Starting phenix.real_space_refine on Mon May 26 14:46:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c6f_45245/05_2025/9c6f_45245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c6f_45245/05_2025/9c6f_45245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c6f_45245/05_2025/9c6f_45245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c6f_45245/05_2025/9c6f_45245.map" model { file = "/net/cci-nas-00/data/ceres_data/9c6f_45245/05_2025/9c6f_45245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c6f_45245/05_2025/9c6f_45245.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 18042 2.51 5 N 4877 2.21 5 O 5265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28361 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4710 Classifications: {'peptide': 598} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 25, 'TRANS': 569} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4710 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 4711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4711 Classifications: {'peptide': 598} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 570} Chain: "D" Number of atoms: 4711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4711 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570} Chain: "E" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4710 Classifications: {'peptide': 598} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 25, 'TRANS': 569} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4710 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.04, per 1000 atoms: 0.60 Number of scatterers: 28361 At special positions: 0 Unit cell: (208.455, 197.765, 97.279, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 9 15.00 Mg 6 11.99 O 5265 8.00 N 4877 7.00 C 18042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 3.6 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 17 sheets defined 53.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.703A pdb=" N GLU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.237A pdb=" N LEU A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 89 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.629A pdb=" N MET A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.674A pdb=" N ILE A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 200 through 206 removed outlier: 4.291A pdb=" N ASN A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 223 removed outlier: 4.557A pdb=" N TRP A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.930A pdb=" N ASP A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 347 through 369 removed outlier: 4.006A pdb=" N LYS A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 4.285A pdb=" N SER A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.930A pdb=" N GLN A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 removed outlier: 3.732A pdb=" N GLU A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.804A pdb=" N THR A 485 " --> pdb=" O ASP A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 557 through 571 Processing helix chain 'A' and resid 575 through 597 Processing helix chain 'B' and resid 14 through 21 removed outlier: 4.031A pdb=" N GLU B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.547A pdb=" N SER B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.703A pdb=" N SER B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.822A pdb=" N ILE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 162 through 167' Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 215 through 223 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.581A pdb=" N ILE B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.512A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 308 through 325 Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 347 through 369 removed outlier: 3.551A pdb=" N LYS B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 404 removed outlier: 4.080A pdb=" N SER B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 430 through 433 removed outlier: 4.137A pdb=" N HIS B 433 " --> pdb=" O TYR B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 434 through 441 removed outlier: 4.360A pdb=" N VAL B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.557A pdb=" N ILE B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 478 removed outlier: 3.869A pdb=" N GLU B 478 " --> pdb=" O ASN B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 557 through 572 removed outlier: 3.609A pdb=" N ALA B 572 " --> pdb=" O SER B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 597 Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.855A pdb=" N GLU C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 4.422A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 88 Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 133 through 143 removed outlier: 4.076A pdb=" N ASP C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.055A pdb=" N GLN C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 Processing helix chain 'C' and resid 227 through 236 removed outlier: 4.286A pdb=" N ALA C 232 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.738A pdb=" N LEU C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.788A pdb=" N GLY C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 307 through 325 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.569A pdb=" N ALA C 340 " --> pdb=" O ASN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.771A pdb=" N LYS C 344 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 369 removed outlier: 3.555A pdb=" N LYS C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 4.028A pdb=" N SER C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 442 removed outlier: 4.141A pdb=" N ARG C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 464 removed outlier: 4.073A pdb=" N GLN C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 4.154A pdb=" N LEU C 477 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 478 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 removed outlier: 3.683A pdb=" N THR C 485 " --> pdb=" O ASP C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 557 through 572 Processing helix chain 'C' and resid 575 through 596 removed outlier: 3.652A pdb=" N ARG C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 70 through 88 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 157 through 162 removed outlier: 4.150A pdb=" N ARG D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 180 through 199 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.794A pdb=" N GLN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.835A pdb=" N ALA D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.616A pdb=" N GLY D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 4.217A pdb=" N LYS D 303 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 325 removed outlier: 3.718A pdb=" N LEU D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 369 removed outlier: 3.632A pdb=" N LYS D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 404 removed outlier: 4.150A pdb=" N SER D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 454 through 465 Processing helix chain 'D' and resid 475 through 478 removed outlier: 3.918A pdb=" N GLU D 478 " --> pdb=" O ASN D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 478' Processing helix chain 'D' and resid 479 through 489 removed outlier: 3.534A pdb=" N ARG D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 541 through 553 removed outlier: 3.805A pdb=" N ALA D 550 " --> pdb=" O LEU D 546 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 571 Processing helix chain 'D' and resid 575 through 598 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.618A pdb=" N GLU E 18 " --> pdb=" O MET E 14 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 removed outlier: 4.233A pdb=" N LEU E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 133 through 144 Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.571A pdb=" N LEU E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 removed outlier: 3.643A pdb=" N MET E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.872A pdb=" N ALA E 212 " --> pdb=" O PRO E 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 213 " --> pdb=" O SER E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 removed outlier: 3.634A pdb=" N GLN E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 230 through 235 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.718A pdb=" N LEU E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 269 removed outlier: 3.716A pdb=" N LEU E 268 " --> pdb=" O GLU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 298 Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 336 through 340 Processing helix chain 'E' and resid 347 through 369 removed outlier: 3.666A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 405 removed outlier: 4.243A pdb=" N SER E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 395 " --> pdb=" O SER E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 425 removed outlier: 3.985A pdb=" N LYS E 424 " --> pdb=" O PHE E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 442 removed outlier: 4.250A pdb=" N HIS E 439 " --> pdb=" O PHE E 435 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG E 440 " --> pdb=" O LYS E 436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 464 removed outlier: 3.715A pdb=" N TRP E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 478 removed outlier: 3.824A pdb=" N LEU E 477 " --> pdb=" O LEU E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 Processing helix chain 'E' and resid 496 through 505 Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 557 through 572 removed outlier: 3.644A pdb=" N ALA E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 600 removed outlier: 3.975A pdb=" N ASN E 600 " --> pdb=" O ILE E 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 23 removed outlier: 3.652A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 70 through 87 Processing helix chain 'F' and resid 103 through 118 Processing helix chain 'F' and resid 133 through 144 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 180 through 199 removed outlier: 3.927A pdb=" N ASP F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 removed outlier: 4.169A pdb=" N GLN F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 215 through 223 Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 254 through 262 Processing helix chain 'F' and resid 307 through 325 Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.511A pdb=" N ALA F 340 " --> pdb=" O PRO F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 369 removed outlier: 3.527A pdb=" N LYS F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 404 removed outlier: 4.277A pdb=" N SER F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 431 through 441 removed outlier: 3.629A pdb=" N PHE F 435 " --> pdb=" O TYR F 431 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 436 " --> pdb=" O GLU F 432 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG F 440 " --> pdb=" O LYS F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 464 Processing helix chain 'F' and resid 475 through 478 removed outlier: 3.796A pdb=" N GLU F 478 " --> pdb=" O ASN F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 475 through 478' Processing helix chain 'F' and resid 479 through 490 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'F' and resid 517 through 525 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 541 through 553 removed outlier: 3.969A pdb=" N ALA F 550 " --> pdb=" O LEU F 546 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 572 removed outlier: 3.519A pdb=" N ALA F 572 " --> pdb=" O SER F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 597 Processing helix chain 'F' and resid 598 through 600 No H-bonds generated for 'chain 'F' and resid 598 through 600' Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.523A pdb=" N VAL A 32 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 5 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE A 33 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS A 7 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 4 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS A 98 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 6 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 245 removed outlier: 7.383A pdb=" N LYS A 239 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 330 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP A 241 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 332 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N HIS A 243 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N CYS A 334 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N HIS A 245 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 328 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN A 377 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA A 330 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU A 379 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 332 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 381 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS A 334 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER A 383 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL A 414 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 378 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 416 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL A 380 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 418 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA A 382 " --> pdb=" O LEU A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 448 removed outlier: 7.231A pdb=" N ALA A 447 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 470 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 61 removed outlier: 6.869A pdb=" N VAL B 30 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR B 60 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 32 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 5 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE B 33 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 7 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL B 4 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS B 98 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 6 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLN B 120 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR B 153 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL B 122 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 240 removed outlier: 7.325A pdb=" N LYS B 239 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 330 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 244 " --> pdb=" O ARG B 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 239 through 240 removed outlier: 7.325A pdb=" N LYS B 239 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 330 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 328 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASN B 377 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 330 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU B 379 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 332 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 381 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 334 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL B 414 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 378 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 416 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 380 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL B 445 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N GLY B 471 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA B 447 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 470 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 61 removed outlier: 6.993A pdb=" N VAL C 30 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 32 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 5 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE C 33 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS C 7 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS C 98 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER C 8 " --> pdb=" O CYS C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 239 through 245 removed outlier: 6.496A pdb=" N LYS C 239 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLU C 331 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP C 241 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG C 333 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N HIS C 243 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N VAL C 414 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU C 378 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 416 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL C 380 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 414 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 469 through 471 removed outlier: 6.252A pdb=" N LEU C 470 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 61 removed outlier: 3.520A pdb=" N SER D 58 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL D 4 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N CYS D 98 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 6 " --> pdb=" O CYS D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 239 through 245 removed outlier: 4.339A pdb=" N VAL D 240 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLU D 331 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU D 242 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG D 333 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS D 244 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA D 328 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ASN D 377 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA D 330 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU D 379 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE D 332 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D 381 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS D 334 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL D 414 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU D 378 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D 416 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL D 380 " --> pdb=" O VAL D 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 469 through 471 removed outlier: 3.593A pdb=" N GLU D 494 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 62 removed outlier: 3.646A pdb=" N SER E 58 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 32 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU E 5 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE E 33 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N CYS E 7 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR E 35 " --> pdb=" O CYS E 7 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS E 98 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLN E 120 " --> pdb=" O TYR E 153 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR E 153 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL E 122 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET E 151 " --> pdb=" O VAL E 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 245 removed outlier: 7.406A pdb=" N LYS E 239 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA E 330 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP E 241 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE E 332 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N HIS E 243 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N CYS E 334 " --> pdb=" O HIS E 243 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N HIS E 245 " --> pdb=" O CYS E 334 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE E 413 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU E 378 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY E 415 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 469 through 471 removed outlier: 6.561A pdb=" N LEU E 470 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 56 through 62 removed outlier: 7.158A pdb=" N VAL F 30 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR F 60 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL F 32 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N CYS F 62 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR F 34 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 33 " --> pdb=" O CYS F 7 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR F 35 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL F 4 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N CYS F 98 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU F 6 " --> pdb=" O CYS F 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 239 through 245 removed outlier: 4.274A pdb=" N VAL F 240 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLU F 331 " --> pdb=" O VAL F 240 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU F 242 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG F 333 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS F 244 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA F 328 " --> pdb=" O HIS F 375 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASN F 377 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA F 330 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU F 379 " --> pdb=" O ALA F 330 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE F 332 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE F 381 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS F 334 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL F 414 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU F 378 " --> pdb=" O VAL F 414 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL F 416 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL F 380 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL F 445 " --> pdb=" O ARG F 469 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N GLY F 471 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA F 447 " --> pdb=" O GLY F 471 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU F 470 " --> pdb=" O GLU F 494 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 493 " --> pdb=" O SER F 529 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3468 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: 9.14 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5024 1.32 - 1.45: 7347 1.45 - 1.57: 16353 1.57 - 1.70: 21 1.70 - 1.82: 246 Bond restraints: 28991 Sorted by residual: bond pdb=" C1' ATP E 701 " pdb=" C2' ATP E 701 " ideal model delta sigma weight residual 1.531 1.303 0.228 1.20e-02 6.94e+03 3.62e+02 bond pdb=" C1' ATP A 701 " pdb=" C2' ATP A 701 " ideal model delta sigma weight residual 1.531 1.303 0.228 1.20e-02 6.94e+03 3.61e+02 bond pdb=" C1' ATP D 701 " pdb=" C2' ATP D 701 " ideal model delta sigma weight residual 1.531 1.303 0.228 1.20e-02 6.94e+03 3.60e+02 bond pdb=" C1' ATP E 701 " pdb=" O4' ATP E 701 " ideal model delta sigma weight residual 1.416 1.620 -0.204 1.30e-02 5.92e+03 2.47e+02 bond pdb=" C1' ATP D 701 " pdb=" O4' ATP D 701 " ideal model delta sigma weight residual 1.416 1.620 -0.204 1.30e-02 5.92e+03 2.46e+02 ... (remaining 28986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 38965 3.50 - 6.99: 258 6.99 - 10.49: 62 10.49 - 13.98: 6 13.98 - 17.48: 7 Bond angle restraints: 39298 Sorted by residual: angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 122.39 17.48 1.00e+00 1.00e+00 3.05e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 122.79 17.08 1.00e+00 1.00e+00 2.92e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 122.80 17.07 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATP E 701 " pdb=" O3A ATP E 701 " pdb=" PB ATP E 701 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 123.98 12.85 1.00e+00 1.00e+00 1.65e+02 ... (remaining 39293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14624 17.86 - 35.71: 2123 35.71 - 53.57: 609 53.57 - 71.42: 117 71.42 - 89.28: 47 Dihedral angle restraints: 17520 sinusoidal: 7080 harmonic: 10440 Sorted by residual: dihedral pdb=" CD ARG D 161 " pdb=" NE ARG D 161 " pdb=" CZ ARG D 161 " pdb=" NH1 ARG D 161 " ideal model delta sinusoidal sigma weight residual 0.00 71.36 -71.36 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CD ARG C 175 " pdb=" NE ARG C 175 " pdb=" CZ ARG C 175 " pdb=" NH1 ARG C 175 " ideal model delta sinusoidal sigma weight residual 0.00 61.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CA GLU D 136 " pdb=" C GLU D 136 " pdb=" N MET D 137 " pdb=" CA MET D 137 " ideal model delta harmonic sigma weight residual 180.00 149.96 30.04 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 17517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3638 0.059 - 0.119: 649 0.119 - 0.178: 53 0.178 - 0.238: 9 0.238 - 0.297: 7 Chirality restraints: 4356 Sorted by residual: chirality pdb=" C2' ATP D 701 " pdb=" C1' ATP D 701 " pdb=" C3' ATP D 701 " pdb=" O2' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP E 701 " pdb=" C1' ATP E 701 " pdb=" C3' ATP E 701 " pdb=" O2' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP A 701 " pdb=" C1' ATP A 701 " pdb=" C3' ATP A 701 " pdb=" O2' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.39 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 4353 not shown) Planarity restraints: 5081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 161 " 1.045 9.50e-02 1.11e+02 4.68e-01 1.32e+02 pdb=" NE ARG D 161 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG D 161 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 161 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 161 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 175 " -0.965 9.50e-02 1.11e+02 4.32e-01 1.13e+02 pdb=" NE ARG C 175 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG C 175 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 175 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 175 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 507 " -0.088 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO F 508 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO F 508 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO F 508 " -0.063 5.00e-02 4.00e+02 ... (remaining 5078 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 464 2.60 - 3.18: 26110 3.18 - 3.75: 47890 3.75 - 4.33: 61096 4.33 - 4.90: 98721 Nonbonded interactions: 234281 Sorted by model distance: nonbonded pdb=" OD1 ASP B 533 " pdb="MG MG B 701 " model vdw 2.031 2.170 nonbonded pdb=" NE2 HIS C 243 " pdb="MG MG C 701 " model vdw 2.083 2.250 nonbonded pdb=" NE2 HIS E 245 " pdb="MG MG E 702 " model vdw 2.110 2.250 nonbonded pdb=" NE2 HIS E 243 " pdb="MG MG E 702 " model vdw 2.117 2.250 nonbonded pdb=" NE2 HIS D 245 " pdb="MG MG D 702 " model vdw 2.119 2.250 ... (remaining 234276 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' and resid 3 through 600) selection = (chain 'B' and resid 3 through 600) selection = (chain 'C' and (resid 3 through 599 or (resid 600 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1)))) selection = (chain 'D' and (resid 3 through 599 or (resid 600 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1)))) selection = (chain 'E' and resid 3 through 600) selection = (chain 'F' and resid 3 through 600) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 59.630 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.120 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:2.670 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.005 0.228 28992 Z= 0.394 Angle : 0.790 17.478 39298 Z= 0.463 Chirality : 0.046 0.297 4356 Planarity : 0.010 0.468 5081 Dihedral : 18.568 89.275 10764 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.70 % Allowed : 5.90 % Favored : 93.40 % Rotamer: Outliers : 1.26 % Allowed : 33.43 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.16 (0.14), residues: 3576 helix: 0.57 (0.13), residues: 1600 sheet: 0.05 (0.27), residues: 396 loop : -0.77 (0.17), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 157 HIS 0.007 0.001 HIS C 576 PHE 0.044 0.001 PHE F 138 TYR 0.030 0.001 TYR B 430 ARG 0.009 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.16030 ( 1209) hydrogen bonds : angle 6.33094 ( 3468) covalent geometry : bond 0.00549 (28991) covalent geometry : angle 0.78987 (39298) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 403 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8585 (pmm) cc_final: 0.8164 (pmm) REVERT: A 154 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 171 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5484 (pm20) REVERT: A 294 MET cc_start: 0.8528 (pmm) cc_final: 0.8246 (tmm) REVERT: A 580 MET cc_start: 0.8633 (mtt) cc_final: 0.8406 (mmp) REVERT: B 17 PRO cc_start: 0.9461 (Cg_exo) cc_final: 0.9198 (Cg_endo) REVERT: B 21 HIS cc_start: 0.8661 (m90) cc_final: 0.8247 (m90) REVERT: B 72 ARG cc_start: 0.8048 (tmt170) cc_final: 0.7696 (tpt90) REVERT: B 106 MET cc_start: 0.6324 (ptp) cc_final: 0.5764 (ptp) REVERT: B 139 ASP cc_start: 0.9130 (m-30) cc_final: 0.8825 (t0) REVERT: B 224 LEU cc_start: 0.8662 (tt) cc_final: 0.8450 (mt) REVERT: B 255 LEU cc_start: 0.8641 (mm) cc_final: 0.8257 (tp) REVERT: C 153 TYR cc_start: 0.9050 (t80) cc_final: 0.8596 (t80) REVERT: C 319 TYR cc_start: 0.8804 (t80) cc_final: 0.8506 (t80) REVERT: C 427 ARG cc_start: 0.4806 (mmm-85) cc_final: 0.4304 (mmp80) REVERT: C 483 MET cc_start: 0.7777 (mmt) cc_final: 0.7492 (mmt) REVERT: C 533 ASP cc_start: 0.8901 (t70) cc_final: 0.8290 (t70) REVERT: C 547 LEU cc_start: 0.8891 (pp) cc_final: 0.8680 (pp) REVERT: D 124 HIS cc_start: 0.8580 (m170) cc_final: 0.8336 (m-70) REVERT: D 211 LEU cc_start: 0.7580 (tt) cc_final: 0.7315 (tt) REVERT: D 294 MET cc_start: 0.8648 (mpp) cc_final: 0.8030 (mmm) REVERT: D 298 ASN cc_start: 0.8758 (t0) cc_final: 0.8237 (m-40) REVERT: D 378 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9056 (mm) REVERT: D 431 TYR cc_start: 0.6144 (m-80) cc_final: 0.5895 (m-80) REVERT: D 432 GLU cc_start: 0.7695 (pm20) cc_final: 0.7232 (mt-10) REVERT: D 456 GLU cc_start: 0.8412 (tp30) cc_final: 0.7845 (tp30) REVERT: D 588 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7792 (ttp80) REVERT: E 151 MET cc_start: 0.7355 (pmm) cc_final: 0.7129 (pmm) REVERT: E 560 ASP cc_start: 0.8612 (m-30) cc_final: 0.8249 (m-30) REVERT: F 25 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8256 (tp30) REVERT: F 588 ARG cc_start: 0.6907 (mtt180) cc_final: 0.6505 (mtt-85) outliers start: 39 outliers final: 19 residues processed: 436 average time/residue: 0.3848 time to fit residues: 266.3174 Evaluate side-chains 331 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 206 optimal weight: 9.9990 chunk 321 optimal weight: 0.0470 overall best weight: 1.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN C 205 GLN C 258 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 ASN ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN F 460 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.145007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098272 restraints weight = 61841.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102066 restraints weight = 39069.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102494 restraints weight = 28366.095| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28992 Z= 0.150 Angle : 0.653 11.223 39298 Z= 0.328 Chirality : 0.044 0.212 4356 Planarity : 0.005 0.116 5081 Dihedral : 8.091 87.397 3993 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.82 % Favored : 93.96 % Rotamer: Outliers : 3.50 % Allowed : 31.23 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: -0.16 (0.14), residues: 3576 helix: 0.61 (0.13), residues: 1671 sheet: 0.02 (0.26), residues: 410 loop : -0.87 (0.17), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 157 HIS 0.005 0.001 HIS C 21 PHE 0.021 0.001 PHE C 138 TYR 0.025 0.001 TYR B 430 ARG 0.009 0.000 ARG D 161 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 1209) hydrogen bonds : angle 4.92471 ( 3468) covalent geometry : bond 0.00348 (28991) covalent geometry : angle 0.65321 (39298) Misc. bond : bond 0.00262 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 340 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7127 (mpp) cc_final: 0.6590 (mpp) REVERT: A 325 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 547 LEU cc_start: 0.9047 (tt) cc_final: 0.8816 (tp) REVERT: B 21 HIS cc_start: 0.8550 (m90) cc_final: 0.8123 (m90) REVERT: B 72 ARG cc_start: 0.7998 (tmt170) cc_final: 0.7676 (tpt90) REVERT: B 81 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8520 (pp) REVERT: B 106 MET cc_start: 0.6429 (ptp) cc_final: 0.6066 (ptp) REVERT: B 224 LEU cc_start: 0.9263 (tt) cc_final: 0.8839 (tp) REVERT: B 255 LEU cc_start: 0.8471 (mm) cc_final: 0.8241 (tp) REVERT: B 468 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7677 (mtm180) REVERT: C 14 MET cc_start: 0.6982 (tpt) cc_final: 0.6247 (tpp) REVERT: C 89 MET cc_start: 0.8399 (mmm) cc_final: 0.7737 (mmm) REVERT: C 151 MET cc_start: 0.8327 (pmm) cc_final: 0.8092 (pmm) REVERT: C 153 TYR cc_start: 0.8867 (t80) cc_final: 0.8452 (t80) REVERT: C 165 LYS cc_start: 0.6836 (tptp) cc_final: 0.6365 (mmtm) REVERT: C 196 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6752 (ptp) REVERT: C 205 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: C 319 TYR cc_start: 0.8949 (t80) cc_final: 0.8743 (t80) REVERT: C 365 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 384 ARG cc_start: 0.3828 (mmt180) cc_final: 0.2437 (mpt90) REVERT: C 494 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: C 533 ASP cc_start: 0.8639 (t70) cc_final: 0.7972 (t70) REVERT: D 11 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6726 (t70) REVERT: D 93 GLU cc_start: 0.8142 (pm20) cc_final: 0.7840 (pm20) REVERT: D 123 PHE cc_start: 0.7844 (p90) cc_final: 0.7591 (p90) REVERT: D 432 GLU cc_start: 0.7694 (pm20) cc_final: 0.7429 (mt-10) REVERT: D 456 GLU cc_start: 0.7897 (tp30) cc_final: 0.7619 (tp30) REVERT: E 246 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9112 (tp) REVERT: E 313 ARG cc_start: 0.8018 (tpm170) cc_final: 0.7177 (tpp-160) REVERT: E 560 ASP cc_start: 0.8482 (m-30) cc_final: 0.8163 (m-30) REVERT: F 25 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8279 (tp30) REVERT: F 117 PHE cc_start: 0.8974 (m-80) cc_final: 0.8763 (m-80) REVERT: F 138 PHE cc_start: 0.7123 (m-10) cc_final: 0.6895 (m-10) REVERT: F 560 ASP cc_start: 0.8381 (m-30) cc_final: 0.8149 (m-30) REVERT: F 588 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6726 (mtt-85) outliers start: 108 outliers final: 41 residues processed: 427 average time/residue: 0.3765 time to fit residues: 258.4284 Evaluate side-chains 356 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 11 HIS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain F residue 76 PHE Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 222 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 0.0010 chunk 196 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 336 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 205 GLN B 375 HIS ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS F 83 GLN ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.141959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094542 restraints weight = 61861.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097886 restraints weight = 39490.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098449 restraints weight = 29105.577| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28992 Z= 0.206 Angle : 0.658 11.929 39298 Z= 0.331 Chirality : 0.045 0.215 4356 Planarity : 0.004 0.117 5081 Dihedral : 7.321 85.507 3962 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.10 % Favored : 93.68 % Rotamer: Outliers : 4.72 % Allowed : 30.42 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: -0.20 (0.14), residues: 3576 helix: 0.64 (0.13), residues: 1663 sheet: 0.04 (0.26), residues: 398 loop : -0.99 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.007 0.001 HIS C 11 PHE 0.019 0.002 PHE E 33 TYR 0.023 0.002 TYR A 153 ARG 0.006 0.000 ARG B 588 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 1209) hydrogen bonds : angle 4.82332 ( 3468) covalent geometry : bond 0.00490 (28991) covalent geometry : angle 0.65790 (39298) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 319 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7181 (tppt) REVERT: A 106 MET cc_start: 0.7237 (mpp) cc_final: 0.6640 (mpp) REVERT: A 110 LEU cc_start: 0.9052 (tp) cc_final: 0.8826 (tp) REVERT: A 404 MET cc_start: 0.8088 (tmm) cc_final: 0.7784 (tmm) REVERT: B 21 HIS cc_start: 0.8629 (m90) cc_final: 0.8174 (m90) REVERT: B 72 ARG cc_start: 0.7950 (tmt170) cc_final: 0.7534 (tpt90) REVERT: B 81 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 106 MET cc_start: 0.6571 (ptp) cc_final: 0.6148 (ptp) REVERT: B 224 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8770 (tp) REVERT: B 255 LEU cc_start: 0.8574 (mm) cc_final: 0.8308 (tp) REVERT: B 484 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7459 (ptp-110) REVERT: B 559 MET cc_start: 0.9076 (tpp) cc_final: 0.8840 (tpp) REVERT: C 14 MET cc_start: 0.7009 (tpt) cc_final: 0.6288 (tpp) REVERT: C 80 MET cc_start: 0.8790 (mmm) cc_final: 0.8439 (mmm) REVERT: C 89 MET cc_start: 0.8501 (mmm) cc_final: 0.7752 (mmm) REVERT: C 153 TYR cc_start: 0.8889 (t80) cc_final: 0.8496 (t80) REVERT: C 157 TRP cc_start: 0.7613 (t60) cc_final: 0.6836 (t-100) REVERT: C 365 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: C 384 ARG cc_start: 0.4346 (mmt180) cc_final: 0.3447 (mmt180) REVERT: C 385 LYS cc_start: 0.5246 (OUTLIER) cc_final: 0.4684 (mmmt) REVERT: C 494 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: C 533 ASP cc_start: 0.8796 (t0) cc_final: 0.8193 (t70) REVERT: D 92 ASN cc_start: 0.8772 (t0) cc_final: 0.8312 (t0) REVERT: D 93 GLU cc_start: 0.8202 (pm20) cc_final: 0.7775 (pm20) REVERT: D 123 PHE cc_start: 0.7978 (p90) cc_final: 0.7716 (p90) REVERT: D 432 GLU cc_start: 0.7815 (pm20) cc_final: 0.7474 (mt-10) REVERT: D 456 GLU cc_start: 0.7928 (tp30) cc_final: 0.7687 (tp30) REVERT: E 246 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9139 (tp) REVERT: E 294 MET cc_start: 0.7727 (mmm) cc_final: 0.7527 (mmt) REVERT: E 313 ARG cc_start: 0.7951 (tpm170) cc_final: 0.7063 (tpp-160) REVERT: E 406 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: E 498 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: E 560 ASP cc_start: 0.8585 (m-30) cc_final: 0.8238 (m-30) REVERT: F 138 PHE cc_start: 0.7205 (m-10) cc_final: 0.6987 (m-10) REVERT: F 188 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: F 560 ASP cc_start: 0.8592 (m-30) cc_final: 0.8314 (m-30) outliers start: 146 outliers final: 69 residues processed: 443 average time/residue: 0.3821 time to fit residues: 273.1460 Evaluate side-chains 370 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 290 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 406 GLN Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 494 GLU Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 119 optimal weight: 40.0000 chunk 190 optimal weight: 0.9990 chunk 335 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN B 500 ASN C 111 GLN ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.142144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095033 restraints weight = 62309.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098564 restraints weight = 39629.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099069 restraints weight = 29062.572| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28992 Z= 0.199 Angle : 0.654 11.093 39298 Z= 0.330 Chirality : 0.045 0.197 4356 Planarity : 0.004 0.116 5081 Dihedral : 7.165 78.071 3955 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.21 % Favored : 93.57 % Rotamer: Outliers : 4.85 % Allowed : 30.81 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: -0.22 (0.14), residues: 3576 helix: 0.60 (0.13), residues: 1666 sheet: -0.09 (0.26), residues: 410 loop : -0.94 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 157 HIS 0.011 0.001 HIS C 576 PHE 0.014 0.001 PHE C 573 TYR 0.020 0.002 TYR B 430 ARG 0.004 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1209) hydrogen bonds : angle 4.77277 ( 3468) covalent geometry : bond 0.00472 (28991) covalent geometry : angle 0.65366 (39298) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 307 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7191 (tppt) REVERT: A 106 MET cc_start: 0.7145 (mpp) cc_final: 0.6377 (mpp) REVERT: A 110 LEU cc_start: 0.9079 (tp) cc_final: 0.8845 (tp) REVERT: B 21 HIS cc_start: 0.8615 (m90) cc_final: 0.8136 (m90) REVERT: B 72 ARG cc_start: 0.7962 (tmt170) cc_final: 0.7671 (tpt90) REVERT: B 81 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 106 MET cc_start: 0.6729 (ptp) cc_final: 0.6241 (ptp) REVERT: B 107 SER cc_start: 0.9360 (p) cc_final: 0.9131 (p) REVERT: B 167 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6647 (mm) REVERT: B 224 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 255 LEU cc_start: 0.8500 (mm) cc_final: 0.8254 (tp) REVERT: B 271 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6800 (mtt180) REVERT: B 314 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 389 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6098 (p0) REVERT: B 484 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7446 (ttp-170) REVERT: C 14 MET cc_start: 0.7305 (tpt) cc_final: 0.6701 (tpp) REVERT: C 89 MET cc_start: 0.8553 (mmm) cc_final: 0.7796 (mmm) REVERT: C 153 TYR cc_start: 0.8879 (t80) cc_final: 0.8515 (t80) REVERT: C 157 TRP cc_start: 0.7627 (t60) cc_final: 0.6902 (t-100) REVERT: C 196 MET cc_start: 0.7165 (ptp) cc_final: 0.6727 (ptp) REVERT: C 365 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: C 385 LYS cc_start: 0.5135 (OUTLIER) cc_final: 0.4385 (mmmt) REVERT: C 494 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: C 533 ASP cc_start: 0.8794 (t0) cc_final: 0.8222 (t70) REVERT: D 92 ASN cc_start: 0.8797 (t0) cc_final: 0.8292 (t0) REVERT: D 93 GLU cc_start: 0.8124 (pm20) cc_final: 0.7720 (pm20) REVERT: D 339 TYR cc_start: 0.8141 (m-10) cc_final: 0.7731 (m-10) REVERT: D 404 MET cc_start: 0.8793 (ppp) cc_final: 0.8591 (ppp) REVERT: D 456 GLU cc_start: 0.7915 (tp30) cc_final: 0.7684 (tp30) REVERT: E 246 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9138 (tp) REVERT: E 294 MET cc_start: 0.7689 (mmm) cc_final: 0.7474 (mmt) REVERT: E 313 ARG cc_start: 0.7937 (tpm170) cc_final: 0.7053 (tpp-160) REVERT: E 404 MET cc_start: 0.7943 (tmm) cc_final: 0.7574 (tmm) REVERT: E 498 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: E 560 ASP cc_start: 0.8589 (m-30) cc_final: 0.8230 (m-30) REVERT: E 580 MET cc_start: 0.8341 (mmm) cc_final: 0.7930 (mmm) REVERT: F 138 PHE cc_start: 0.7502 (m-10) cc_final: 0.7251 (m-10) REVERT: F 560 ASP cc_start: 0.8608 (m-30) cc_final: 0.8297 (m-30) outliers start: 150 outliers final: 92 residues processed: 438 average time/residue: 0.3670 time to fit residues: 262.4474 Evaluate side-chains 390 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 285 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 345 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 138 optimal weight: 0.0970 chunk 201 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 338 optimal weight: 0.9980 chunk 1 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN D 576 HIS ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 405 GLN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.144736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097239 restraints weight = 61447.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102808 restraints weight = 37629.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102861 restraints weight = 24875.252| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28992 Z= 0.118 Angle : 0.622 10.296 39298 Z= 0.307 Chirality : 0.043 0.204 4356 Planarity : 0.004 0.116 5081 Dihedral : 6.991 74.386 3955 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.37 % Favored : 94.41 % Rotamer: Outliers : 4.69 % Allowed : 31.52 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: -0.00 (0.14), residues: 3576 helix: 0.82 (0.13), residues: 1649 sheet: 0.10 (0.26), residues: 406 loop : -0.88 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 157 HIS 0.006 0.001 HIS C 21 PHE 0.020 0.001 PHE E 33 TYR 0.019 0.001 TYR B 430 ARG 0.004 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1209) hydrogen bonds : angle 4.50029 ( 3468) covalent geometry : bond 0.00278 (28991) covalent geometry : angle 0.62208 (39298) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 334 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8082 (mtpt) REVERT: A 88 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7213 (ttmm) REVERT: A 106 MET cc_start: 0.7048 (mpp) cc_final: 0.6231 (mpp) REVERT: A 110 LEU cc_start: 0.9021 (tp) cc_final: 0.8802 (tp) REVERT: A 303 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7095 (ptpp) REVERT: A 404 MET cc_start: 0.7940 (tmm) cc_final: 0.7562 (tmm) REVERT: A 478 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: A 531 ASN cc_start: 0.9144 (m110) cc_final: 0.8883 (m-40) REVERT: B 21 HIS cc_start: 0.8519 (m90) cc_final: 0.8045 (m90) REVERT: B 72 ARG cc_start: 0.7930 (tmt170) cc_final: 0.7453 (tpt90) REVERT: B 81 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8433 (pp) REVERT: B 106 MET cc_start: 0.6778 (ptp) cc_final: 0.6256 (ptp) REVERT: B 196 MET cc_start: 0.6816 (ppp) cc_final: 0.5442 (ppp) REVERT: B 224 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8740 (tp) REVERT: B 255 LEU cc_start: 0.8470 (mm) cc_final: 0.8254 (tp) REVERT: B 271 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6645 (mtt180) REVERT: B 298 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8565 (m110) REVERT: B 389 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.5685 (p0) REVERT: B 454 ASP cc_start: 0.7705 (p0) cc_final: 0.7346 (p0) REVERT: B 484 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7385 (ttp-170) REVERT: B 559 MET cc_start: 0.8938 (tpp) cc_final: 0.8712 (tpp) REVERT: C 14 MET cc_start: 0.7536 (tpt) cc_final: 0.6991 (tpp) REVERT: C 89 MET cc_start: 0.8403 (mmm) cc_final: 0.7758 (mmm) REVERT: C 141 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6923 (tt) REVERT: C 153 TYR cc_start: 0.8889 (t80) cc_final: 0.8508 (t80) REVERT: C 157 TRP cc_start: 0.7555 (t60) cc_final: 0.6979 (t-100) REVERT: C 196 MET cc_start: 0.7055 (ptp) cc_final: 0.6771 (ptp) REVERT: C 365 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: C 385 LYS cc_start: 0.5224 (OUTLIER) cc_final: 0.4398 (mmmt) REVERT: C 460 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: C 483 MET cc_start: 0.8173 (tpp) cc_final: 0.7819 (mmt) REVERT: C 494 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: C 533 ASP cc_start: 0.8670 (t0) cc_final: 0.8113 (t70) REVERT: D 20 PHE cc_start: 0.7908 (t80) cc_final: 0.7693 (t80) REVERT: D 92 ASN cc_start: 0.8781 (t0) cc_final: 0.8297 (t0) REVERT: D 93 GLU cc_start: 0.8030 (pm20) cc_final: 0.7697 (pm20) REVERT: D 339 TYR cc_start: 0.8071 (m-10) cc_final: 0.7671 (m-10) REVERT: D 432 GLU cc_start: 0.7782 (pm20) cc_final: 0.7448 (mt-10) REVERT: E 103 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5709 (tt) REVERT: E 112 LYS cc_start: 0.8699 (tptt) cc_final: 0.8147 (tptp) REVERT: E 165 LYS cc_start: 0.8232 (pttt) cc_final: 0.7864 (pttt) REVERT: E 246 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9137 (tp) REVERT: E 313 ARG cc_start: 0.7912 (tpm170) cc_final: 0.7083 (tpp-160) REVERT: E 498 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: E 560 ASP cc_start: 0.8499 (m-30) cc_final: 0.8169 (m-30) REVERT: F 138 PHE cc_start: 0.7567 (m-10) cc_final: 0.7269 (m-10) REVERT: F 560 ASP cc_start: 0.8415 (m-30) cc_final: 0.7966 (m-30) outliers start: 145 outliers final: 75 residues processed: 456 average time/residue: 0.3740 time to fit residues: 275.9376 Evaluate side-chains 400 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 308 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 234 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 351 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 353 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN B 326 ASN C 124 HIS ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.143171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095177 restraints weight = 63025.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100610 restraints weight = 38697.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100669 restraints weight = 24873.305| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28992 Z= 0.151 Angle : 0.643 12.674 39298 Z= 0.317 Chirality : 0.044 0.232 4356 Planarity : 0.004 0.117 5081 Dihedral : 6.920 74.688 3955 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.04 % Rotamer: Outliers : 4.82 % Allowed : 31.42 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: 0.00 (0.14), residues: 3576 helix: 0.84 (0.13), residues: 1646 sheet: -0.03 (0.26), residues: 416 loop : -0.86 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 82 HIS 0.006 0.001 HIS C 21 PHE 0.026 0.001 PHE C 27 TYR 0.030 0.001 TYR A 153 ARG 0.005 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1209) hydrogen bonds : angle 4.52516 ( 3468) covalent geometry : bond 0.00362 (28991) covalent geometry : angle 0.64261 (39298) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 314 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8081 (mtpt) REVERT: A 88 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7201 (ttmm) REVERT: A 106 MET cc_start: 0.7038 (mpp) cc_final: 0.6180 (mpp) REVERT: A 110 LEU cc_start: 0.9037 (tp) cc_final: 0.8796 (tp) REVERT: A 303 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7158 (ptpp) REVERT: A 478 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: A 531 ASN cc_start: 0.9148 (m110) cc_final: 0.8867 (m-40) REVERT: B 21 HIS cc_start: 0.8604 (m90) cc_final: 0.8106 (m90) REVERT: B 72 ARG cc_start: 0.7778 (tmt170) cc_final: 0.7099 (tpt90) REVERT: B 81 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 106 MET cc_start: 0.6804 (ptp) cc_final: 0.6261 (ptp) REVERT: B 107 SER cc_start: 0.9372 (p) cc_final: 0.9148 (p) REVERT: B 167 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6579 (mm) REVERT: B 206 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8751 (pp) REVERT: B 224 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8793 (tp) REVERT: B 255 LEU cc_start: 0.8518 (mm) cc_final: 0.8305 (tp) REVERT: B 271 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6820 (mtt180) REVERT: B 314 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: B 484 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7407 (ttp-170) REVERT: B 559 MET cc_start: 0.9024 (tpp) cc_final: 0.8800 (tpp) REVERT: C 89 MET cc_start: 0.8462 (mmm) cc_final: 0.7658 (mmm) REVERT: C 141 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6976 (tt) REVERT: C 151 MET cc_start: 0.8312 (pmm) cc_final: 0.7809 (ptp) REVERT: C 153 TYR cc_start: 0.8899 (t80) cc_final: 0.8514 (t80) REVERT: C 157 TRP cc_start: 0.7621 (t60) cc_final: 0.6979 (t-100) REVERT: C 196 MET cc_start: 0.7052 (ptp) cc_final: 0.6798 (ptp) REVERT: C 365 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: C 385 LYS cc_start: 0.5266 (OUTLIER) cc_final: 0.4461 (mmmt) REVERT: C 460 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: C 494 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: C 533 ASP cc_start: 0.8743 (t0) cc_final: 0.8187 (t70) REVERT: D 58 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8480 (p) REVERT: D 92 ASN cc_start: 0.8816 (t0) cc_final: 0.8213 (t0) REVERT: D 93 GLU cc_start: 0.8047 (pm20) cc_final: 0.7578 (pm20) REVERT: D 199 ASP cc_start: 0.7917 (t0) cc_final: 0.7517 (t0) REVERT: D 339 TYR cc_start: 0.8123 (m-10) cc_final: 0.7765 (m-10) REVERT: E 103 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5673 (tt) REVERT: E 112 LYS cc_start: 0.8699 (tptt) cc_final: 0.8135 (tptp) REVERT: E 246 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9145 (tp) REVERT: E 313 ARG cc_start: 0.7899 (tpm170) cc_final: 0.7117 (tpp-160) REVERT: E 498 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: E 560 ASP cc_start: 0.8540 (m-30) cc_final: 0.8213 (m-30) REVERT: E 580 MET cc_start: 0.8440 (mmm) cc_final: 0.7809 (mmm) REVERT: F 138 PHE cc_start: 0.7527 (m-10) cc_final: 0.7224 (m-10) REVERT: F 560 ASP cc_start: 0.8521 (m-30) cc_final: 0.8070 (m-30) outliers start: 149 outliers final: 94 residues processed: 443 average time/residue: 0.3776 time to fit residues: 273.9960 Evaluate side-chains 409 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 296 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 264 optimal weight: 20.0000 chunk 250 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 228 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN B 46 ASN C 219 GLN ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 405 GLN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.145189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103442 restraints weight = 61495.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102129 restraints weight = 39568.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103616 restraints weight = 36075.239| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28992 Z= 0.119 Angle : 0.650 15.564 39298 Z= 0.316 Chirality : 0.044 0.264 4356 Planarity : 0.004 0.117 5081 Dihedral : 6.825 77.921 3955 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % Rotamer: Outliers : 4.27 % Allowed : 32.20 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: 0.05 (0.14), residues: 3576 helix: 0.86 (0.13), residues: 1659 sheet: 0.05 (0.26), residues: 415 loop : -0.85 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 82 HIS 0.014 0.001 HIS C 124 PHE 0.031 0.001 PHE B 49 TYR 0.028 0.001 TYR A 153 ARG 0.006 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 1209) hydrogen bonds : angle 4.42049 ( 3468) covalent geometry : bond 0.00278 (28991) covalent geometry : angle 0.65042 (39298) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 332 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7218 (ttmm) REVERT: A 106 MET cc_start: 0.7087 (mpp) cc_final: 0.6217 (mpp) REVERT: A 303 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7219 (ptpp) REVERT: A 404 MET cc_start: 0.8098 (tmm) cc_final: 0.7717 (tmm) REVERT: A 478 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: A 531 ASN cc_start: 0.9102 (m110) cc_final: 0.8889 (m-40) REVERT: B 21 HIS cc_start: 0.8550 (m90) cc_final: 0.8054 (m90) REVERT: B 81 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8376 (pp) REVERT: B 106 MET cc_start: 0.6931 (ptp) cc_final: 0.6592 (ptp) REVERT: B 167 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6537 (mm) REVERT: B 224 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8770 (tp) REVERT: B 255 LEU cc_start: 0.8522 (mm) cc_final: 0.8301 (tp) REVERT: B 271 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6924 (mtt180) REVERT: B 314 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 559 MET cc_start: 0.9014 (tpp) cc_final: 0.8756 (tpp) REVERT: C 14 MET cc_start: 0.7822 (tpp) cc_final: 0.7252 (tpp) REVERT: C 89 MET cc_start: 0.8245 (mmm) cc_final: 0.7585 (mmm) REVERT: C 141 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6862 (tt) REVERT: C 151 MET cc_start: 0.8213 (pmm) cc_final: 0.7586 (ptp) REVERT: C 153 TYR cc_start: 0.8820 (t80) cc_final: 0.8477 (t80) REVERT: C 157 TRP cc_start: 0.7585 (t60) cc_final: 0.7035 (t-100) REVERT: C 196 MET cc_start: 0.7042 (ptp) cc_final: 0.6818 (ptp) REVERT: C 365 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: C 385 LYS cc_start: 0.5239 (OUTLIER) cc_final: 0.4464 (mmmt) REVERT: C 460 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: C 494 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: C 533 ASP cc_start: 0.8593 (t0) cc_final: 0.8154 (t70) REVERT: D 58 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8469 (p) REVERT: D 199 ASP cc_start: 0.7840 (t0) cc_final: 0.7389 (t0) REVERT: D 293 TYR cc_start: 0.8371 (t80) cc_final: 0.8140 (t80) REVERT: D 339 TYR cc_start: 0.8118 (m-10) cc_final: 0.7730 (m-10) REVERT: D 432 GLU cc_start: 0.7870 (pm20) cc_final: 0.7476 (mt-10) REVERT: E 103 ILE cc_start: 0.6053 (OUTLIER) cc_final: 0.5679 (tt) REVERT: E 112 LYS cc_start: 0.8787 (tptt) cc_final: 0.8163 (tptp) REVERT: E 246 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9130 (tp) REVERT: E 313 ARG cc_start: 0.7734 (tpm170) cc_final: 0.7048 (tpp-160) REVERT: E 560 ASP cc_start: 0.8431 (m-30) cc_final: 0.8169 (m-30) REVERT: E 580 MET cc_start: 0.8268 (mmm) cc_final: 0.7784 (mmm) REVERT: F 25 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8430 (tm-30) REVERT: F 138 PHE cc_start: 0.7527 (m-10) cc_final: 0.7243 (m-10) REVERT: F 560 ASP cc_start: 0.8381 (m-30) cc_final: 0.7974 (m-30) outliers start: 132 outliers final: 84 residues processed: 442 average time/residue: 0.3675 time to fit residues: 262.4714 Evaluate side-chains 406 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 306 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 158 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 119 optimal weight: 40.0000 chunk 197 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS B 326 ASN C 124 HIS ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 460 GLN ** F 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.144728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097100 restraints weight = 61762.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102833 restraints weight = 37561.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102851 restraints weight = 24860.954| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28992 Z= 0.133 Angle : 0.662 14.496 39298 Z= 0.321 Chirality : 0.044 0.203 4356 Planarity : 0.004 0.117 5081 Dihedral : 6.712 85.498 3953 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.56 % Favored : 94.21 % Rotamer: Outliers : 4.47 % Allowed : 32.20 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: 0.02 (0.14), residues: 3576 helix: 0.83 (0.13), residues: 1665 sheet: 0.08 (0.26), residues: 411 loop : -0.87 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.006 0.001 HIS C 21 PHE 0.030 0.001 PHE A 138 TYR 0.021 0.001 TYR A 153 ARG 0.006 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1209) hydrogen bonds : angle 4.42664 ( 3468) covalent geometry : bond 0.00320 (28991) covalent geometry : angle 0.66157 (39298) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 312 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8115 (mtpt) REVERT: A 88 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7185 (ttmm) REVERT: A 106 MET cc_start: 0.7050 (mpp) cc_final: 0.6163 (mpp) REVERT: A 179 LYS cc_start: 0.5845 (tmtt) cc_final: 0.5606 (tptp) REVERT: A 303 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7150 (ptpp) REVERT: A 404 MET cc_start: 0.8101 (tmm) cc_final: 0.7715 (tmm) REVERT: A 531 ASN cc_start: 0.9099 (m110) cc_final: 0.8858 (m-40) REVERT: B 21 HIS cc_start: 0.8569 (m90) cc_final: 0.8043 (m90) REVERT: B 81 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 106 MET cc_start: 0.6916 (ptp) cc_final: 0.6580 (ptp) REVERT: B 167 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6485 (mm) REVERT: B 224 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 271 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6738 (mtt180) REVERT: B 314 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: B 559 MET cc_start: 0.9010 (tpp) cc_final: 0.8752 (tpp) REVERT: C 14 MET cc_start: 0.7926 (tpp) cc_final: 0.7391 (tpp) REVERT: C 89 MET cc_start: 0.8273 (mmm) cc_final: 0.7514 (mmm) REVERT: C 141 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7010 (tt) REVERT: C 151 MET cc_start: 0.8221 (pmm) cc_final: 0.7685 (ptp) REVERT: C 153 TYR cc_start: 0.8901 (t80) cc_final: 0.8529 (t80) REVERT: C 157 TRP cc_start: 0.7565 (t60) cc_final: 0.6958 (t-100) REVERT: C 196 MET cc_start: 0.7068 (ptp) cc_final: 0.6862 (ptp) REVERT: C 365 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: C 460 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: C 483 MET cc_start: 0.8136 (tpp) cc_final: 0.7723 (mmm) REVERT: C 494 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: C 533 ASP cc_start: 0.8807 (t0) cc_final: 0.8280 (t70) REVERT: D 58 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8501 (p) REVERT: D 93 GLU cc_start: 0.8066 (pm20) cc_final: 0.7621 (pm20) REVERT: D 199 ASP cc_start: 0.7824 (t0) cc_final: 0.7449 (t0) REVERT: D 339 TYR cc_start: 0.8141 (m-10) cc_final: 0.7786 (m-10) REVERT: E 112 LYS cc_start: 0.8700 (tptt) cc_final: 0.8088 (tptp) REVERT: E 313 ARG cc_start: 0.7868 (tpm170) cc_final: 0.7217 (tpp-160) REVERT: E 560 ASP cc_start: 0.8498 (m-30) cc_final: 0.8143 (m-30) REVERT: E 580 MET cc_start: 0.8333 (mmm) cc_final: 0.7899 (mmm) REVERT: F 25 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8427 (tm-30) REVERT: F 138 PHE cc_start: 0.7669 (m-10) cc_final: 0.7373 (m-10) REVERT: F 560 ASP cc_start: 0.8504 (m-30) cc_final: 0.8052 (m-30) outliers start: 138 outliers final: 95 residues processed: 427 average time/residue: 0.3695 time to fit residues: 257.0357 Evaluate side-chains 413 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 306 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 177 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 240 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN C 124 HIS ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** F 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.141416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093570 restraints weight = 61703.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.099035 restraints weight = 38558.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099039 restraints weight = 25854.145| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28992 Z= 0.236 Angle : 0.726 15.971 39298 Z= 0.359 Chirality : 0.046 0.301 4356 Planarity : 0.005 0.116 5081 Dihedral : 6.715 75.979 3953 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.29 % Favored : 93.48 % Rotamer: Outliers : 4.30 % Allowed : 32.17 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3576 helix: 0.68 (0.13), residues: 1657 sheet: -0.09 (0.27), residues: 398 loop : -0.98 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 82 HIS 0.006 0.001 HIS C 21 PHE 0.025 0.002 PHE D 273 TYR 0.022 0.002 TYR C 77 ARG 0.006 0.001 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 1209) hydrogen bonds : angle 4.70376 ( 3468) covalent geometry : bond 0.00560 (28991) covalent geometry : angle 0.72555 (39298) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 295 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8136 (mtpt) REVERT: A 88 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7277 (ttmm) REVERT: A 106 MET cc_start: 0.7060 (mpp) cc_final: 0.6129 (mpp) REVERT: A 110 LEU cc_start: 0.9098 (tp) cc_final: 0.8873 (tp) REVERT: A 303 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7164 (ptpp) REVERT: B 21 HIS cc_start: 0.8668 (m90) cc_final: 0.8120 (m90) REVERT: B 81 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 106 MET cc_start: 0.7046 (ptp) cc_final: 0.6702 (ptp) REVERT: B 107 SER cc_start: 0.9419 (p) cc_final: 0.9217 (p) REVERT: B 167 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6608 (mm) REVERT: B 271 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6752 (mtt180) REVERT: B 314 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: B 559 MET cc_start: 0.9066 (tpp) cc_final: 0.8800 (tpp) REVERT: C 141 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7059 (tt) REVERT: C 151 MET cc_start: 0.8394 (pmm) cc_final: 0.8048 (ptp) REVERT: C 153 TYR cc_start: 0.8861 (t80) cc_final: 0.8535 (t80) REVERT: C 157 TRP cc_start: 0.7724 (t60) cc_final: 0.6942 (t-100) REVERT: C 196 MET cc_start: 0.7132 (ptp) cc_final: 0.6891 (ptp) REVERT: C 365 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: C 460 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: C 494 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: D 58 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8539 (p) REVERT: D 93 GLU cc_start: 0.8156 (pm20) cc_final: 0.7690 (pm20) REVERT: D 199 ASP cc_start: 0.7908 (t0) cc_final: 0.7418 (t0) REVERT: D 293 TYR cc_start: 0.8299 (t80) cc_final: 0.7934 (t80) REVERT: D 339 TYR cc_start: 0.8213 (m-10) cc_final: 0.7921 (m-10) REVERT: E 112 LYS cc_start: 0.8733 (tptt) cc_final: 0.8168 (tptp) REVERT: E 313 ARG cc_start: 0.7847 (tpm170) cc_final: 0.7073 (tpp-160) REVERT: E 560 ASP cc_start: 0.8495 (m-30) cc_final: 0.8224 (m-30) REVERT: E 574 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8930 (pt) REVERT: F 25 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8149 (tp30) REVERT: F 138 PHE cc_start: 0.7645 (m-10) cc_final: 0.7218 (m-10) REVERT: F 560 ASP cc_start: 0.8584 (m-30) cc_final: 0.8196 (m-30) outliers start: 133 outliers final: 99 residues processed: 409 average time/residue: 0.3686 time to fit residues: 243.9447 Evaluate side-chains 394 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 283 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 326 optimal weight: 0.6980 chunk 347 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 341 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 319 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN C 124 HIS ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.144547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097134 restraints weight = 61339.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103347 restraints weight = 37504.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103251 restraints weight = 25255.834| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28992 Z= 0.125 Angle : 0.701 14.808 39298 Z= 0.339 Chirality : 0.045 0.221 4356 Planarity : 0.004 0.116 5081 Dihedral : 6.511 66.309 3953 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.20 % Favored : 94.57 % Rotamer: Outliers : 3.40 % Allowed : 33.27 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: -0.00 (0.14), residues: 3576 helix: 0.86 (0.13), residues: 1651 sheet: 0.03 (0.26), residues: 405 loop : -0.92 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 221 HIS 0.028 0.001 HIS C 124 PHE 0.031 0.001 PHE E 33 TYR 0.038 0.001 TYR C 77 ARG 0.015 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 1209) hydrogen bonds : angle 4.44346 ( 3468) covalent geometry : bond 0.00290 (28991) covalent geometry : angle 0.70133 (39298) Misc. bond : bond 0.00012 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 320 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8188 (mtpt) REVERT: A 88 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7178 (ttmm) REVERT: A 106 MET cc_start: 0.6870 (mpp) cc_final: 0.6007 (mpp) REVERT: A 123 PHE cc_start: 0.7948 (p90) cc_final: 0.7627 (p90) REVERT: A 303 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7257 (ptpp) REVERT: A 404 MET cc_start: 0.8019 (tmm) cc_final: 0.7672 (tmm) REVERT: A 531 ASN cc_start: 0.9136 (m110) cc_final: 0.8890 (m-40) REVERT: B 21 HIS cc_start: 0.8548 (m90) cc_final: 0.8019 (m90) REVERT: B 81 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8277 (pp) REVERT: B 106 MET cc_start: 0.7041 (ptp) cc_final: 0.6728 (ptp) REVERT: B 167 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6336 (mm) REVERT: B 271 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6649 (mtt180) REVERT: B 314 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: B 325 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7786 (t0) REVERT: B 404 MET cc_start: 0.8504 (ppp) cc_final: 0.8281 (ppp) REVERT: B 405 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 468 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7671 (mtm180) REVERT: B 559 MET cc_start: 0.8934 (tpp) cc_final: 0.8705 (tpp) REVERT: C 14 MET cc_start: 0.7913 (tpp) cc_final: 0.7363 (tpp) REVERT: C 89 MET cc_start: 0.8124 (mmm) cc_final: 0.7240 (mmm) REVERT: C 141 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7068 (tt) REVERT: C 151 MET cc_start: 0.8262 (pmm) cc_final: 0.7752 (ptp) REVERT: C 153 TYR cc_start: 0.8901 (t80) cc_final: 0.8559 (t80) REVERT: C 157 TRP cc_start: 0.7554 (t60) cc_final: 0.6996 (t-100) REVERT: C 365 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: C 460 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: C 483 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7736 (mmt) REVERT: C 494 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: C 533 ASP cc_start: 0.8792 (t0) cc_final: 0.8252 (t70) REVERT: D 58 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8492 (p) REVERT: D 93 GLU cc_start: 0.8050 (pm20) cc_final: 0.7611 (pm20) REVERT: D 199 ASP cc_start: 0.7845 (t0) cc_final: 0.7439 (t0) REVERT: D 293 TYR cc_start: 0.8230 (t80) cc_final: 0.7888 (t80) REVERT: D 339 TYR cc_start: 0.8143 (m-10) cc_final: 0.7768 (m-10) REVERT: E 85 TYR cc_start: 0.8840 (t80) cc_final: 0.8442 (t80) REVERT: E 89 MET cc_start: 0.7698 (mmm) cc_final: 0.7103 (tpt) REVERT: E 112 LYS cc_start: 0.8691 (tptt) cc_final: 0.8106 (tptp) REVERT: E 313 ARG cc_start: 0.7831 (tpm170) cc_final: 0.7187 (tpp-160) REVERT: E 574 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8872 (pt) REVERT: F 25 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8127 (tp30) REVERT: F 138 PHE cc_start: 0.7557 (m-10) cc_final: 0.7218 (m-10) REVERT: F 560 ASP cc_start: 0.8300 (m-30) cc_final: 0.7896 (m-30) outliers start: 105 outliers final: 74 residues processed: 409 average time/residue: 0.3742 time to fit residues: 249.6154 Evaluate side-chains 399 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 311 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 21 HIS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 433 HIS Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 12 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 257 optimal weight: 0.0980 chunk 256 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 271 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN B 314 GLN B 326 ASN C 124 HIS ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.145232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098145 restraints weight = 61549.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103385 restraints weight = 37285.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.103597 restraints weight = 24292.766| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28992 Z= 0.122 Angle : 0.690 14.982 39298 Z= 0.333 Chirality : 0.044 0.224 4356 Planarity : 0.004 0.117 5081 Dihedral : 6.361 64.789 3953 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.40 % Favored : 94.38 % Rotamer: Outliers : 3.43 % Allowed : 33.43 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: 0.05 (0.14), residues: 3576 helix: 0.91 (0.13), residues: 1649 sheet: 0.03 (0.26), residues: 413 loop : -0.90 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 221 HIS 0.009 0.001 HIS A 576 PHE 0.028 0.001 PHE D 273 TYR 0.030 0.001 TYR C 77 ARG 0.010 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 1209) hydrogen bonds : angle 4.40494 ( 3468) covalent geometry : bond 0.00288 (28991) covalent geometry : angle 0.69045 (39298) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9057.25 seconds wall clock time: 160 minutes 4.08 seconds (9604.08 seconds total)