0.7710 (mttt) cc_final: 0.7181 (ttpt) REVERT: C 241 MET cc_start: 0.7451 (tpp) cc_final: 0.6995 (tpp) REVERT: C 687 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: D 144 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8507 (tt) REVERT: E 525 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6722 (tt) outliers start: 81 outliers final: 47 residues processed: 281 average time/residue: 0.2887 time to fit residues: 124.1493 Evaluate side-chains 260 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 348 LEU Chi-restraints excluded: chain A residue 696 ILE 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 568 VAL 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 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 275 THR 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 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 566 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 52 GLN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123175 restraints weight = 21690.001| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.01 r_work: 0.3300 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1426 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= 0.109 Angle : 0.584 8.520 22538 Z= 0.270 Chirality : 0.045 0.325 2695 Planarity : 0.004 0.059 2716 Dihedral : 11.703 85.933 2587 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 4.34 % Allowed : 25.99 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1899 helix: 2.58 (0.20), residues: 701 sheet: -0.52 (0.28), residues: 379 loop : -2.17 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 85 HIS 0.002 0.001 HIS A 88 PHE 0.017 0.001 PHE A 256 TYR 0.010 0.001 TYR B 224 ARG 0.005 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 8) link_NAG-ASN : angle 2.72935 ( 24) link_BETA1-4 : bond 0.00876 ( 16) link_BETA1-4 : angle 3.80719 ( 48) hydrogen bonds : bond 0.05268 ( 687) hydrogen bonds : angle 4.04364 ( 2091) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.58355 ( 10) covalent geometry : bond 0.00239 (16458) covalent geometry : angle 0.55015 (22456) *********************** 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 296 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 218 time to evaluate : 1.645 Fit side-chains REVERT: A 64 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 185 GLU cc_start: 0.8369 (mp0) cc_final: 0.8116 (mp0) REVERT: C 141 LYS cc_start: 0.7678 (mttt) cc_final: 0.7006 (ttpt) REVERT: C 241 MET cc_start: 0.7424 (tpp) cc_final: 0.7036 (tpp) REVERT: C 687 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: D 59 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7707 (tp40) REVERT: D 144 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8455 (tt) REVERT: E 525 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6591 (tt) outliers start: 78 outliers final: 47 residues processed: 279 average time/residue: 0.2650 time to fit residues: 111.5065 Evaluate side-chains 263 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 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 225 ASP Chi-restraints excluded: chain B residue 281 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 C residue 108 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 167 PHE 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 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 59 GLN Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 186 MET 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 555 VAL 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 21 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 85 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 overall best weight: 1.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN C 44 HIS D 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117805 restraints weight = 22277.142| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.11 r_work: 0.3224 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16487 Z= 0.190 Angle : 0.650 8.037 22538 Z= 0.306 Chirality : 0.048 0.361 2695 Planarity : 0.004 0.064 2716 Dihedral : 11.064 77.579 2587 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.00 % Favored : 92.94 % Rotamer: Outliers : 5.84 % Allowed : 25.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1899 helix: 2.27 (0.20), residues: 701 sheet: -0.71 (0.27), residues: 384 loop : -2.29 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 85 HIS 0.005 0.001 HIS C 216 PHE 0.014 0.001 PHE B 162 TYR 0.012 0.001 TYR A 142 ARG 0.003 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 8) link_NAG-ASN : angle 2.86888 ( 24) link_BETA1-4 : bond 0.00764 ( 16) link_BETA1-4 : angle 3.78719 ( 48) hydrogen bonds : bond 0.06795 ( 687) hydrogen bonds : angle 4.36809 ( 2091) SS BOND : bond 0.00394 ( 5) SS BOND : angle 0.71565 ( 10) covalent geometry : bond 0.00468 (16458) covalent geometry : angle 0.62046 (22456) *********************** 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 308 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 203 time to evaluate : 1.697 Fit side-chains REVERT: A 64 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 144 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9032 (tt) REVERT: C 209 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (pt) REVERT: C 687 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: D 59 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7836 (tp40) REVERT: D 144 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8643 (tt) REVERT: D 165 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8171 (mp-120) REVERT: E 525 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6754 (tt) outliers start: 105 outliers final: 66 residues processed: 289 average time/residue: 0.2635 time to fit residues: 116.3402 Evaluate side-chains 267 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 193 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 217 ASP Chi-restraints excluded: chain A residue 226 ILE 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 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 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 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 121 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 189 LEU 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 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 148 ILE Chi-restraints excluded: chain D residue 165 GLN 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 279 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 CYS 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 126 GLU Chi-restraints excluded: chain E residue 127 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 137 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 57 optimal weight: 0.0050 chunk 84 optimal weight: 4.9990 chunk 4 optimal weight: 0.0030 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.148413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124398 restraints weight = 21856.639| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.05 r_work: 0.3306 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16487 Z= 0.107 Angle : 0.588 8.367 22538 Z= 0.273 Chirality : 0.044 0.325 2695 Planarity : 0.004 0.059 2716 Dihedral : 10.174 69.783 2587 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.85 % Favored : 94.10 % Rotamer: Outliers : 3.39 % Allowed : 27.71 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1899 helix: 2.64 (0.20), residues: 701 sheet: -0.51 (0.27), residues: 385 loop : -2.14 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 90 HIS 0.003 0.001 HIS C 216 PHE 0.016 0.001 PHE C 313 TYR 0.008 0.001 TYR B 224 ARG 0.004 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 8) link_NAG-ASN : angle 2.86487 ( 24) link_BETA1-4 : bond 0.00940 ( 16) link_BETA1-4 : angle 3.68322 ( 48) hydrogen bonds : bond 0.05218 ( 687) hydrogen bonds : angle 3.97980 ( 2091) SS BOND : bond 0.00214 ( 5) SS BOND : angle 0.54321 ( 10) covalent geometry : bond 0.00228 (16458) covalent geometry : angle 0.55633 (22456) *********************** 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 269 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 1.763 Fit side-chains REVERT: A 64 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: C 241 MET cc_start: 0.7426 (tpp) cc_final: 0.7032 (tpp) REVERT: C 687 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: D 144 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8448 (tt) REVERT: E 525 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6658 (tt) outliers start: 61 outliers final: 41 residues processed: 255 average time/residue: 0.2632 time to fit residues: 100.7157 Evaluate side-chains 246 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain A residue 327 ILE 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 100 VAL Chi-restraints excluded: chain B residue 118 TYR 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 295 ILE Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 541 ASP 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 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 695 ILE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain D residue 32 ASP 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 229 LYS Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 292 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 135 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 228 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 566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN C 44 HIS E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117746 restraints weight = 22339.191| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.21 r_work: 0.3208 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16487 Z= 0.181 Angle : 0.650 8.858 22538 Z= 0.304 Chirality : 0.047 0.391 2695 Planarity : 0.004 0.062 2716 Dihedral : 9.545 65.825 2587 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.21 % Favored : 92.68 % Rotamer: Outliers : 4.84 % Allowed : 26.04 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1899 helix: 2.28 (0.20), residues: 702 sheet: -0.71 (0.27), residues: 393 loop : -2.22 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 85 HIS 0.005 0.001 HIS C 216 PHE 0.013 0.001 PHE B 162 TYR 0.012 0.001 TYR A 142 ARG 0.006 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 2.86394 ( 24) link_BETA1-4 : bond 0.00900 ( 16) link_BETA1-4 : angle 3.87865 ( 48) hydrogen bonds : bond 0.06752 ( 687) hydrogen bonds : angle 4.30176 ( 2091) SS BOND : bond 0.00360 ( 5) SS BOND : angle 0.60145 ( 10) covalent geometry : bond 0.00439 (16458) covalent geometry : angle 0.61868 (22456) *********************** 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 286 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 199 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: B 144 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8948 (tt) REVERT: C 80 MET cc_start: 0.8876 (ttp) cc_final: 0.8676 (ttm) REVERT: C 687 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: D 59 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7730 (tp40) REVERT: D 144 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8530 (tt) REVERT: E 525 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6984 (tt) outliers start: 87 outliers final: 63 residues processed: 263 average time/residue: 0.2518 time to fit residues: 100.1687 Evaluate side-chains 260 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 108 LEU 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 352 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 144 LEU 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 323 SER 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 189 LEU 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 285 PHE 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 44 ILE 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 203 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 239 LEU 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 336 CYS Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 568 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 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 160 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 26 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.147981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123244 restraints weight = 21870.082| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.06 r_work: 0.3277 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1710 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= 0.109 Angle : 0.584 8.626 22538 Z= 0.271 Chirality : 0.044 0.345 2695 Planarity : 0.004 0.059 2716 Dihedral : 8.731 62.706 2587 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 3.12 % Allowed : 27.77 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1899 helix: 2.64 (0.20), residues: 702 sheet: -0.50 (0.27), residues: 391 loop : -2.12 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 90 HIS 0.004 0.001 HIS A 62 PHE 0.017 0.001 PHE C 313 TYR 0.008 0.001 TYR B 97 ARG 0.006 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 8) link_NAG-ASN : angle 2.76298 ( 24) link_BETA1-4 : bond 0.01043 ( 16) link_BETA1-4 : angle 3.76514 ( 48) hydrogen bonds : bond 0.05177 ( 687) hydrogen bonds : angle 3.91320 ( 2091) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.62737 ( 10) covalent geometry : bond 0.00233 (16458) covalent geometry : angle 0.55144 (22456) *********************** 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 260 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.896 Fit side-chains REVERT: A 64 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: C 241 MET cc_start: 0.7546 (tpp) cc_final: 0.7314 (tpt) REVERT: C 687 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: D 144 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8418 (tt) REVERT: E 525 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6899 (tt) outliers start: 56 outliers final: 42 residues processed: 246 average time/residue: 0.2593 time to fit residues: 95.5006 Evaluate side-chains 246 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 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 167 PHE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 321 THR 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 144 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 THR 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 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 162 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 168 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 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 = 0.3691 r_free = 0.3691 target = 0.147187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123821 restraints weight = 21952.896| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.95 r_work: 0.3285 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1759 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= 0.115 Angle : 0.586 9.331 22538 Z= 0.271 Chirality : 0.044 0.371 2695 Planarity : 0.004 0.058 2716 Dihedral : 8.138 59.965 2587 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 2.89 % Allowed : 28.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1899 helix: 2.66 (0.20), residues: 702 sheet: -0.50 (0.27), residues: 387 loop : -2.07 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 90 HIS 0.002 0.001 HIS C 216 PHE 0.015 0.001 PHE C 313 TYR 0.011 0.001 TYR A 142 ARG 0.007 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 2.74880 ( 24) link_BETA1-4 : bond 0.00991 ( 16) link_BETA1-4 : angle 3.77083 ( 48) hydrogen bonds : bond 0.05227 ( 687) hydrogen bonds : angle 3.87600 ( 2091) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.57486 ( 10) covalent geometry : bond 0.00261 (16458) covalent geometry : angle 0.55323 (22456) *********************** 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 253 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 1.738 Fit side-chains REVERT: A 64 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: C 687 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: D 144 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8425 (tt) REVERT: D 276 PHE cc_start: 0.7047 (m-10) cc_final: 0.6832 (m-80) REVERT: E 525 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6971 (tt) outliers start: 52 outliers final: 44 residues processed: 239 average time/residue: 0.2753 time to fit residues: 99.4405 Evaluate side-chains 246 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 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 218 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 321 THR 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 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 545 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 39 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 chunk 149 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.146452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123029 restraints weight = 22022.859| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.94 r_work: 0.3273 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1777 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= 0.123 Angle : 0.588 9.618 22538 Z= 0.273 Chirality : 0.044 0.379 2695 Planarity : 0.004 0.059 2716 Dihedral : 7.666 58.101 2587 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.37 % Favored : 93.52 % Rotamer: Outliers : 3.01 % Allowed : 28.05 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1899 helix: 2.61 (0.20), residues: 704 sheet: -0.49 (0.27), residues: 390 loop : -2.08 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 90 HIS 0.003 0.001 HIS C 216 PHE 0.016 0.001 PHE A 256 TYR 0.010 0.001 TYR A 142 ARG 0.006 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 8) link_NAG-ASN : angle 2.83426 ( 24) link_BETA1-4 : bond 0.01057 ( 16) link_BETA1-4 : angle 3.80916 ( 48) hydrogen bonds : bond 0.05444 ( 687) hydrogen bonds : angle 3.92211 ( 2091) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.60522 ( 10) covalent geometry : bond 0.00281 (16458) covalent geometry : angle 0.55440 (22456) ********************** 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 254 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 1.715 Fit side-chains REVERT: A 64 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: B 39 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7635 (mmm160) REVERT: C 80 MET cc_start: 0.8864 (ttp) cc_final: 0.8638 (ttm) REVERT: C 687 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 144 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8470 (tt) REVERT: D 276 PHE cc_start: 0.7020 (m-10) cc_final: 0.6820 (m-80) REVERT: E 525 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6944 (tt) outliers start: 54 outliers final: 46 residues processed: 242 average time/residue: 0.2634 time to fit residues: 96.6978 Evaluate side-chains 248 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 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 218 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 321 THR 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 140 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 545 VAL 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 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 57 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 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 = 0.3690 r_free = 0.3690 target = 0.147077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123135 restraints weight = 21904.427| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.98 r_work: 0.3277 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1814 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= 0.118 Angle : 0.580 9.779 22538 Z= 0.270 Chirality : 0.044 0.379 2695 Planarity : 0.004 0.059 2716 Dihedral : 7.397 57.738 2587 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 3.34 % Allowed : 27.88 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1899 helix: 2.65 (0.20), residues: 703 sheet: -0.46 (0.27), residues: 389 loop : -2.06 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.002 0.001 HIS C 216 PHE 0.016 0.001 PHE C 313 TYR 0.009 0.001 TYR A 142 ARG 0.007 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 8) link_NAG-ASN : angle 2.82200 ( 24) link_BETA1-4 : bond 0.01065 ( 16) link_BETA1-4 : angle 3.76387 ( 48) hydrogen bonds : bond 0.05318 ( 687) hydrogen bonds : angle 3.88539 ( 2091) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.61161 ( 10) covalent geometry : bond 0.00267 (16458) covalent geometry : angle 0.54659 (22456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8195.27 seconds wall clock time: 142 minutes 39.09 seconds (8559.09 seconds total)