Starting phenix.real_space_refine on Tue Jun 24 00:12:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c6c_45244/06_2025/9c6c_45244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c6c_45244/06_2025/9c6c_45244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c6c_45244/06_2025/9c6c_45244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c6c_45244/06_2025/9c6c_45244.map" model { file = "/net/cci-nas-00/data/ceres_data/9c6c_45244/06_2025/9c6c_45244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c6c_45244/06_2025/9c6c_45244.cif" } resolution = 3.4 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= 0.057 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 17693 2.51 5 N 4787 2.21 5 O 5151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27808 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "B" Number of atoms: 4589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4589 Classifications: {'peptide': 582} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 556} Chain breaks: 1 Chain: "C" Number of atoms: 4654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4654 Classifications: {'peptide': 590} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 562} Chain breaks: 1 Chain: "D" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4580 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 555} Chain breaks: 1 Chain: "E" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4674 Classifications: {'peptide': 593} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "F" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4546 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 553} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" 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} Time building chain proxies: 16.43, per 1000 atoms: 0.59 Number of scatterers: 27808 At special positions: 0 Unit cell: (200.972, 200.972, 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 5151 8.00 N 4787 7.00 C 17693 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=0, symmetry=0 Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 3.4 seconds 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6618 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 16 sheets defined 55.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.388A pdb=" N LEU A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.877A pdb=" N LYS A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 224 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 252 through 261 removed outlier: 3.863A pdb=" N LEU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 347 through 369 removed outlier: 3.869A pdb=" N LYS A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.952A pdb=" N SER A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.672A pdb=" N ALA A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.537A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 4.400A pdb=" N LEU A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 534 through 539 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 572 removed outlier: 3.549A pdb=" N ALA A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'B' and resid 14 through 23 removed outlier: 4.105A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 4.482A pdb=" N LEU B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.958A pdb=" N PHE B 178 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 198 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.988A pdb=" N GLN B 205 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 230 through 237 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 252 through 262 removed outlier: 3.741A pdb=" N LEU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.873A pdb=" N GLY B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 325 removed outlier: 3.549A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 347 through 369 removed outlier: 3.720A pdb=" N LYS B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 4.517A pdb=" N SER B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.573A pdb=" N ARG B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 441 removed outlier: 4.390A pdb=" N ALA B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 475 through 478 removed outlier: 3.819A 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 490 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 534 through 539 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 Processing helix chain 'B' and resid 575 through 600 removed outlier: 3.897A pdb=" N LYS B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 20 removed outlier: 3.778A pdb=" N GLU C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 4.020A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 89 Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 133 through 143 removed outlier: 4.282A 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 180 through 188 removed outlier: 4.684A pdb=" N GLU C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.862A pdb=" N LEU C 268 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 269' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 307 through 325 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.549A pdb=" N LYS C 344 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 369 removed outlier: 3.828A pdb=" N LYS C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 4.138A pdb=" N SER C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 434 removed outlier: 3.716A pdb=" N ASP C 434 " --> pdb=" O TYR C 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 431 through 434' Processing helix chain 'C' and resid 435 through 442 removed outlier: 4.231A pdb=" N HIS C 439 " --> pdb=" O PHE C 435 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 464 removed outlier: 3.659A pdb=" N GLN C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 478 Processing helix chain 'C' and resid 479 through 489 removed outlier: 3.561A 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 597 Processing helix chain 'C' and resid 598 through 600 No H-bonds generated for 'chain 'C' and resid 598 through 600' Processing helix chain 'D' and resid 14 through 23 removed outlier: 3.934A pdb=" N GLU D 18 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) 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 143 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.873A pdb=" N LYS D 164 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 199 Processing helix chain 'D' and resid 200 through 206 removed outlier: 4.569A pdb=" N LEU D 206 " --> pdb=" O LYS D 202 " (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 253 through 262 removed outlier: 4.395A pdb=" N ASP D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 4.215A pdb=" N ALA D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 325 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.524A pdb=" N TYR D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 369 Processing helix chain 'D' and resid 391 through 404 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 431 through 435 removed outlier: 3.613A pdb=" N PHE D 435 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 475 through 478 removed outlier: 3.578A 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 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 removed outlier: 3.548A pdb=" N SER D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 553 removed outlier: 3.848A pdb=" N LEU D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) removed outlier: 4.238A 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 removed outlier: 3.854A pdb=" N VAL D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 562 " --> pdb=" O ARG D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 600 removed outlier: 4.391A pdb=" N LYS D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN D 600 " --> pdb=" O ILE D 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.882A pdb=" N GLU E 18 " --> pdb=" O MET E 14 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 51 removed outlier: 3.899A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 89 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 134 through 144 removed outlier: 4.144A pdb=" N PHE E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.646A pdb=" N PHE E 178 " --> pdb=" O ARG E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 190 removed outlier: 4.523A pdb=" N LEU E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 230 through 237 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 253 through 262 Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 341 through 345 removed outlier: 3.550A pdb=" N LYS E 344 " --> pdb=" O ASP E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 369 removed outlier: 3.674A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 406 removed outlier: 4.356A pdb=" N SER E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 435 through 442 removed outlier: 3.663A pdb=" N HIS E 439 " --> pdb=" O PHE E 435 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY E 442 " --> pdb=" O VAL E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 464 Processing helix chain 'E' and resid 475 through 478 Processing helix chain 'E' and resid 479 through 490 Processing helix chain 'E' and resid 496 through 504 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: 3.739A pdb=" N VAL E 561 " --> pdb=" O SER E 557 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 562 " --> pdb=" O ARG E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 598 removed outlier: 4.583A pdb=" N ILE E 598 " --> pdb=" O CYS E 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 removed outlier: 3.973A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 4.237A pdb=" N LEU F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 88 Processing helix chain 'F' and resid 103 through 118 removed outlier: 3.785A pdb=" N SER F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 144 removed outlier: 3.741A pdb=" N MET F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.996A pdb=" N ARG F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 removed outlier: 3.562A pdb=" N ILE F 166 " --> pdb=" O LEU F 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 166' Processing helix chain 'F' and resid 180 through 199 Processing helix chain 'F' and resid 215 through 224 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 252 through 262 removed outlier: 3.719A pdb=" N LEU F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.793A pdb=" N GLY F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.522A pdb=" N LYS F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 325 Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 347 through 369 Processing helix chain 'F' and resid 390 through 405 removed outlier: 4.314A pdb=" N SER F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 437 removed outlier: 4.154A pdb=" N HIS F 433 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE F 435 " --> pdb=" O GLU F 432 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS F 436 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA F 437 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 465 removed outlier: 3.505A pdb=" N ILE F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 489 removed outlier: 3.694A pdb=" N ARG F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) 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 548 Processing helix chain 'F' and resid 548 through 553 Processing helix chain 'F' and resid 558 through 571 removed outlier: 4.208A pdb=" N LEU F 562 " --> pdb=" O ARG F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 600 removed outlier: 3.895A pdb=" N LYS F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN F 600 " --> pdb=" O ILE F 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 62 removed outlier: 7.184A pdb=" N VAL A 30 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR A 60 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 32 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS A 62 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR A 34 " --> pdb=" O CYS A 62 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU A 5 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE A 33 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N CYS A 7 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N THR A 35 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 9 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 4 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS A 98 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU A 6 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 123 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 126 " --> pdb=" O HIS A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 245 removed outlier: 4.477A pdb=" N VAL A 240 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU A 331 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU A 242 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG A 333 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 244 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 328 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ASN A 377 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 330 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU A 379 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 332 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 381 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS A 334 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N SER A 383 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N VAL A 376 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N GLY A 415 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 378 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP A 417 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 380 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA A 419 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA A 382 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 446 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 418 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 445 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLY A 471 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA A 447 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 62 removed outlier: 6.867A pdb=" N VAL B 30 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR B 60 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 32 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N CYS B 62 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR B 34 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 4 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N CYS B 98 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 6 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 97 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL B 125 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN B 120 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B 153 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL B 122 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 151 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 245 removed outlier: 4.550A pdb=" N VAL B 240 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLU B 331 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU B 242 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG B 333 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N CYS B 244 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 328 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ASN B 377 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 330 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 379 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 332 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 381 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS B 334 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N VAL B 376 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N GLY B 415 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU B 378 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP B 417 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 380 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 414 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 446 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B 416 " --> pdb=" O THR B 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 471 removed outlier: 7.858A pdb=" N LEU B 470 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 493 " --> pdb=" O SER B 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 62 removed outlier: 6.705A pdb=" N VAL C 30 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL C 32 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS C 62 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR C 34 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 7 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL C 4 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N CYS C 98 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 6 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 123 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLN C 120 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR C 153 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL C 122 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET C 151 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 239 through 245 removed outlier: 4.515A pdb=" N VAL C 240 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLU C 331 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU C 242 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG C 333 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS C 244 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 328 " --> pdb=" O HIS C 375 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN C 377 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 330 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 379 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE C 332 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE C 381 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N CYS C 334 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER C 383 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 413 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 378 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 415 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 419 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 469 through 471 Processing sheet with id=AA9, first strand: chain 'D' and resid 56 through 62 removed outlier: 7.031A pdb=" N VAL D 30 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR D 60 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 32 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N CYS D 62 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR D 34 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR D 35 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL D 4 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N CYS D 98 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU D 6 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL D 97 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL D 125 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL D 122 " --> pdb=" O MET D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS D 147 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 239 through 245 removed outlier: 4.576A pdb=" N VAL D 240 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU D 331 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 242 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG D 333 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS D 244 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 328 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ASN D 377 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 330 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 379 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 332 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE D 413 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 378 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY D 415 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 493 through 494 removed outlier: 6.368A pdb=" N VAL D 493 " --> pdb=" O SER D 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.735A pdb=" N VAL E 30 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 58 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU E 5 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE E 33 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS E 7 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL E 4 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS E 98 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU E 6 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 97 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL E 125 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLN E 120 " --> pdb=" O TYR E 153 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR E 153 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL E 122 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET E 151 " --> pdb=" O VAL E 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 245 removed outlier: 4.497A pdb=" N VAL E 240 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLU E 331 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU E 242 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG E 333 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS E 244 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA E 328 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N ASN E 377 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA E 330 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU E 379 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE E 332 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE E 381 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS E 334 " --> pdb=" O ILE E 381 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER E 383 " --> pdb=" O CYS E 334 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE E 413 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 378 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY E 415 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 419 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG E 469 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL E 493 " --> pdb=" O SER E 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.719A pdb=" N LEU F 5 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE F 33 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS F 7 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL F 4 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N CYS F 98 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU F 6 " --> pdb=" O CYS F 98 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL F 97 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER F 121 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY F 152 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE F 123 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU F 150 " --> pdb=" O PHE F 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 239 through 245 removed outlier: 4.639A pdb=" N VAL F 240 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLU F 331 " --> pdb=" O VAL F 240 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU F 242 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG F 333 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS F 244 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL F 414 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU F 378 " --> pdb=" O VAL F 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 493 through 494 removed outlier: 6.488A pdb=" N VAL F 493 " --> pdb=" O SER F 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 1201 hydrogen bonds defined for protein. 3444 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: 9.09 Time building geometry restraints manager: 7.73 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: 5071 1.32 - 1.45: 7066 1.45 - 1.57: 16015 1.57 - 1.69: 21 1.69 - 1.82: 246 Bond restraints: 28419 Sorted by residual: 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 3.61e+02 bond pdb=" C1' ATP B 701 " pdb=" C2' ATP B 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 F 701 " pdb=" C2' ATP F 701 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.59e+02 bond pdb=" C1' ATP B 701 " pdb=" O4' ATP B 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 2.47e+02 ... (remaining 28414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 38219 3.47 - 6.95: 227 6.95 - 10.42: 49 10.42 - 13.89: 11 13.89 - 17.37: 4 Bond angle restraints: 38510 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 122.50 17.37 1.00e+00 1.00e+00 3.02e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 122.53 17.34 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 122.63 17.24 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 123.63 13.20 1.00e+00 1.00e+00 1.74e+02 angle pdb=" PA ATP F 701 " pdb=" O3A ATP F 701 " pdb=" PB ATP F 701 " ideal model delta sigma weight residual 136.83 123.63 13.20 1.00e+00 1.00e+00 1.74e+02 ... (remaining 38505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14321 17.99 - 35.98: 2075 35.98 - 53.97: 597 53.97 - 71.96: 129 71.96 - 89.95: 37 Dihedral angle restraints: 17159 sinusoidal: 6935 harmonic: 10224 Sorted by residual: dihedral pdb=" CA MET F 89 " pdb=" C MET F 89 " pdb=" N PRO F 90 " pdb=" CA PRO F 90 " ideal model delta harmonic sigma weight residual 180.00 -143.93 -36.07 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA PHE D 208 " pdb=" C PHE D 208 " pdb=" N PRO D 209 " pdb=" CA PRO D 209 " ideal model delta harmonic sigma weight residual -180.00 -144.83 -35.17 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" C PHE F 208 " pdb=" N PHE F 208 " pdb=" CA PHE F 208 " pdb=" CB PHE F 208 " ideal model delta harmonic sigma weight residual -122.60 -135.88 13.28 0 2.50e+00 1.60e-01 2.82e+01 ... (remaining 17156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3911 0.076 - 0.153: 344 0.153 - 0.229: 10 0.229 - 0.306: 3 0.306 - 0.382: 1 Chirality restraints: 4269 Sorted by residual: chirality pdb=" CA PHE F 208 " pdb=" N PHE F 208 " pdb=" C PHE F 208 " pdb=" CB PHE F 208 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C2' ATP F 701 " pdb=" C1' ATP F 701 " pdb=" C3' ATP F 701 " pdb=" O2' ATP F 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.39 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2' ATP B 701 " pdb=" C1' ATP B 701 " pdb=" C3' ATP B 701 " pdb=" O2' ATP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.39 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4266 not shown) Planarity restraints: 4973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 179 " 0.137 5.00e-02 4.00e+02 1.96e-01 6.12e+01 pdb=" N PRO E 180 " -0.338 5.00e-02 4.00e+02 pdb=" CA PRO E 180 " 0.112 5.00e-02 4.00e+02 pdb=" CD PRO E 180 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 89 " 0.098 5.00e-02 4.00e+02 1.48e-01 3.50e+01 pdb=" N PRO F 90 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO F 90 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO F 90 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 208 " 0.102 5.00e-02 4.00e+02 1.48e-01 3.49e+01 pdb=" N PRO F 209 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO F 209 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO F 209 " 0.083 5.00e-02 4.00e+02 ... (remaining 4970 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 420 2.63 - 3.19: 25888 3.19 - 3.76: 45781 3.76 - 4.33: 59331 4.33 - 4.90: 97779 Nonbonded interactions: 229199 Sorted by model distance: nonbonded pdb=" NE2 HIS C 243 " pdb="MG MG C 701 " model vdw 2.058 2.250 nonbonded pdb=" NE2 HIS E 243 " pdb="MG MG E 701 " model vdw 2.063 2.250 nonbonded pdb=" NE2 HIS A 243 " pdb="MG MG A 701 " model vdw 2.066 2.250 nonbonded pdb=" O GLN B 460 " pdb=" OG SER B 464 " model vdw 2.074 3.040 nonbonded pdb=" NE2 HIS B 243 " pdb="MG MG B 702 " model vdw 2.119 2.250 ... (remaining 229194 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 190 or resid 200 through 262 or resid 286 throug \ h 600)) selection = (chain 'B' and (resid 3 through 190 or resid 200 through 262 or resid 286 throug \ h 600)) selection = (chain 'C' and (resid 3 through 190 or resid 200 through 262 or resid 286 throug \ h 600)) selection = (chain 'D' and (resid 3 through 190 or resid 200 through 262 or resid 286 throug \ h 600)) selection = (chain 'E' and (resid 3 through 190 or resid 200 through 262 or resid 286 throug \ h 600)) selection = (chain 'F' and (resid 3 through 190 or resid 200 through 262 or resid 286 throug \ h 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 60.410 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 28419 Z= 0.383 Angle : 0.736 17.365 38510 Z= 0.424 Chirality : 0.043 0.382 4269 Planarity : 0.006 0.196 4973 Dihedral : 18.579 89.949 10541 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.24 % Favored : 94.44 % Rotamer: Outliers : 0.26 % Allowed : 34.31 % Favored : 65.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3492 helix: 1.27 (0.13), residues: 1619 sheet: 0.05 (0.28), residues: 359 loop : -0.90 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 221 HIS 0.013 0.001 HIS D 21 PHE 0.093 0.001 PHE F 208 TYR 0.013 0.001 TYR E 77 ARG 0.010 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.15152 ( 1201) hydrogen bonds : angle 5.94615 ( 3444) covalent geometry : bond 0.00538 (28419) covalent geometry : angle 0.73607 (38510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 424 time to evaluate : 3.386 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 3 ARG cc_start: 0.6023 (mmm-85) cc_final: 0.5352 (mmt90) REVERT: A 31 HIS cc_start: 0.8461 (m90) cc_final: 0.7523 (m170) REVERT: A 112 LYS cc_start: 0.6984 (ttpp) cc_final: 0.6658 (tttt) REVERT: B 8 SER cc_start: 0.7723 (t) cc_final: 0.7193 (p) REVERT: B 39 LYS cc_start: 0.8092 (pttp) cc_final: 0.7686 (tttt) REVERT: B 224 LEU cc_start: 0.8612 (mm) cc_final: 0.8280 (mt) REVERT: B 436 LYS cc_start: 0.7740 (tppt) cc_final: 0.6821 (mmpt) REVERT: B 515 LEU cc_start: 0.8910 (tt) cc_final: 0.8655 (mp) REVERT: B 547 LEU cc_start: 0.8863 (mm) cc_final: 0.8440 (mm) REVERT: C 154 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 397 LEU cc_start: 0.8165 (mp) cc_final: 0.7951 (mp) REVERT: C 496 CYS cc_start: 0.8494 (m) cc_final: 0.7624 (p) REVERT: C 509 MET cc_start: 0.6061 (tpp) cc_final: 0.5810 (ttp) REVERT: D 138 PHE cc_start: 0.8691 (m-80) cc_final: 0.8491 (m-10) REVERT: D 294 MET cc_start: 0.3369 (tmm) cc_final: 0.3061 (ttp) REVERT: D 316 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6551 (mt-10) REVERT: D 353 GLN cc_start: 0.6760 (tp40) cc_final: 0.6484 (tp-100) REVERT: D 547 LEU cc_start: 0.8674 (mm) cc_final: 0.8415 (mm) REVERT: E 1 MET cc_start: 0.0979 (tpt) cc_final: 0.0109 (tpt) REVERT: E 14 MET cc_start: 0.7904 (pmm) cc_final: 0.7689 (pmm) REVERT: E 28 GLU cc_start: 0.7670 (mp0) cc_final: 0.7231 (mm-30) REVERT: E 75 GLU cc_start: 0.8272 (pp20) cc_final: 0.7989 (pp20) REVERT: E 120 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7211 (tm-30) REVERT: E 123 PHE cc_start: 0.7510 (p90) cc_final: 0.7064 (p90) REVERT: E 161 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7656 (mmt90) REVERT: E 406 GLN cc_start: 0.7130 (pp30) cc_final: 0.6898 (pt0) REVERT: F 14 MET cc_start: 0.8531 (mmp) cc_final: 0.7947 (mmt) REVERT: F 88 LYS cc_start: 0.7052 (tttt) cc_final: 0.6378 (mmtt) REVERT: F 548 ILE cc_start: 0.8701 (tp) cc_final: 0.8280 (tt) REVERT: F 584 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7660 (mtmt) REVERT: F 593 VAL cc_start: 0.8451 (t) cc_final: 0.8207 (p) outliers start: 8 outliers final: 5 residues processed: 431 average time/residue: 0.3924 time to fit residues: 267.0617 Evaluate side-chains 351 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 346 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain F residue 374 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 HIS ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 472 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.162414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112926 restraints weight = 42023.220| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.45 r_work: 0.3243 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 28419 Z= 0.259 Angle : 0.717 11.807 38510 Z= 0.363 Chirality : 0.047 0.251 4269 Planarity : 0.006 0.156 4973 Dihedral : 7.013 76.968 3869 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.33 % Favored : 93.41 % Rotamer: Outliers : 4.79 % Allowed : 29.13 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: -0.03 (0.15), residues: 3492 helix: 0.93 (0.13), residues: 1643 sheet: -0.50 (0.26), residues: 422 loop : -0.92 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 84 HIS 0.009 0.001 HIS D 124 PHE 0.035 0.002 PHE F 208 TYR 0.020 0.002 TYR F 463 ARG 0.008 0.001 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 1201) hydrogen bonds : angle 5.11583 ( 3444) covalent geometry : bond 0.00626 (28419) covalent geometry : angle 0.71697 (38510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 377 time to evaluate : 3.223 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 31 HIS cc_start: 0.8013 (m90) cc_final: 0.7339 (m170) REVERT: A 112 LYS cc_start: 0.7831 (ttpp) cc_final: 0.7225 (tttt) REVERT: A 137 MET cc_start: 0.8732 (ppp) cc_final: 0.8452 (tmm) REVERT: A 151 MET cc_start: 0.8188 (pmm) cc_final: 0.7955 (pmm) REVERT: B 39 LYS cc_start: 0.8027 (pttp) cc_final: 0.7624 (tttt) REVERT: B 124 HIS cc_start: 0.8149 (m-70) cc_final: 0.7930 (m-70) REVERT: B 151 MET cc_start: 0.7066 (pmm) cc_final: 0.6158 (pmm) REVERT: B 249 PHE cc_start: 0.2778 (t80) cc_final: 0.2535 (t80) REVERT: B 443 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 495 MET cc_start: 0.8792 (ttt) cc_final: 0.8575 (tpt) REVERT: B 547 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 29 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: C 76 PHE cc_start: 0.8573 (t80) cc_final: 0.8051 (t80) REVERT: C 116 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 136 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8665 (mt-10) REVERT: C 154 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 265 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: C 490 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7314 (mmtp) REVERT: D 162 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8062 (mmp80) REVERT: D 219 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: D 294 MET cc_start: 0.4173 (tmm) cc_final: 0.3130 (ttp) REVERT: D 547 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8389 (mm) REVERT: E 1 MET cc_start: 0.0705 (tpt) cc_final: 0.0043 (tpt) REVERT: E 75 GLU cc_start: 0.8326 (pp20) cc_final: 0.7986 (pp20) REVERT: E 220 GLN cc_start: 0.8401 (pp30) cc_final: 0.7967 (pp30) REVERT: E 586 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7241 (t80) REVERT: F 14 MET cc_start: 0.8656 (mmp) cc_final: 0.7712 (mmt) REVERT: F 56 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7032 (tmt-80) REVERT: F 88 LYS cc_start: 0.7593 (tttt) cc_final: 0.6994 (mmtt) REVERT: F 219 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: F 526 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7834 (mt) REVERT: F 548 ILE cc_start: 0.8857 (tp) cc_final: 0.8478 (tt) outliers start: 145 outliers final: 84 residues processed: 486 average time/residue: 0.3881 time to fit residues: 299.7523 Evaluate side-chains 428 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 331 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 564 ILE Chi-restraints excluded: chain F residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 21 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 263 optimal weight: 0.5980 chunk 225 optimal weight: 7.9990 chunk 347 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 HIS ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN D 472 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN E 534 ASN F 406 GLN ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116254 restraints weight = 41658.454| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.34 r_work: 0.3309 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28419 Z= 0.127 Angle : 0.608 10.546 38510 Z= 0.304 Chirality : 0.043 0.256 4269 Planarity : 0.005 0.151 4973 Dihedral : 6.608 74.429 3867 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.07 % Favored : 94.67 % Rotamer: Outliers : 3.80 % Allowed : 29.76 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3492 helix: 1.21 (0.13), residues: 1634 sheet: -0.44 (0.26), residues: 417 loop : -0.83 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 84 HIS 0.008 0.001 HIS D 124 PHE 0.042 0.002 PHE F 208 TYR 0.014 0.001 TYR F 463 ARG 0.007 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1201) hydrogen bonds : angle 4.75656 ( 3444) covalent geometry : bond 0.00299 (28419) covalent geometry : angle 0.60849 (38510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 375 time to evaluate : 3.068 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 31 HIS cc_start: 0.8094 (m90) cc_final: 0.7494 (m170) REVERT: A 80 MET cc_start: 0.8554 (mmm) cc_final: 0.8292 (mmm) REVERT: A 104 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7397 (mmtt) REVERT: A 112 LYS cc_start: 0.7728 (ttpp) cc_final: 0.7144 (tttt) REVERT: A 151 MET cc_start: 0.8090 (pmm) cc_final: 0.7863 (pmm) REVERT: A 483 MET cc_start: 0.8486 (mtp) cc_final: 0.8073 (mmm) REVERT: A 487 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 494 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: A 495 MET cc_start: 0.8577 (mtp) cc_final: 0.8368 (mtp) REVERT: B 151 MET cc_start: 0.7169 (pmm) cc_final: 0.5876 (pmm) REVERT: B 166 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7998 (tt) REVERT: B 378 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7851 (mm) REVERT: B 488 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: B 515 LEU cc_start: 0.8709 (tt) cc_final: 0.8495 (mp) REVERT: B 547 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 29 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: C 56 ARG cc_start: 0.8238 (tpt170) cc_final: 0.7797 (tpt170) REVERT: C 76 PHE cc_start: 0.8530 (t80) cc_final: 0.8255 (t80) REVERT: C 120 GLN cc_start: 0.7435 (tm-30) cc_final: 0.7080 (tm-30) REVERT: C 136 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8616 (mt-10) REVERT: C 154 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 162 ARG cc_start: 0.7196 (mmt180) cc_final: 0.6513 (mmm160) REVERT: C 184 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8350 (mtmm) REVERT: C 296 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8340 (mm) REVERT: C 386 PHE cc_start: 0.4127 (OUTLIER) cc_final: 0.2850 (p90) REVERT: D 34 THR cc_start: 0.7980 (m) cc_final: 0.7516 (p) REVERT: D 104 LYS cc_start: 0.6659 (mmtm) cc_final: 0.5785 (mmmt) REVERT: D 138 PHE cc_start: 0.8723 (m-80) cc_final: 0.8455 (m-10) REVERT: D 219 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: D 224 LEU cc_start: 0.9122 (mt) cc_final: 0.8886 (mp) REVERT: D 353 GLN cc_start: 0.7070 (tp-100) cc_final: 0.6794 (tp-100) REVERT: D 547 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8338 (mm) REVERT: E 1 MET cc_start: 0.0976 (tpt) cc_final: 0.0255 (tpt) REVERT: E 75 GLU cc_start: 0.8384 (pp20) cc_final: 0.7713 (pp20) REVERT: E 178 PHE cc_start: 0.8066 (p90) cc_final: 0.7431 (t80) REVERT: E 495 MET cc_start: 0.8579 (mtp) cc_final: 0.8009 (mtp) REVERT: E 498 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: E 586 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7258 (t80) REVERT: F 14 MET cc_start: 0.8654 (mmp) cc_final: 0.7719 (mmt) REVERT: F 56 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7009 (tmt-80) REVERT: F 88 LYS cc_start: 0.7510 (tttt) cc_final: 0.6916 (mmtt) REVERT: F 219 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: F 389 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7767 (p0) REVERT: F 548 ILE cc_start: 0.8799 (tp) cc_final: 0.8412 (tt) outliers start: 115 outliers final: 56 residues processed: 463 average time/residue: 0.3978 time to fit residues: 293.7585 Evaluate side-chains 401 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 329 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 231 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 79 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 340 optimal weight: 0.8980 chunk 264 optimal weight: 0.7980 chunk 335 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 HIS ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 HIS F 500 ASN ** F 531 ASN ** 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 = 0.4202 r_free = 0.4202 target = 0.166462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.116370 restraints weight = 41852.708| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.52 r_work: 0.3298 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 28419 Z= 0.123 Angle : 0.591 10.383 38510 Z= 0.295 Chirality : 0.042 0.258 4269 Planarity : 0.005 0.150 4973 Dihedral : 6.394 72.379 3866 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.10 % Favored : 94.64 % Rotamer: Outliers : 3.80 % Allowed : 29.46 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 0.28 (0.15), residues: 3492 helix: 1.28 (0.13), residues: 1628 sheet: -0.33 (0.26), residues: 424 loop : -0.87 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 82 HIS 0.004 0.001 HIS B 243 PHE 0.040 0.001 PHE F 208 TYR 0.014 0.001 TYR F 463 ARG 0.008 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 1201) hydrogen bonds : angle 4.62398 ( 3444) covalent geometry : bond 0.00292 (28419) covalent geometry : angle 0.59080 (38510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 362 time to evaluate : 3.613 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 31 HIS cc_start: 0.8135 (m90) cc_final: 0.7561 (m170) REVERT: A 80 MET cc_start: 0.8616 (mmm) cc_final: 0.8270 (mmm) REVERT: A 112 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7189 (tttt) REVERT: A 141 LEU cc_start: 0.7916 (pp) cc_final: 0.7573 (pp) REVERT: A 487 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 488 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: B 151 MET cc_start: 0.7135 (pmm) cc_final: 0.5624 (pmm) REVERT: B 166 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8047 (tt) REVERT: B 249 PHE cc_start: 0.2435 (t80) cc_final: 0.2193 (t80) REVERT: B 378 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7871 (mm) REVERT: B 443 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8345 (tp) REVERT: B 460 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: B 488 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: B 515 LEU cc_start: 0.8638 (tt) cc_final: 0.8432 (mp) REVERT: B 547 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8624 (mm) REVERT: C 29 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: C 76 PHE cc_start: 0.8540 (t80) cc_final: 0.8101 (t80) REVERT: C 120 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 136 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8731 (mt-10) REVERT: C 154 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 162 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6536 (mmm160) REVERT: C 186 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7077 (tp) REVERT: C 296 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8400 (mm) REVERT: C 386 PHE cc_start: 0.4107 (OUTLIER) cc_final: 0.2841 (p90) REVERT: C 597 SER cc_start: 0.7546 (t) cc_final: 0.7201 (p) REVERT: D 34 THR cc_start: 0.7913 (m) cc_final: 0.7494 (p) REVERT: D 162 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7693 (mmp80) REVERT: D 219 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: D 353 GLN cc_start: 0.7121 (tp-100) cc_final: 0.6904 (tp-100) REVERT: D 547 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8311 (mm) REVERT: E 1 MET cc_start: 0.0971 (tpt) cc_final: 0.0168 (tpt) REVERT: E 75 GLU cc_start: 0.8070 (pp20) cc_final: 0.7651 (pp20) REVERT: E 80 MET cc_start: 0.8512 (mmm) cc_final: 0.8171 (mmm) REVERT: E 167 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6335 (tp) REVERT: E 178 PHE cc_start: 0.7585 (p90) cc_final: 0.7326 (t80) REVERT: E 220 GLN cc_start: 0.8247 (pp30) cc_final: 0.7738 (pp30) REVERT: E 357 ASP cc_start: 0.7747 (m-30) cc_final: 0.7379 (m-30) REVERT: E 384 ARG cc_start: 0.3146 (OUTLIER) cc_final: 0.2121 (tpp80) REVERT: E 440 ARG cc_start: 0.6824 (tpt-90) cc_final: 0.6618 (tpp-160) REVERT: E 495 MET cc_start: 0.8554 (mtp) cc_final: 0.8128 (mtp) REVERT: E 498 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: E 586 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7218 (t80) REVERT: F 88 LYS cc_start: 0.7599 (tttt) cc_final: 0.6985 (mmtt) REVERT: F 219 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: F 389 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7748 (p0) REVERT: F 509 MET cc_start: 0.0964 (mmm) cc_final: 0.0525 (mmm) REVERT: F 548 ILE cc_start: 0.8813 (tp) cc_final: 0.8433 (tt) outliers start: 115 outliers final: 70 residues processed: 456 average time/residue: 0.4000 time to fit residues: 287.8646 Evaluate side-chains 422 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 331 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 198 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 336 optimal weight: 0.7980 chunk 273 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 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 = 0.4192 r_free = 0.4192 target = 0.165625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115181 restraints weight = 41685.991| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.74 r_work: 0.3281 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28419 Z= 0.143 Angle : 0.603 10.845 38510 Z= 0.300 Chirality : 0.043 0.259 4269 Planarity : 0.005 0.152 4973 Dihedral : 6.349 71.344 3866 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.24 % Favored : 94.50 % Rotamer: Outliers : 4.76 % Allowed : 29.03 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 0.28 (0.15), residues: 3492 helix: 1.29 (0.13), residues: 1630 sheet: -0.28 (0.26), residues: 418 loop : -0.92 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 84 HIS 0.005 0.001 HIS B 124 PHE 0.041 0.001 PHE F 208 TYR 0.024 0.001 TYR B 521 ARG 0.010 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1201) hydrogen bonds : angle 4.58651 ( 3444) covalent geometry : bond 0.00345 (28419) covalent geometry : angle 0.60288 (38510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 349 time to evaluate : 3.103 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 29 GLU cc_start: 0.7155 (mp0) cc_final: 0.6894 (mp0) REVERT: A 31 HIS cc_start: 0.8167 (m90) cc_final: 0.7573 (m170) REVERT: A 80 MET cc_start: 0.8654 (mmm) cc_final: 0.8299 (mmm) REVERT: A 112 LYS cc_start: 0.7786 (ttpp) cc_final: 0.7194 (tttt) REVERT: A 487 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (mp) REVERT: A 488 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: B 151 MET cc_start: 0.7297 (pmm) cc_final: 0.5583 (pmm) REVERT: B 166 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8041 (tt) REVERT: B 378 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 443 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 460 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: B 547 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8666 (mm) REVERT: C 29 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6829 (tp30) REVERT: C 76 PHE cc_start: 0.8535 (t80) cc_final: 0.8161 (t80) REVERT: C 120 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 136 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8671 (mt-10) REVERT: C 138 PHE cc_start: 0.7117 (m-10) cc_final: 0.6867 (m-10) REVERT: C 154 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 162 ARG cc_start: 0.7238 (mmt180) cc_final: 0.6590 (mmm160) REVERT: C 296 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8380 (mm) REVERT: C 386 PHE cc_start: 0.4151 (OUTLIER) cc_final: 0.2880 (p90) REVERT: C 405 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: D 27 PHE cc_start: 0.7324 (m-80) cc_final: 0.6670 (m-10) REVERT: D 36 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: D 124 HIS cc_start: 0.7495 (m90) cc_final: 0.7033 (m-70) REVERT: D 162 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7774 (mmp80) REVERT: D 219 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: D 353 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6897 (tp-100) REVERT: D 454 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: D 547 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8361 (mm) REVERT: E 1 MET cc_start: 0.1085 (tpt) cc_final: 0.0306 (tpt) REVERT: E 3 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7455 (ptp90) REVERT: E 75 GLU cc_start: 0.8085 (pp20) cc_final: 0.7657 (pp20) REVERT: E 80 MET cc_start: 0.8538 (mmm) cc_final: 0.8172 (mmm) REVERT: E 123 PHE cc_start: 0.7612 (p90) cc_final: 0.7372 (p90) REVERT: E 167 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6401 (tp) REVERT: E 178 PHE cc_start: 0.7659 (p90) cc_final: 0.7319 (t80) REVERT: E 220 GLN cc_start: 0.8374 (pp30) cc_final: 0.7833 (pp30) REVERT: E 357 ASP cc_start: 0.7780 (m-30) cc_final: 0.7333 (m-30) REVERT: E 384 ARG cc_start: 0.3296 (OUTLIER) cc_final: 0.2163 (tpp80) REVERT: E 498 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: E 586 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7351 (t80) REVERT: F 56 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7119 (tmt-80) REVERT: F 88 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7001 (mmtt) REVERT: F 219 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: F 509 MET cc_start: 0.0758 (mmm) cc_final: 0.0434 (mmm) REVERT: F 548 ILE cc_start: 0.8826 (tp) cc_final: 0.8435 (tt) outliers start: 144 outliers final: 89 residues processed: 466 average time/residue: 0.3981 time to fit residues: 297.8822 Evaluate side-chains 433 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 320 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 211 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.161863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112250 restraints weight = 42184.541| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.24 r_work: 0.3245 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28419 Z= 0.238 Angle : 0.674 12.376 38510 Z= 0.339 Chirality : 0.046 0.261 4269 Planarity : 0.005 0.157 4973 Dihedral : 6.556 71.249 3866 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 5.18 % Allowed : 28.53 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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 (0.15), residues: 3492 helix: 0.98 (0.13), residues: 1639 sheet: -0.52 (0.25), residues: 436 loop : -0.90 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 157 HIS 0.006 0.001 HIS C 472 PHE 0.043 0.002 PHE F 208 TYR 0.023 0.002 TYR B 521 ARG 0.018 0.001 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 1201) hydrogen bonds : angle 4.78811 ( 3444) covalent geometry : bond 0.00573 (28419) covalent geometry : angle 0.67370 (38510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 340 time to evaluate : 3.992 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 29 GLU cc_start: 0.7180 (mp0) cc_final: 0.6941 (mp0) REVERT: A 31 HIS cc_start: 0.8158 (m90) cc_final: 0.7535 (m170) REVERT: A 80 MET cc_start: 0.8673 (mmm) cc_final: 0.8315 (mmm) REVERT: A 487 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 488 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: B 151 MET cc_start: 0.7620 (pmm) cc_final: 0.5644 (pmm) REVERT: B 166 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8064 (tt) REVERT: B 320 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6459 (tp40) REVERT: B 378 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 460 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: B 495 MET cc_start: 0.8948 (mmm) cc_final: 0.8663 (tpt) REVERT: B 547 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8780 (mm) REVERT: C 29 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: C 56 ARG cc_start: 0.8236 (tpt90) cc_final: 0.8018 (tpt90) REVERT: C 76 PHE cc_start: 0.8567 (t80) cc_final: 0.8050 (t80) REVERT: C 120 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7236 (tm-30) REVERT: C 136 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8637 (mt-10) REVERT: C 138 PHE cc_start: 0.7243 (m-10) cc_final: 0.6851 (m-10) REVERT: C 162 ARG cc_start: 0.7364 (mmt180) cc_final: 0.6764 (mmm160) REVERT: C 296 LEU cc_start: 0.8643 (mm) cc_final: 0.8384 (mm) REVERT: C 386 PHE cc_start: 0.4230 (OUTLIER) cc_final: 0.2915 (p90) REVERT: C 404 MET cc_start: 0.7848 (tmm) cc_final: 0.7568 (ttp) REVERT: C 405 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: C 490 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7271 (mmtp) REVERT: C 594 CYS cc_start: 0.8090 (m) cc_final: 0.7826 (m) REVERT: D 14 MET cc_start: 0.5084 (mmm) cc_final: 0.4859 (mmm) REVERT: D 27 PHE cc_start: 0.7401 (m-80) cc_final: 0.6760 (m-10) REVERT: D 162 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8134 (mmp80) REVERT: D 213 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8660 (mm) REVERT: D 219 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: D 353 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6898 (tp-100) REVERT: D 454 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: D 547 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8320 (mm) REVERT: E 1 MET cc_start: 0.1704 (tpt) cc_final: 0.0867 (tpt) REVERT: E 3 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7154 (ptp90) REVERT: E 75 GLU cc_start: 0.8070 (pp20) cc_final: 0.7595 (pp20) REVERT: E 80 MET cc_start: 0.8561 (mmm) cc_final: 0.8180 (mmm) REVERT: E 154 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: E 178 PHE cc_start: 0.7793 (p90) cc_final: 0.7326 (t80) REVERT: E 220 GLN cc_start: 0.8337 (pp30) cc_final: 0.7856 (pp30) REVERT: E 357 ASP cc_start: 0.7709 (m-30) cc_final: 0.7169 (m-30) REVERT: E 384 ARG cc_start: 0.3550 (OUTLIER) cc_final: 0.2299 (tpp80) REVERT: E 495 MET cc_start: 0.8496 (mtp) cc_final: 0.8228 (mtp) REVERT: E 509 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6677 (tpt) REVERT: E 586 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7357 (t80) REVERT: F 56 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7114 (tmt-80) REVERT: F 88 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7325 (mmtt) REVERT: F 186 ILE cc_start: 0.8343 (mm) cc_final: 0.8081 (mm) REVERT: F 219 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: F 509 MET cc_start: 0.0644 (mmm) cc_final: 0.0375 (mmm) outliers start: 157 outliers final: 106 residues processed: 462 average time/residue: 0.5350 time to fit residues: 398.7032 Evaluate side-chains 447 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 317 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Chi-restraints excluded: chain F residue 485 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 219 optimal weight: 0.0070 chunk 324 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 255 optimal weight: 0.4980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.166911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117622 restraints weight = 41611.924| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.47 r_work: 0.3318 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 28419 Z= 0.113 Angle : 0.604 14.352 38510 Z= 0.298 Chirality : 0.042 0.270 4269 Planarity : 0.005 0.151 4973 Dihedral : 6.272 69.711 3866 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.87 % Favored : 94.87 % Rotamer: Outliers : 3.86 % Allowed : 29.95 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 0.29 (0.15), residues: 3492 helix: 1.26 (0.13), residues: 1629 sheet: -0.20 (0.26), residues: 416 loop : -0.88 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 82 HIS 0.007 0.001 HIS F 433 PHE 0.040 0.001 PHE F 208 TYR 0.017 0.001 TYR B 521 ARG 0.011 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 1201) hydrogen bonds : angle 4.50490 ( 3444) covalent geometry : bond 0.00264 (28419) covalent geometry : angle 0.60384 (38510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 348 time to evaluate : 3.402 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 31 HIS cc_start: 0.8118 (m90) cc_final: 0.7633 (m170) REVERT: A 80 MET cc_start: 0.8675 (mmm) cc_final: 0.8289 (mmm) REVERT: A 112 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7179 (tttt) REVERT: A 487 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 520 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7523 (mtmm) REVERT: B 133 ASN cc_start: 0.8539 (t0) cc_final: 0.8266 (t0) REVERT: B 151 MET cc_start: 0.7477 (pmm) cc_final: 0.5270 (pmm) REVERT: B 166 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8115 (tt) REVERT: B 196 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7641 (tpp) REVERT: B 378 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (mm) REVERT: B 443 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8382 (tp) REVERT: B 460 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 547 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8697 (mm) REVERT: C 29 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: C 120 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7118 (tm-30) REVERT: C 136 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8632 (mt-10) REVERT: C 138 PHE cc_start: 0.7396 (m-10) cc_final: 0.7148 (m-10) REVERT: C 154 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 162 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6653 (mmm160) REVERT: C 184 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8270 (mttt) REVERT: C 210 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.7948 (t) REVERT: C 386 PHE cc_start: 0.4103 (OUTLIER) cc_final: 0.2803 (p90) REVERT: C 404 MET cc_start: 0.7773 (tmm) cc_final: 0.7528 (ttp) REVERT: C 405 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: C 594 CYS cc_start: 0.7848 (m) cc_final: 0.7542 (m) REVERT: D 14 MET cc_start: 0.5244 (mmm) cc_final: 0.4813 (mmm) REVERT: D 27 PHE cc_start: 0.7295 (m-80) cc_final: 0.6678 (m-10) REVERT: D 36 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: D 137 MET cc_start: 0.7622 (mmm) cc_final: 0.6945 (mmm) REVERT: D 213 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8545 (mm) REVERT: D 219 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: D 454 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: D 547 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (mm) REVERT: E 1 MET cc_start: 0.1984 (tpt) cc_final: 0.0620 (tpt) REVERT: E 3 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.6882 (ptp90) REVERT: E 75 GLU cc_start: 0.8072 (pp20) cc_final: 0.7636 (pp20) REVERT: E 78 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8485 (tp-100) REVERT: E 80 MET cc_start: 0.8588 (mmm) cc_final: 0.8225 (mmm) REVERT: E 123 PHE cc_start: 0.7440 (p90) cc_final: 0.7044 (p90) REVERT: E 167 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6059 (tp) REVERT: E 178 PHE cc_start: 0.7622 (p90) cc_final: 0.7278 (t80) REVERT: E 220 GLN cc_start: 0.8095 (pp30) cc_final: 0.7497 (pp30) REVERT: E 357 ASP cc_start: 0.7734 (m-30) cc_final: 0.7173 (m-30) REVERT: E 384 ARG cc_start: 0.3186 (OUTLIER) cc_final: 0.2054 (tpp-160) REVERT: E 495 MET cc_start: 0.8406 (mtp) cc_final: 0.8149 (mtp) REVERT: E 509 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6673 (tpt) REVERT: E 586 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7339 (t80) REVERT: F 56 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7123 (tpt-90) REVERT: F 88 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7108 (mmtt) REVERT: F 219 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: F 484 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7415 (ttp-110) REVERT: F 509 MET cc_start: 0.0842 (mmm) cc_final: 0.0584 (mmm) outliers start: 117 outliers final: 70 residues processed: 435 average time/residue: 0.4000 time to fit residues: 276.2195 Evaluate side-chains 412 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 315 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 83 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 254 optimal weight: 0.0870 chunk 185 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 HIS ** F 531 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.165577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116086 restraints weight = 41692.651| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.45 r_work: 0.3291 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28419 Z= 0.140 Angle : 0.616 12.280 38510 Z= 0.304 Chirality : 0.043 0.264 4269 Planarity : 0.005 0.152 4973 Dihedral : 6.225 65.551 3866 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.44 % Favored : 94.33 % Rotamer: Outliers : 4.26 % Allowed : 29.95 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 0.28 (0.15), residues: 3492 helix: 1.25 (0.13), residues: 1628 sheet: -0.23 (0.26), residues: 422 loop : -0.86 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 82 HIS 0.005 0.001 HIS F 433 PHE 0.039 0.002 PHE F 208 TYR 0.029 0.001 TYR C 77 ARG 0.010 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 1201) hydrogen bonds : angle 4.49524 ( 3444) covalent geometry : bond 0.00337 (28419) covalent geometry : angle 0.61554 (38510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 335 time to evaluate : 3.756 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 29 GLU cc_start: 0.7175 (mp0) cc_final: 0.6889 (mp0) REVERT: A 31 HIS cc_start: 0.8124 (m90) cc_final: 0.7683 (m170) REVERT: A 80 MET cc_start: 0.8656 (mmm) cc_final: 0.8259 (mmm) REVERT: A 112 LYS cc_start: 0.7833 (ttpp) cc_final: 0.7188 (tttt) REVERT: A 487 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 488 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: A 520 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7522 (mtmm) REVERT: B 133 ASN cc_start: 0.8490 (t0) cc_final: 0.8204 (t0) REVERT: B 151 MET cc_start: 0.7544 (pmm) cc_final: 0.5359 (pmm) REVERT: B 166 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 196 MET cc_start: 0.7934 (tpp) cc_final: 0.7648 (tpp) REVERT: B 378 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 443 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (tp) REVERT: B 460 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: B 483 MET cc_start: 0.8218 (mmm) cc_final: 0.7970 (mtp) REVERT: B 509 MET cc_start: 0.1192 (mmm) cc_final: 0.0681 (mmm) REVERT: B 547 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8707 (mm) REVERT: C 29 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: C 31 HIS cc_start: 0.7971 (m-70) cc_final: 0.7760 (m-70) REVERT: C 76 PHE cc_start: 0.8448 (t80) cc_final: 0.8108 (t80) REVERT: C 120 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7164 (tm-30) REVERT: C 136 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8667 (mt-10) REVERT: C 138 PHE cc_start: 0.7414 (m-10) cc_final: 0.7080 (m-10) REVERT: C 154 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 162 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6683 (mmm160) REVERT: C 184 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8286 (mttt) REVERT: C 210 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8035 (t) REVERT: C 386 PHE cc_start: 0.4226 (OUTLIER) cc_final: 0.2906 (p90) REVERT: C 404 MET cc_start: 0.7778 (tmm) cc_final: 0.7518 (ttp) REVERT: C 405 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: C 520 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: C 594 CYS cc_start: 0.7883 (m) cc_final: 0.7581 (m) REVERT: D 14 MET cc_start: 0.5384 (mmm) cc_final: 0.4830 (mmm) REVERT: D 27 PHE cc_start: 0.7351 (m-80) cc_final: 0.6713 (m-10) REVERT: D 36 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: D 137 MET cc_start: 0.7557 (mmm) cc_final: 0.6872 (mmm) REVERT: D 162 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7640 (mmp80) REVERT: D 205 GLN cc_start: 0.5335 (OUTLIER) cc_final: 0.4457 (mt0) REVERT: D 213 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8557 (mm) REVERT: D 219 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: D 454 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: D 547 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8300 (mm) REVERT: E 1 MET cc_start: 0.2076 (tpt) cc_final: 0.0697 (tpt) REVERT: E 3 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6828 (ptp90) REVERT: E 75 GLU cc_start: 0.8044 (pp20) cc_final: 0.7602 (pp20) REVERT: E 78 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8514 (tp-100) REVERT: E 80 MET cc_start: 0.8620 (mmm) cc_final: 0.8260 (mmm) REVERT: E 123 PHE cc_start: 0.7463 (p90) cc_final: 0.7227 (p90) REVERT: E 154 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: E 167 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6087 (tp) REVERT: E 178 PHE cc_start: 0.7660 (p90) cc_final: 0.7276 (t80) REVERT: E 221 TRP cc_start: 0.8644 (OUTLIER) cc_final: 0.8139 (t60) REVERT: E 357 ASP cc_start: 0.7781 (m-30) cc_final: 0.7209 (m-30) REVERT: E 384 ARG cc_start: 0.3228 (OUTLIER) cc_final: 0.1851 (tpp80) REVERT: E 509 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6619 (tpt) REVERT: E 586 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7368 (t80) REVERT: F 56 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7138 (tpt-90) REVERT: F 88 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7244 (mmtt) REVERT: F 186 ILE cc_start: 0.8066 (mm) cc_final: 0.7830 (mm) REVERT: F 219 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7792 (mt0) outliers start: 129 outliers final: 80 residues processed: 432 average time/residue: 0.3922 time to fit residues: 270.0302 Evaluate side-chains 427 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 315 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Chi-restraints excluded: chain F residue 485 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 11 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 130 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 313 optimal weight: 0.8980 chunk 336 optimal weight: 0.9980 chunk 312 optimal weight: 0.9990 chunk 193 optimal weight: 0.0770 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.167424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117980 restraints weight = 41599.774| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.42 r_work: 0.3324 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 28419 Z= 0.112 Angle : 0.604 10.322 38510 Z= 0.298 Chirality : 0.043 0.265 4269 Planarity : 0.005 0.149 4973 Dihedral : 6.134 63.792 3864 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.13 % Favored : 94.64 % Rotamer: Outliers : 3.70 % Allowed : 30.58 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 0.38 (0.15), residues: 3492 helix: 1.31 (0.13), residues: 1628 sheet: -0.12 (0.26), residues: 416 loop : -0.83 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 82 HIS 0.005 0.001 HIS F 433 PHE 0.037 0.001 PHE F 208 TYR 0.017 0.001 TYR F 153 ARG 0.017 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1201) hydrogen bonds : angle 4.42993 ( 3444) covalent geometry : bond 0.00264 (28419) covalent geometry : angle 0.60362 (38510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 329 time to evaluate : 3.097 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 29 GLU cc_start: 0.7250 (mp0) cc_final: 0.6963 (mp0) REVERT: A 31 HIS cc_start: 0.8053 (m90) cc_final: 0.7634 (m170) REVERT: A 72 ARG cc_start: 0.6064 (tmt170) cc_final: 0.5837 (tmt-80) REVERT: A 80 MET cc_start: 0.8674 (mmm) cc_final: 0.8267 (mmm) REVERT: A 112 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7205 (tttt) REVERT: A 487 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8791 (mt) REVERT: A 520 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7479 (mtmm) REVERT: B 133 ASN cc_start: 0.8462 (t0) cc_final: 0.8180 (t0) REVERT: B 151 MET cc_start: 0.7419 (pmm) cc_final: 0.5313 (pmm) REVERT: B 166 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8116 (tt) REVERT: B 196 MET cc_start: 0.7859 (tpp) cc_final: 0.7632 (tpp) REVERT: B 378 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7959 (mm) REVERT: B 443 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8350 (tp) REVERT: B 460 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: B 483 MET cc_start: 0.8205 (mmm) cc_final: 0.7933 (mtp) REVERT: B 501 TYR cc_start: 0.8053 (t80) cc_final: 0.7850 (t80) REVERT: B 509 MET cc_start: 0.1439 (mmm) cc_final: 0.1099 (mmm) REVERT: B 547 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8707 (mm) REVERT: C 29 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: C 76 PHE cc_start: 0.8401 (t80) cc_final: 0.8146 (t80) REVERT: C 120 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7151 (tm-30) REVERT: C 136 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8618 (mt-10) REVERT: C 138 PHE cc_start: 0.7332 (m-10) cc_final: 0.7042 (m-10) REVERT: C 154 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 162 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6783 (mmm160) REVERT: C 184 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8279 (mttt) REVERT: C 210 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7820 (t) REVERT: C 386 PHE cc_start: 0.4129 (OUTLIER) cc_final: 0.2832 (p90) REVERT: C 390 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6017 (tt) REVERT: C 404 MET cc_start: 0.7714 (tmm) cc_final: 0.7470 (ttp) REVERT: C 520 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8232 (mmtp) REVERT: C 594 CYS cc_start: 0.7783 (m) cc_final: 0.7575 (m) REVERT: D 27 PHE cc_start: 0.7289 (m-80) cc_final: 0.6676 (m-10) REVERT: D 36 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: D 137 MET cc_start: 0.7477 (mmm) cc_final: 0.6944 (mmm) REVERT: D 151 MET cc_start: 0.7788 (tpp) cc_final: 0.7277 (mmm) REVERT: D 162 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7651 (mmp80) REVERT: D 196 MET cc_start: 0.7678 (mmp) cc_final: 0.7350 (mmm) REVERT: D 205 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4470 (mt0) REVERT: D 213 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8537 (mm) REVERT: D 219 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: D 454 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: D 547 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8249 (mm) REVERT: E 1 MET cc_start: 0.2064 (tpt) cc_final: 0.0853 (tpt) REVERT: E 3 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.6806 (ptp90) REVERT: E 75 GLU cc_start: 0.8048 (pp20) cc_final: 0.7613 (pp20) REVERT: E 78 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8516 (tp-100) REVERT: E 80 MET cc_start: 0.8643 (mmm) cc_final: 0.8301 (mmm) REVERT: E 123 PHE cc_start: 0.7395 (p90) cc_final: 0.7037 (p90) REVERT: E 154 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: E 167 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5914 (tp) REVERT: E 178 PHE cc_start: 0.7599 (p90) cc_final: 0.7245 (t80) REVERT: E 220 GLN cc_start: 0.8043 (pp30) cc_final: 0.7565 (pp30) REVERT: E 221 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8183 (t60) REVERT: E 357 ASP cc_start: 0.7733 (m-30) cc_final: 0.7170 (m-30) REVERT: E 384 ARG cc_start: 0.3168 (OUTLIER) cc_final: 0.2071 (tpp-160) REVERT: E 509 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6621 (tpt) REVERT: E 586 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7230 (t80) REVERT: F 56 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7212 (tpt-90) REVERT: F 88 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7157 (mmtt) REVERT: F 219 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: F 509 MET cc_start: 0.1067 (mmm) cc_final: 0.0570 (mmm) outliers start: 112 outliers final: 72 residues processed: 420 average time/residue: 0.4162 time to fit residues: 280.2152 Evaluate side-chains 417 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 314 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Chi-restraints excluded: chain F residue 485 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 253 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN D 472 HIS D 502 GLN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.165058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115569 restraints weight = 41835.205| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.47 r_work: 0.3279 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28419 Z= 0.165 Angle : 0.642 11.541 38510 Z= 0.318 Chirality : 0.044 0.264 4269 Planarity : 0.005 0.152 4973 Dihedral : 6.190 63.132 3864 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.53 % Favored : 94.27 % Rotamer: Outliers : 3.83 % Allowed : 30.52 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 0.26 (0.15), residues: 3492 helix: 1.20 (0.13), residues: 1639 sheet: -0.14 (0.26), residues: 409 loop : -0.89 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 157 HIS 0.004 0.001 HIS F 433 PHE 0.039 0.002 PHE F 208 TYR 0.017 0.002 TYR C 77 ARG 0.013 0.001 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1201) hydrogen bonds : angle 4.51926 ( 3444) covalent geometry : bond 0.00401 (28419) covalent geometry : angle 0.64218 (38510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 317 time to evaluate : 3.251 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 29 GLU cc_start: 0.7223 (mp0) cc_final: 0.6923 (mp0) REVERT: A 31 HIS cc_start: 0.8153 (m90) cc_final: 0.7749 (m170) REVERT: A 33 PHE cc_start: 0.8461 (t80) cc_final: 0.8238 (t80) REVERT: A 72 ARG cc_start: 0.6212 (tmt170) cc_final: 0.6010 (tmt-80) REVERT: A 80 MET cc_start: 0.8647 (mmm) cc_final: 0.8231 (mmm) REVERT: A 112 LYS cc_start: 0.7861 (ttpp) cc_final: 0.7057 (tttt) REVERT: A 487 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 520 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7520 (mtmm) REVERT: B 133 ASN cc_start: 0.8510 (t0) cc_final: 0.8220 (t0) REVERT: B 151 MET cc_start: 0.7521 (pmm) cc_final: 0.5502 (pmm) REVERT: B 166 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 196 MET cc_start: 0.7946 (tpp) cc_final: 0.7675 (tpp) REVERT: B 378 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 443 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (tp) REVERT: B 460 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: B 509 MET cc_start: 0.1580 (mmm) cc_final: 0.1234 (mmm) REVERT: B 547 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8776 (mm) REVERT: C 29 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: C 31 HIS cc_start: 0.7952 (m-70) cc_final: 0.7410 (m-70) REVERT: C 56 ARG cc_start: 0.8628 (tpt90) cc_final: 0.8230 (tpt90) REVERT: C 76 PHE cc_start: 0.8423 (t80) cc_final: 0.7940 (t80) REVERT: C 120 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 136 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 138 PHE cc_start: 0.7448 (m-10) cc_final: 0.7106 (m-10) REVERT: C 154 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 162 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6815 (mmm160) REVERT: C 184 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8302 (mttt) REVERT: C 210 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8136 (t) REVERT: C 386 PHE cc_start: 0.4237 (OUTLIER) cc_final: 0.2946 (p90) REVERT: C 390 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.5988 (tt) REVERT: C 594 CYS cc_start: 0.8031 (m) cc_final: 0.7793 (m) REVERT: D 14 MET cc_start: 0.5749 (mmp) cc_final: 0.5255 (mmm) REVERT: D 27 PHE cc_start: 0.7341 (m-80) cc_final: 0.6696 (m-10) REVERT: D 36 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: D 162 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7738 (mmp80) REVERT: D 213 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8595 (mm) REVERT: D 219 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: D 454 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: D 483 MET cc_start: 0.8185 (mtp) cc_final: 0.7913 (ttt) REVERT: D 547 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8263 (mm) REVERT: E 1 MET cc_start: 0.2135 (tpt) cc_final: 0.0901 (tpt) REVERT: E 3 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6769 (ptp90) REVERT: E 75 GLU cc_start: 0.8059 (pp20) cc_final: 0.7619 (pp20) REVERT: E 80 MET cc_start: 0.8629 (mmm) cc_final: 0.8282 (mmm) REVERT: E 123 PHE cc_start: 0.7475 (p90) cc_final: 0.7070 (p90) REVERT: E 154 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: E 167 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6037 (tp) REVERT: E 178 PHE cc_start: 0.7719 (p90) cc_final: 0.7334 (t80) REVERT: E 220 GLN cc_start: 0.8099 (pp30) cc_final: 0.7647 (pp30) REVERT: E 221 TRP cc_start: 0.8664 (OUTLIER) cc_final: 0.8203 (t60) REVERT: E 357 ASP cc_start: 0.7787 (m-30) cc_final: 0.7208 (m-30) REVERT: E 384 ARG cc_start: 0.3207 (OUTLIER) cc_final: 0.1842 (tpp80) REVERT: E 509 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6599 (tpt) REVERT: E 586 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7237 (t80) REVERT: F 56 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7164 (tpt-90) REVERT: F 88 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7254 (mmtt) REVERT: F 219 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: F 453 ASP cc_start: 0.6299 (t70) cc_final: 0.6031 (t70) REVERT: F 509 MET cc_start: 0.0956 (mmm) cc_final: 0.0459 (mmm) outliers start: 116 outliers final: 77 residues processed: 409 average time/residue: 0.3984 time to fit residues: 262.1298 Evaluate side-chains 413 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 308 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 GLN Chi-restraints excluded: chain F residue 483 MET Chi-restraints excluded: chain F residue 485 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 253 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 331 optimal weight: 4.9990 chunk 217 optimal weight: 0.0770 chunk 175 optimal weight: 0.2980 chunk 188 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 HIS ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 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 = 0.4182 r_free = 0.4182 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114883 restraints weight = 41108.288| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.41 r_work: 0.3283 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28419 Z= 0.146 Angle : 0.637 14.783 38510 Z= 0.313 Chirality : 0.044 0.265 4269 Planarity : 0.005 0.152 4973 Dihedral : 6.206 63.593 3864 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 3.63 % Allowed : 30.61 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3492 helix: 1.21 (0.13), residues: 1633 sheet: -0.16 (0.26), residues: 409 loop : -0.87 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 157 HIS 0.004 0.001 HIS F 433 PHE 0.039 0.002 PHE F 208 TYR 0.019 0.001 TYR B 521 ARG 0.013 0.001 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1201) hydrogen bonds : angle 4.50910 ( 3444) covalent geometry : bond 0.00354 (28419) covalent geometry : angle 0.63652 (38510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15571.90 seconds wall clock time: 270 minutes 4.94 seconds (16204.94 seconds total)