Starting phenix.real_space_refine on Fri Jul 3 18:35:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.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/7d7e_30606/07_2026/7d7e_30606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d7e_30606/07_2026/7d7e_30606.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 60 5.16 5 C 10186 2.51 5 N 2489 2.21 5 O 2763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15501 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3960 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 11, 'TRANS': 470} Chain: "C" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3898 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 11, 'TRANS': 462} Chain: "D" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3862 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 11, 'TRANS': 459} Chain breaks: 1 Chain: "A" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3638 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 10, 'TRANS': 440} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.24, per 1000 atoms: 0.21 Number of scatterers: 15501 At special positions: 0 Unit cell: (110.874, 119.57, 116.309, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 60 16.00 O 2763 8.00 N 2489 7.00 C 10186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 223 " distance=2.02 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 223 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2500 " - " ASN A1822 " " NAG A2501 " - " ASN A1712 " " NAG B 701 " - " ASN B 177 " " NAG B 702 " - " ASN B 207 " " NAG B 703 " - " ASN B 241 " " NAG C 701 " - " ASN C 177 " " NAG C 702 " - " ASN C 207 " " NAG C 703 " - " ASN C 241 " " NAG D 801 " - " ASN D 207 " " NAG D 802 " - " ASN D 241 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 640.9 milliseconds 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 53.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.836A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.742A pdb=" N TYR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.509A pdb=" N PHE B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.939A pdb=" N GLY B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 377 removed outlier: 3.525A pdb=" N ILE B 352 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 385 through 421 removed outlier: 3.694A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.724A pdb=" N THR B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 499 removed outlier: 3.787A pdb=" N GLY B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.778A pdb=" N LEU B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 533 removed outlier: 3.594A pdb=" N ILE B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 575 removed outlier: 3.909A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 120 removed outlier: 3.676A pdb=" N VAL C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.878A pdb=" N THR C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.568A pdb=" N PHE C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.572A pdb=" N GLY C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 376 removed outlier: 3.712A pdb=" N CYS C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.696A pdb=" N SER C 383 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 384 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 421 removed outlier: 3.805A pdb=" N HIS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 452 Processing helix chain 'C' and resid 453 through 456 Processing helix chain 'C' and resid 466 through 473 removed outlier: 3.826A pdb=" N ARG C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.549A pdb=" N PHE C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 481 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 removed outlier: 3.672A pdb=" N LEU C 521 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 533 removed outlier: 4.257A pdb=" N ILE C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 564 removed outlier: 3.892A pdb=" N VAL C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 115 removed outlier: 3.893A pdb=" N LEU D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.772A pdb=" N THR D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.564A pdb=" N PHE D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 162 " --> pdb=" O TRP D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 278 through 291 removed outlier: 3.545A pdb=" N GLY D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 373 removed outlier: 3.589A pdb=" N PHE D 350 " --> pdb=" O ASN D 346 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 421 removed outlier: 3.629A pdb=" N LEU D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D 391 " --> pdb=" O ASN D 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 452 Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 460 through 465 removed outlier: 3.544A pdb=" N THR D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 477 through 499 removed outlier: 3.844A pdb=" N ILE D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.596A pdb=" N LEU D 521 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.724A pdb=" N ILE D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 572 removed outlier: 4.139A pdb=" N VAL D 539 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR D 564 " --> pdb=" O ILE D 560 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1678 removed outlier: 3.935A pdb=" N ALA A1678 " --> pdb=" O THR A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1695 removed outlier: 3.724A pdb=" N PHE A1685 " --> pdb=" O SER A1681 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1686 " --> pdb=" O SER A1682 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A1687 " --> pdb=" O ARG A1683 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A1695 " --> pdb=" O TRP A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1720 Processing helix chain 'A' and resid 1823 through 1836 removed outlier: 3.918A pdb=" N VAL A1829 " --> pdb=" O ALA A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1920 Processing helix chain 'A' and resid 1928 through 1965 removed outlier: 3.763A pdb=" N LEU A1932 " --> pdb=" O ARG A1928 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1933 " --> pdb=" O LYS A1929 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A1934 " --> pdb=" O ARG A1930 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1938 " --> pdb=" O ASP A1934 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A1952 " --> pdb=" O SER A1948 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A1965 " --> pdb=" O GLN A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 2001 removed outlier: 3.770A pdb=" N LEU A1991 " --> pdb=" O GLY A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2043 removed outlier: 3.731A pdb=" N TYR A2035 " --> pdb=" O LEU A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2066 Processing helix chain 'A' and resid 2071 through 2077 Processing helix chain 'A' and resid 2079 through 2107 removed outlier: 3.930A pdb=" N ALA A2107 " --> pdb=" O ALA A2103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 193 through 194 removed outlier: 3.635A pdb=" N TYR B 308 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 300 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 193 through 194 removed outlier: 3.635A pdb=" N TYR B 308 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 323 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 188 removed outlier: 4.680A pdb=" N SER C 306 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 197 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP C 304 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG C 199 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE C 302 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG C 201 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 300 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU C 203 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR C 298 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 307 " --> pdb=" O CYS C 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 258 through 259 Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AA8, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.934A pdb=" N LEU D 195 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR D 308 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 197 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER D 306 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 199 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP D 304 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 300 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 314 " --> pdb=" O ASN D 309 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU D 323 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1815 through 1818 removed outlier: 6.932A pdb=" N PHE A1733 " --> pdb=" O ASN A1854 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN A1854 " --> pdb=" O PHE A1733 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A1735 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A1852 " --> pdb=" O LEU A1735 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN A1737 " --> pdb=" O PHE A1850 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE A1850 " --> pdb=" O ASN A1737 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A1739 " --> pdb=" O VAL A1848 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A1848 " --> pdb=" O LEU A1739 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A1741 " --> pdb=" O LEU A1846 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A1846 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR A1743 " --> pdb=" O LYS A1844 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A1844 " --> pdb=" O SER A1869 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER A1869 " --> pdb=" O LYS A1844 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4749 1.34 - 1.46: 3686 1.46 - 1.58: 7396 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 15922 Sorted by residual: bond pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 1.521 1.443 0.077 1.36e-02 5.41e+03 3.25e+01 bond pdb=" N VAL A1704 " pdb=" CA VAL A1704 " ideal model delta sigma weight residual 1.459 1.493 -0.035 9.10e-03 1.21e+04 1.47e+01 bond pdb=" N GLN A1888 " pdb=" CA GLN A1888 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.25e-02 6.40e+03 8.61e+00 bond pdb=" N ILE A1897 " pdb=" CA ILE A1897 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.17e+00 bond pdb=" N LEU A1887 " pdb=" CA LEU A1887 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.17e+00 ... (remaining 15917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 21298 2.51 - 5.02: 311 5.02 - 7.53: 32 7.53 - 10.05: 3 10.05 - 12.56: 2 Bond angle restraints: 21646 Sorted by residual: angle pdb=" N VAL B 345 " pdb=" CA VAL B 345 " pdb=" C VAL B 345 " ideal model delta sigma weight residual 113.20 107.69 5.51 9.60e-01 1.09e+00 3.30e+01 angle pdb=" N HIS B 213 " pdb=" CA HIS B 213 " pdb=" C HIS B 213 " ideal model delta sigma weight residual 110.80 122.94 -12.14 2.13e+00 2.20e-01 3.25e+01 angle pdb=" N ILE D 374 " pdb=" CA ILE D 374 " pdb=" C ILE D 374 " ideal model delta sigma weight residual 112.29 107.00 5.29 9.40e-01 1.13e+00 3.17e+01 angle pdb=" N ILE A1749 " pdb=" CA ILE A1749 " pdb=" C ILE A1749 " ideal model delta sigma weight residual 112.98 107.01 5.97 1.25e+00 6.40e-01 2.28e+01 angle pdb=" N VAL A1704 " pdb=" CA VAL A1704 " pdb=" C VAL A1704 " ideal model delta sigma weight residual 113.47 108.73 4.74 1.01e+00 9.80e-01 2.20e+01 ... (remaining 21641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7793 17.82 - 35.64: 949 35.64 - 53.45: 231 53.45 - 71.27: 50 71.27 - 89.09: 8 Dihedral angle restraints: 9031 sinusoidal: 3523 harmonic: 5508 Sorted by residual: dihedral pdb=" CB CYS B 210 " pdb=" SG CYS B 210 " pdb=" SG CYS B 223 " pdb=" CB CYS B 223 " ideal model delta sinusoidal sigma weight residual -86.00 -21.22 -64.78 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CA HIS B 213 " pdb=" C HIS B 213 " pdb=" N GLU B 214 " pdb=" CA GLU B 214 " ideal model delta harmonic sigma weight residual 180.00 145.97 34.03 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA LYS D 98 " pdb=" C LYS D 98 " pdb=" N THR D 99 " pdb=" CA THR D 99 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 9028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1982 0.063 - 0.125: 406 0.125 - 0.188: 40 0.188 - 0.251: 4 0.251 - 0.313: 3 Chirality restraints: 2435 Sorted by residual: chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 207 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG D 801 " pdb=" ND2 ASN D 207 " pdb=" C2 NAG D 801 " pdb=" O5 NAG D 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C1 NAG A2501 " pdb=" ND2 ASN A1712 " pdb=" C2 NAG A2501 " pdb=" O5 NAG A2501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2432 not shown) Planarity restraints: 2696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 238 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.30e+00 pdb=" N PRO D 239 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 239 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 239 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 163 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO B 164 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 238 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO B 239 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 239 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 239 " -0.028 5.00e-02 4.00e+02 ... (remaining 2693 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 72 2.48 - 3.08: 10946 3.08 - 3.69: 21924 3.69 - 4.29: 32850 4.29 - 4.90: 56342 Nonbonded interactions: 122134 Sorted by model distance: nonbonded pdb=" OD1 ASN D 387 " pdb="CA CA D 803 " model vdw 1.870 2.510 nonbonded pdb=" O THR C 99 " pdb=" OG1 THR C 100 " model vdw 2.080 3.040 nonbonded pdb=" O VAL B 212 " pdb=" ND1 HIS B 213 " model vdw 2.129 3.120 nonbonded pdb=" OH TYR D 119 " pdb=" ND2 ASN A2040 " model vdw 2.131 3.120 nonbonded pdb=" N ASP C 304 " pdb=" OD1 ASP C 304 " model vdw 2.154 3.120 ... (remaining 122129 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 'B' and (resid 94 through 173 or resid 183 through 567 or resid 702 throu \ gh 704)) selection = (chain 'C' and (resid 94 through 173 or resid 183 through 567 or resid 702 throu \ gh 704)) selection = (chain 'D' and (resid 94 through 567 or resid 801 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.050 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.007 0.077 15934 Z= 0.348 Angle : 0.782 13.830 21680 Z= 0.457 Chirality : 0.051 0.313 2435 Planarity : 0.004 0.063 2686 Dihedral : 16.567 89.089 5497 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 10.81 % Allowed : 20.85 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.17), residues: 1868 helix: -1.15 (0.15), residues: 999 sheet: -1.64 (0.33), residues: 193 loop : -3.80 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1996 TYR 0.022 0.002 TYR B 438 PHE 0.017 0.002 PHE B 302 TRP 0.011 0.001 TRP C 434 HIS 0.006 0.001 HIS A1765 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.35 (15922) covalent geometry : angle 0.75916 / 0.45 (21646) SS BOND : bond 0.00787 / 0.40 ( 2) SS BOND : angle 4.00429 / 2.05 ( 4) hydrogen bonds : bond 0.14253 / 9.45 ( 793) hydrogen bonds : angle 5.59579 / 3.81 ( 2319) link_NAG-ASN : bond 0.00885 / 0.44 ( 10) link_NAG-ASN : angle 4.92670 / 3.10 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 228 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8106 (m) REVERT: B 135 GLU cc_start: 0.8134 (pt0) cc_final: 0.7912 (tm-30) REVERT: B 138 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8739 (pp) REVERT: B 323 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8619 (mt-10) REVERT: B 356 GLU cc_start: 0.5734 (mm-30) cc_final: 0.5459 (tp30) REVERT: B 360 CYS cc_start: 0.8968 (t) cc_final: 0.8540 (m) REVERT: B 420 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 461 LYS cc_start: 0.7403 (mmpt) cc_final: 0.6896 (mmmt) REVERT: B 465 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7507 (mp10) REVERT: C 131 LYS cc_start: 0.8346 (tttt) cc_final: 0.8042 (tttp) REVERT: C 173 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8547 (mttm) REVERT: C 317 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8541 (mm) REVERT: C 349 ASP cc_start: 0.8725 (m-30) cc_final: 0.8202 (m-30) REVERT: C 356 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4724 (mm-30) REVERT: C 378 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7329 (mmm160) REVERT: C 390 ASP cc_start: 0.6990 (m-30) cc_final: 0.6634 (m-30) REVERT: C 465 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7356 (mm-40) REVERT: C 472 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8399 (ptp-170) REVERT: C 526 TYR cc_start: 0.8803 (t80) cc_final: 0.8408 (t80) REVERT: C 555 MET cc_start: 0.7326 (mtt) cc_final: 0.6659 (ttp) REVERT: D 102 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7624 (ttp-110) REVERT: D 113 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8679 (t0) REVERT: D 121 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8371 (mmm) REVERT: D 304 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7779 (p0) REVERT: D 313 ASN cc_start: 0.7870 (p0) cc_final: 0.7402 (p0) REVERT: D 376 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4610 (mt) REVERT: D 410 GLU cc_start: 0.7979 (tp30) cc_final: 0.7573 (tp30) REVERT: D 421 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8814 (pp30) REVERT: D 466 LEU cc_start: 0.8778 (tt) cc_final: 0.8569 (tp) REVERT: D 480 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7788 (t80) REVERT: D 483 MET cc_start: 0.8222 (ttm) cc_final: 0.7997 (ttm) REVERT: D 499 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: D 502 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8338 (mm110) REVERT: D 504 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 549 PHE cc_start: 0.6771 (m-10) cc_final: 0.6378 (t80) REVERT: D 554 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7706 (t0) REVERT: A 1705 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: A 1729 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6099 (t0) REVERT: A 1807 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8734 (pp) REVERT: A 1919 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8000 (tptp) REVERT: A 1930 ARG cc_start: 0.7620 (ttt180) cc_final: 0.7343 (tmm-80) REVERT: A 1959 MET cc_start: 0.9208 (mmm) cc_final: 0.8966 (tpp) REVERT: A 2069 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (mmtt) REVERT: A 2070 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.8057 (p-80) REVERT: A 2098 ASN cc_start: 0.8778 (t0) cc_final: 0.8151 (t0) outliers start: 181 outliers final: 99 residues processed: 383 average time/residue: 0.1088 time to fit residues: 63.4890 Evaluate side-chains 290 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 171 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 485 PHE Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain D residue 502 GLN Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 555 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1729 ASP Chi-restraints excluded: chain A residue 1732 SER Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1777 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1849 GLU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1872 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1888 GLN Chi-restraints excluded: chain A residue 1907 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1919 LYS Chi-restraints excluded: chain A residue 1926 PHE Chi-restraints excluded: chain A residue 1951 SER Chi-restraints excluded: chain A residue 1991 LEU Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2034 SER Chi-restraints excluded: chain A residue 2043 PHE Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2068 SER Chi-restraints excluded: chain A residue 2069 LYS Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2073 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 HIS B 258 HIS B 313 ASN B 377 HIS B 412 ASN B 516 GLN B 574 GLN C 139 HIS C 178 GLN C 222 ASN C 258 HIS C 412 ASN C 421 GLN C 460 ASN C 516 GLN C 527 ASN C 554 ASN D 139 HIS D 192 ASN D 202 GLN D 258 HIS D 347 ASN D 377 HIS ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 GLN D 516 GLN D 554 ASN A1664 GLN A1756 HIS A1856 ASN A1950 GLN A1961 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.087105 restraints weight = 20788.872| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 1.71 r_work: 0.2550 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15934 Z= 0.140 Angle : 0.627 13.174 21680 Z= 0.321 Chirality : 0.043 0.252 2435 Planarity : 0.004 0.055 2686 Dihedral : 9.250 67.531 2267 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.73 % Allowed : 21.57 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.19), residues: 1868 helix: 0.15 (0.16), residues: 1013 sheet: -0.84 (0.36), residues: 192 loop : -3.27 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 337 TYR 0.014 0.001 TYR B 438 PHE 0.017 0.001 PHE B 480 TRP 0.011 0.001 TRP C 434 HIS 0.005 0.001 HIS B 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (15922) covalent geometry : angle 0.60562 / 0.32 (21646) SS BOND : bond 0.00470 / 0.24 ( 2) SS BOND : angle 3.76375 / 1.97 ( 4) hydrogen bonds : bond 0.04983 / 3.26 ( 793) hydrogen bonds : angle 3.87033 / 2.65 ( 2319) link_NAG-ASN : bond 0.00712 / 0.31 ( 10) link_NAG-ASN : angle 4.15070 / 2.58 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 191 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9069 (pp) REVERT: B 360 CYS cc_start: 0.9092 (t) cc_final: 0.8785 (m) REVERT: B 420 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 461 LYS cc_start: 0.7476 (mmpt) cc_final: 0.6972 (mmmt) REVERT: B 504 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8638 (tp30) REVERT: C 103 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 349 ASP cc_start: 0.8939 (m-30) cc_final: 0.8293 (m-30) REVERT: C 356 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5433 (mm-30) REVERT: C 375 HIS cc_start: 0.8604 (t-170) cc_final: 0.8364 (t-170) REVERT: C 378 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7135 (mmm160) REVERT: C 465 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7692 (mm-40) REVERT: C 555 MET cc_start: 0.8072 (mtt) cc_final: 0.7329 (ttp) REVERT: D 118 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9149 (m) REVERT: D 376 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4361 (mt) REVERT: D 410 GLU cc_start: 0.8396 (tp30) cc_final: 0.8032 (tp30) REVERT: D 421 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8110 (pp30) REVERT: D 480 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8199 (t80) REVERT: D 549 PHE cc_start: 0.7450 (m-10) cc_final: 0.7228 (t80) REVERT: D 554 ASN cc_start: 0.8777 (t0) cc_final: 0.8221 (t0) REVERT: A 1904 TYR cc_start: 0.8575 (m-80) cc_final: 0.8370 (m-80) REVERT: A 1930 ARG cc_start: 0.7724 (ttt180) cc_final: 0.7247 (ttm110) REVERT: A 1965 ASP cc_start: 0.7859 (t0) cc_final: 0.7642 (t0) REVERT: A 2070 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8094 (p-80) REVERT: A 2098 ASN cc_start: 0.8978 (t0) cc_final: 0.8359 (t0) outliers start: 96 outliers final: 48 residues processed: 269 average time/residue: 0.0960 time to fit residues: 39.8468 Evaluate side-chains 230 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1872 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 162 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 GLN D 258 HIS A1823 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.084843 restraints weight = 21214.440| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 1.88 r_work: 0.2488 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15934 Z= 0.183 Angle : 0.639 12.840 21680 Z= 0.323 Chirality : 0.044 0.248 2435 Planarity : 0.004 0.055 2686 Dihedral : 7.018 57.907 2122 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.20 % Allowed : 22.70 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1868 helix: 0.61 (0.17), residues: 1015 sheet: -0.57 (0.36), residues: 192 loop : -3.06 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1920 TYR 0.018 0.001 TYR C 438 PHE 0.015 0.001 PHE C 488 TRP 0.009 0.001 TRP B 434 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (15922) covalent geometry : angle 0.61864 / 0.32 (21646) SS BOND : bond 0.00615 / 0.32 ( 2) SS BOND : angle 3.39311 / 1.76 ( 4) hydrogen bonds : bond 0.05148 / 3.37 ( 793) hydrogen bonds : angle 3.71098 / 2.54 ( 2319) link_NAG-ASN : bond 0.00681 / 0.30 ( 10) link_NAG-ASN : angle 4.12419 / 2.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 183 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8337 (mmm) cc_final: 0.8063 (mmm) REVERT: B 138 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9122 (pp) REVERT: B 360 CYS cc_start: 0.9097 (t) cc_final: 0.8784 (m) REVERT: B 368 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8646 (p) REVERT: B 420 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 504 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8621 (tp30) REVERT: C 343 ARG cc_start: 0.8305 (ptp-170) cc_final: 0.8079 (ptm160) REVERT: C 349 ASP cc_start: 0.8925 (m-30) cc_final: 0.8267 (m-30) REVERT: C 356 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5368 (mm-30) REVERT: C 378 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7207 (mmm160) REVERT: C 555 MET cc_start: 0.8166 (mtt) cc_final: 0.7362 (ttp) REVERT: D 376 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4462 (mt) REVERT: D 382 LEU cc_start: 0.8481 (pt) cc_final: 0.8221 (tp) REVERT: D 410 GLU cc_start: 0.8477 (tp30) cc_final: 0.8082 (tp30) REVERT: D 421 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8492 (pp30) REVERT: D 480 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8184 (t80) REVERT: D 549 PHE cc_start: 0.7425 (m-10) cc_final: 0.7216 (t80) REVERT: D 554 ASN cc_start: 0.8753 (t0) cc_final: 0.8161 (t0) REVERT: A 1904 TYR cc_start: 0.8623 (m-80) cc_final: 0.8403 (m-80) REVERT: A 1930 ARG cc_start: 0.7769 (ttt180) cc_final: 0.7294 (ttm110) REVERT: A 2070 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8065 (p-80) REVERT: A 2098 ASN cc_start: 0.8971 (t0) cc_final: 0.8211 (t0) REVERT: A 2108 PHE cc_start: 0.8333 (t80) cc_final: 0.8082 (t80) outliers start: 87 outliers final: 57 residues processed: 253 average time/residue: 0.0973 time to fit residues: 38.4642 Evaluate side-chains 232 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1695 SER Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1872 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1994 THR Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Chi-restraints excluded: chain A residue 2104 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 121 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 117 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 375 HIS D 258 HIS ** D 493 GLN ** 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 = 0.3339 r_free = 0.3339 target = 0.117951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.087482 restraints weight = 21055.036| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 1.86 r_work: 0.2531 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15934 Z= 0.142 Angle : 0.599 12.846 21680 Z= 0.302 Chirality : 0.043 0.249 2435 Planarity : 0.003 0.052 2686 Dihedral : 6.704 56.114 2118 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.96 % Allowed : 23.30 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1868 helix: 0.88 (0.17), residues: 1019 sheet: -0.34 (0.37), residues: 192 loop : -2.91 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 343 TYR 0.014 0.001 TYR B 438 PHE 0.015 0.001 PHE D 403 TRP 0.010 0.001 TRP B 434 HIS 0.007 0.001 HIS C 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15922) covalent geometry : angle 0.57943 / 0.30 (21646) SS BOND : bond 0.00495 / 0.26 ( 2) SS BOND : angle 2.90716 / 1.51 ( 4) hydrogen bonds : bond 0.04612 / 3.02 ( 793) hydrogen bonds : angle 3.57882 / 2.45 ( 2319) link_NAG-ASN : bond 0.00718 / 0.32 ( 10) link_NAG-ASN : angle 4.00732 / 2.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 179 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9063 (pp) REVERT: B 360 CYS cc_start: 0.9099 (t) cc_final: 0.8760 (m) REVERT: B 368 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 420 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 504 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8653 (tp30) REVERT: C 349 ASP cc_start: 0.8878 (m-30) cc_final: 0.8249 (m-30) REVERT: C 356 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5532 (mm-30) REVERT: C 378 ARG cc_start: 0.7433 (tpp80) cc_final: 0.7217 (mmm160) REVERT: C 465 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7785 (mm-40) REVERT: C 555 MET cc_start: 0.8082 (mtt) cc_final: 0.7323 (ttp) REVERT: D 382 LEU cc_start: 0.8378 (pt) cc_final: 0.8091 (tt) REVERT: D 410 GLU cc_start: 0.8436 (tp30) cc_final: 0.8044 (tp30) REVERT: D 480 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8143 (t80) REVERT: D 549 PHE cc_start: 0.7425 (m-10) cc_final: 0.7187 (t80) REVERT: D 554 ASN cc_start: 0.8641 (t0) cc_final: 0.8123 (t0) REVERT: A 1930 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7319 (ttm110) REVERT: A 2070 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8082 (p-80) REVERT: A 2098 ASN cc_start: 0.8916 (t0) cc_final: 0.8190 (t0) REVERT: A 2108 PHE cc_start: 0.8379 (t80) cc_final: 0.8109 (t80) outliers start: 83 outliers final: 58 residues processed: 248 average time/residue: 0.0936 time to fit residues: 36.3612 Evaluate side-chains 228 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1695 SER Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1809 THR Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1872 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1991 LEU Chi-restraints excluded: chain A residue 1994 THR Chi-restraints excluded: chain A residue 2013 THR Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Chi-restraints excluded: chain A residue 2104 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 222 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.089959 restraints weight = 20887.350| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.80 r_work: 0.2593 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15934 Z= 0.107 Angle : 0.567 12.357 21680 Z= 0.283 Chirality : 0.042 0.248 2435 Planarity : 0.003 0.045 2686 Dihedral : 6.019 58.743 2103 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.24 % Allowed : 23.60 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1868 helix: 1.17 (0.17), residues: 1018 sheet: -0.07 (0.38), residues: 192 loop : -2.71 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 204 TYR 0.014 0.001 TYR D 456 PHE 0.014 0.001 PHE D 403 TRP 0.009 0.001 TRP C 434 HIS 0.003 0.001 HIS A1765 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (15922) covalent geometry : angle 0.54829 / 0.28 (21646) SS BOND : bond 0.00374 / 0.20 ( 2) SS BOND : angle 2.51632 / 1.31 ( 4) hydrogen bonds : bond 0.04013 / 2.63 ( 793) hydrogen bonds : angle 3.44194 / 2.36 ( 2319) link_NAG-ASN : bond 0.00747 / 0.34 ( 10) link_NAG-ASN : angle 3.84163 / 2.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9054 (pp) REVERT: B 360 CYS cc_start: 0.9070 (t) cc_final: 0.8762 (m) REVERT: B 368 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8558 (p) REVERT: B 420 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 463 MET cc_start: 0.8205 (mtp) cc_final: 0.7900 (mtp) REVERT: B 504 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8615 (tp30) REVERT: C 349 ASP cc_start: 0.8836 (m-30) cc_final: 0.8364 (m-30) REVERT: C 415 MET cc_start: 0.9078 (mmt) cc_final: 0.8843 (mmt) REVERT: C 419 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7418 (mt) REVERT: C 555 MET cc_start: 0.8032 (mtt) cc_final: 0.7324 (ttp) REVERT: D 290 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8430 (mm-30) REVERT: D 382 LEU cc_start: 0.8235 (pt) cc_final: 0.8023 (tt) REVERT: D 410 GLU cc_start: 0.8407 (tp30) cc_final: 0.8036 (tp30) REVERT: D 480 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8115 (t80) REVERT: D 483 MET cc_start: 0.8535 (ttm) cc_final: 0.8043 (ttm) REVERT: D 549 PHE cc_start: 0.7562 (m-10) cc_final: 0.7294 (t80) REVERT: D 554 ASN cc_start: 0.8537 (t0) cc_final: 0.8029 (t0) REVERT: A 1930 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7293 (ttm110) REVERT: A 2070 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.7977 (p-80) REVERT: A 2098 ASN cc_start: 0.8840 (t0) cc_final: 0.8186 (t0) REVERT: A 2108 PHE cc_start: 0.8315 (t80) cc_final: 0.8085 (t80) outliers start: 71 outliers final: 47 residues processed: 241 average time/residue: 0.0909 time to fit residues: 34.6559 Evaluate side-chains 224 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2013 THR Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 151 optimal weight: 40.0000 chunk 128 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 460 ASN D 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.080857 restraints weight = 21241.154| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 1.81 r_work: 0.2521 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15934 Z= 0.204 Angle : 0.627 12.365 21680 Z= 0.317 Chirality : 0.045 0.250 2435 Planarity : 0.004 0.048 2686 Dihedral : 5.942 57.518 2096 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.42 % Rotamer: Outliers : 5.26 % Allowed : 23.42 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1868 helix: 1.20 (0.17), residues: 1008 sheet: -0.06 (0.38), residues: 192 loop : -2.68 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 204 TYR 0.019 0.002 TYR C 438 PHE 0.017 0.002 PHE C 488 TRP 0.009 0.001 TRP B 434 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (15922) covalent geometry : angle 0.60947 / 0.31 (21646) SS BOND : bond 0.00593 / 0.31 ( 2) SS BOND : angle 2.96338 / 1.55 ( 4) hydrogen bonds : bond 0.04954 / 3.24 ( 793) hydrogen bonds : angle 3.57220 / 2.45 ( 2319) link_NAG-ASN : bond 0.00578 / 0.26 ( 10) link_NAG-ASN : angle 3.91755 / 2.42 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 170 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9152 (pp) REVERT: B 317 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 360 CYS cc_start: 0.8987 (t) cc_final: 0.8758 (m) REVERT: B 368 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 504 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8594 (tp30) REVERT: C 349 ASP cc_start: 0.8870 (m-30) cc_final: 0.8286 (m-30) REVERT: C 555 MET cc_start: 0.8213 (mtt) cc_final: 0.7562 (ttp) REVERT: D 290 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 410 GLU cc_start: 0.8570 (tp30) cc_final: 0.8241 (tp30) REVERT: D 475 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6604 (mmtp) REVERT: D 480 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8295 (t80) REVERT: D 554 ASN cc_start: 0.8744 (t0) cc_final: 0.8294 (t0) REVERT: A 1930 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7427 (ttm110) REVERT: A 2070 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.8019 (p-80) REVERT: A 2098 ASN cc_start: 0.8949 (t0) cc_final: 0.8294 (t0) outliers start: 88 outliers final: 66 residues processed: 242 average time/residue: 0.1085 time to fit residues: 41.4693 Evaluate side-chains 235 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1695 SER Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1777 VAL Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1809 THR Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1849 GLU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1878 SER Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1991 LEU Chi-restraints excluded: chain A residue 2013 THR Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Chi-restraints excluded: chain A residue 2104 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN B 420 GLN D 222 ASN D 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.086585 restraints weight = 20643.961| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.80 r_work: 0.2663 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 15934 Z= 0.103 Angle : 0.567 12.303 21680 Z= 0.281 Chirality : 0.041 0.249 2435 Planarity : 0.003 0.045 2686 Dihedral : 5.629 58.918 2096 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.00 % Allowed : 25.09 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1868 helix: 1.48 (0.17), residues: 1009 sheet: 0.23 (0.38), residues: 192 loop : -2.54 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.013 0.001 TYR D 456 PHE 0.014 0.001 PHE A1925 TRP 0.009 0.001 TRP C 434 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (15922) covalent geometry : angle 0.55001 / 0.28 (21646) SS BOND : bond 0.00320 / 0.17 ( 2) SS BOND : angle 2.12937 / 1.11 ( 4) hydrogen bonds : bond 0.03812 / 2.49 ( 793) hydrogen bonds : angle 3.40860 / 2.34 ( 2319) link_NAG-ASN : bond 0.00715 / 0.32 ( 10) link_NAG-ASN : angle 3.67576 / 2.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 CYS cc_start: 0.8921 (t) cc_final: 0.8687 (m) REVERT: C 349 ASP cc_start: 0.8799 (m-30) cc_final: 0.8376 (m-30) REVERT: C 415 MET cc_start: 0.9102 (mmt) cc_final: 0.8880 (mmt) REVERT: C 419 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7560 (mp) REVERT: C 555 MET cc_start: 0.8072 (mtt) cc_final: 0.7467 (ttp) REVERT: D 341 LEU cc_start: 0.7685 (tt) cc_final: 0.7296 (tp) REVERT: D 410 GLU cc_start: 0.8480 (tp30) cc_final: 0.8197 (tp30) REVERT: D 475 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6500 (mmtp) REVERT: D 480 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (t80) REVERT: D 554 ASN cc_start: 0.8562 (t0) cc_final: 0.8186 (t0) REVERT: A 1930 ARG cc_start: 0.7660 (ttt180) cc_final: 0.7289 (ttm110) REVERT: A 2070 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8038 (p-80) REVERT: A 2098 ASN cc_start: 0.8837 (t0) cc_final: 0.8214 (t0) REVERT: A 2108 PHE cc_start: 0.8278 (t80) cc_final: 0.8069 (t80) outliers start: 67 outliers final: 50 residues processed: 234 average time/residue: 0.1125 time to fit residues: 41.0785 Evaluate side-chains 223 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1991 LEU Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 141 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 375 HIS D 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.085582 restraints weight = 20859.900| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.81 r_work: 0.2632 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15934 Z= 0.113 Angle : 0.573 12.176 21680 Z= 0.284 Chirality : 0.042 0.250 2435 Planarity : 0.003 0.043 2686 Dihedral : 5.516 58.365 2093 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.46 % Allowed : 25.51 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1868 helix: 1.58 (0.17), residues: 1009 sheet: 0.33 (0.38), residues: 190 loop : -2.51 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 337 TYR 0.012 0.001 TYR B 127 PHE 0.016 0.001 PHE B 364 TRP 0.009 0.001 TRP C 434 HIS 0.005 0.000 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15922) covalent geometry : angle 0.55642 / 0.28 (21646) SS BOND : bond 0.00389 / 0.20 ( 2) SS BOND : angle 2.27445 / 1.19 ( 4) hydrogen bonds : bond 0.03931 / 2.57 ( 793) hydrogen bonds : angle 3.37743 / 2.32 ( 2319) link_NAG-ASN : bond 0.00652 / 0.30 ( 10) link_NAG-ASN : angle 3.60168 / 2.22 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9090 (pp) REVERT: B 360 CYS cc_start: 0.8884 (t) cc_final: 0.8653 (m) REVERT: B 368 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8643 (p) REVERT: C 349 ASP cc_start: 0.8776 (m-30) cc_final: 0.8263 (m-30) REVERT: C 380 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7768 (ttm-80) REVERT: C 415 MET cc_start: 0.9131 (mmt) cc_final: 0.8910 (mmt) REVERT: C 419 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 555 MET cc_start: 0.8084 (mtt) cc_final: 0.7529 (ttp) REVERT: D 341 LEU cc_start: 0.7692 (tt) cc_final: 0.7381 (tp) REVERT: D 410 GLU cc_start: 0.8451 (tp30) cc_final: 0.8174 (tp30) REVERT: D 475 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6515 (mmtp) REVERT: D 480 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8235 (t80) REVERT: D 483 MET cc_start: 0.8318 (ttm) cc_final: 0.8059 (ttm) REVERT: D 554 ASN cc_start: 0.8609 (t0) cc_final: 0.8177 (t0) REVERT: A 1930 ARG cc_start: 0.7670 (ttt180) cc_final: 0.7390 (ttm110) REVERT: A 2070 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7976 (p-80) REVERT: A 2098 ASN cc_start: 0.8809 (t0) cc_final: 0.8198 (t0) outliers start: 58 outliers final: 46 residues processed: 225 average time/residue: 0.1102 time to fit residues: 39.0477 Evaluate side-chains 216 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1991 LEU Chi-restraints excluded: chain A residue 2013 THR Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 166 optimal weight: 0.2980 chunk 117 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 chunk 14 optimal weight: 0.0070 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 375 HIS D 222 ASN A1961 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.088802 restraints weight = 20627.912| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.78 r_work: 0.2687 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15934 Z= 0.096 Angle : 0.552 12.248 21680 Z= 0.272 Chirality : 0.041 0.249 2435 Planarity : 0.003 0.041 2686 Dihedral : 5.298 59.799 2090 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.29 % Allowed : 25.57 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1868 helix: 1.76 (0.17), residues: 1007 sheet: 0.47 (0.39), residues: 189 loop : -2.42 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 337 TYR 0.013 0.001 TYR D 456 PHE 0.015 0.001 PHE B 459 TRP 0.009 0.001 TRP C 434 HIS 0.005 0.000 HIS C 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (15922) covalent geometry : angle 0.53697 / 0.27 (21646) SS BOND : bond 0.00293 / 0.15 ( 2) SS BOND : angle 2.02918 / 1.07 ( 4) hydrogen bonds : bond 0.03485 / 2.28 ( 793) hydrogen bonds : angle 3.30063 / 2.27 ( 2319) link_NAG-ASN : bond 0.00654 / 0.30 ( 10) link_NAG-ASN : angle 3.40334 / 2.10 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8989 (pp) REVERT: B 360 CYS cc_start: 0.8883 (t) cc_final: 0.8672 (m) REVERT: C 349 ASP cc_start: 0.8775 (m-30) cc_final: 0.8240 (m-30) REVERT: C 380 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7744 (ttm-80) REVERT: C 415 MET cc_start: 0.9067 (mmt) cc_final: 0.8814 (mmt) REVERT: C 419 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7466 (mp) REVERT: C 555 MET cc_start: 0.8045 (mtt) cc_final: 0.7486 (ttp) REVERT: D 217 ARG cc_start: 0.8623 (ptp-110) cc_final: 0.8324 (ttm110) REVERT: D 341 LEU cc_start: 0.7613 (tt) cc_final: 0.7321 (tp) REVERT: D 410 GLU cc_start: 0.8391 (tp30) cc_final: 0.8132 (tp30) REVERT: D 480 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8215 (t80) REVERT: D 554 ASN cc_start: 0.8486 (t0) cc_final: 0.7915 (t0) REVERT: A 1930 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7384 (ttm110) REVERT: A 2070 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8005 (p-80) REVERT: A 2098 ASN cc_start: 0.8762 (t0) cc_final: 0.8101 (t0) outliers start: 55 outliers final: 39 residues processed: 240 average time/residue: 0.1078 time to fit residues: 40.2459 Evaluate side-chains 212 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 375 HIS D 222 ASN D 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.084593 restraints weight = 20856.882| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.86 r_work: 0.2569 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15934 Z= 0.147 Angle : 0.601 12.101 21680 Z= 0.297 Chirality : 0.043 0.249 2435 Planarity : 0.003 0.042 2686 Dihedral : 5.437 59.983 2090 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.69 % Allowed : 26.46 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1868 helix: 1.73 (0.17), residues: 1005 sheet: 0.38 (0.39), residues: 190 loop : -2.43 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 337 TYR 0.016 0.001 TYR C 438 PHE 0.019 0.001 PHE A2108 TRP 0.010 0.001 TRP C 434 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15922) covalent geometry : angle 0.58569 / 0.29 (21646) SS BOND : bond 0.00519 / 0.27 ( 2) SS BOND : angle 2.71625 / 1.49 ( 4) hydrogen bonds : bond 0.04262 / 2.80 ( 793) hydrogen bonds : angle 3.37791 / 2.32 ( 2319) link_NAG-ASN : bond 0.00557 / 0.26 ( 10) link_NAG-ASN : angle 3.49235 / 2.15 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: B 138 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9040 (pp) REVERT: B 360 CYS cc_start: 0.8884 (t) cc_final: 0.8623 (m) REVERT: C 349 ASP cc_start: 0.8809 (m-30) cc_final: 0.8283 (m-30) REVERT: C 415 MET cc_start: 0.9170 (mmt) cc_final: 0.8947 (mmt) REVERT: C 419 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7756 (mt) REVERT: C 555 MET cc_start: 0.8092 (mtt) cc_final: 0.7530 (ttp) REVERT: D 341 LEU cc_start: 0.7716 (tt) cc_final: 0.7420 (tp) REVERT: D 410 GLU cc_start: 0.8495 (tp30) cc_final: 0.8233 (tp30) REVERT: D 480 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8141 (t80) REVERT: D 554 ASN cc_start: 0.8609 (t0) cc_final: 0.8277 (t0) REVERT: A 1930 ARG cc_start: 0.7661 (ttt180) cc_final: 0.7364 (ttm110) REVERT: A 2070 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8016 (p-80) REVERT: A 2098 ASN cc_start: 0.8812 (t0) cc_final: 0.8176 (t0) outliers start: 45 outliers final: 37 residues processed: 205 average time/residue: 0.1006 time to fit residues: 32.8863 Evaluate side-chains 206 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain A residue 1727 ILE Chi-restraints excluded: chain A residue 1797 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1874 THR Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2070 HIS Chi-restraints excluded: chain A residue 2097 ILE Chi-restraints excluded: chain A residue 2102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 147 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 375 HIS D 222 ASN A2040 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.085318 restraints weight = 20710.649| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.72 r_work: 0.2605 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15934 Z= 0.117 Angle : 0.582 12.138 21680 Z= 0.287 Chirality : 0.042 0.249 2435 Planarity : 0.003 0.045 2686 Dihedral : 5.382 59.103 2090 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.51 % Allowed : 26.88 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1868 helix: 1.81 (0.17), residues: 1004 sheet: 0.38 (0.38), residues: 190 loop : -2.40 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 337 TYR 0.018 0.001 TYR D 526 PHE 0.016 0.001 PHE A2108 TRP 0.010 0.001 TRP C 434 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15922) covalent geometry : angle 0.56769 / 0.28 (21646) SS BOND : bond 0.00505 / 0.27 ( 2) SS BOND : angle 2.07392 / 1.13 ( 4) hydrogen bonds : bond 0.03974 / 2.61 ( 793) hydrogen bonds : angle 3.33738 / 2.29 ( 2319) link_NAG-ASN : bond 0.00574 / 0.26 ( 10) link_NAG-ASN : angle 3.40199 / 2.09 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.49 seconds wall clock time: 56 minutes 46.15 seconds (3406.15 seconds total)