Starting phenix.real_space_refine on Fri Feb 23 03:17:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo8_29341/02_2024/8fo8_29341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo8_29341/02_2024/8fo8_29341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo8_29341/02_2024/8fo8_29341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo8_29341/02_2024/8fo8_29341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo8_29341/02_2024/8fo8_29341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo8_29341/02_2024/8fo8_29341.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 P 10 5.49 5 S 226 5.16 5 C 23259 2.51 5 N 6263 2.21 5 O 6674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36432 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1115 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1115 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 192 Chain: "C" Number of atoms: 17037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2270, 17037 Classifications: {'peptide': 2270} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2184} Chain breaks: 19 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 860 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 11, 'GLU:plan': 49, 'HIS:plan': 11} Unresolved non-hydrogen planarities: 613 Chain: "E" Number of atoms: 17047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2270, 17047 Classifications: {'peptide': 2270} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2184} Chain breaks: 19 Unresolved non-hydrogen bonds: 1013 Unresolved non-hydrogen angles: 1242 Unresolved non-hydrogen dihedrals: 850 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 11, 'GLU:plan': 49, 'HIS:plan': 11} Unresolved non-hydrogen planarities: 603 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.14, per 1000 atoms: 0.53 Number of scatterers: 36432 At special positions: 0 Unit cell: (200.34, 157.94, 206.7, 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) S 226 16.00 P 10 15.00 O 6674 8.00 N 6263 7.00 C 23259 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.08 Conformation dependent library (CDL) restraints added in 7.0 seconds 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9332 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 38 sheets defined 45.6% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 removed outlier: 4.023A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.282A pdb=" N TYR A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 removed outlier: 3.842A pdb=" N PHE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.976A pdb=" N ARG A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.515A pdb=" N ASN A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.670A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 4.266A pdb=" N TYR B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.571A pdb=" N PHE B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.962A pdb=" N ARG B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'C' and resid 13 through 24 removed outlier: 3.502A pdb=" N ASN C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 44 Processing helix chain 'C' and resid 57 through 60 Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 92 removed outlier: 3.715A pdb=" N GLN C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.953A pdb=" N HIS C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.657A pdb=" N ILE C 134 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.590A pdb=" N HIS C 185 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL C 186 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 190 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 215 removed outlier: 4.187A pdb=" N SER C 210 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 211 " --> pdb=" O MET C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 Processing helix chain 'C' and resid 237 through 243 removed outlier: 4.327A pdb=" N VAL C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 284 through 302 Processing helix chain 'C' and resid 308 through 325 removed outlier: 3.768A pdb=" N LEU C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 363 through 381 removed outlier: 3.576A pdb=" N GLN C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 380 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 removed outlier: 4.374A pdb=" N GLU C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 408 removed outlier: 3.866A pdb=" N GLU C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.808A pdb=" N PHE C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 471 removed outlier: 3.934A pdb=" N ALA C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 Proline residue: C 485 - end of helix Processing helix chain 'C' and resid 497 through 513 removed outlier: 4.410A pdb=" N VAL C 513 " --> pdb=" O LEU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 540 removed outlier: 3.697A pdb=" N MET C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 553 Processing helix chain 'C' and resid 556 through 572 removed outlier: 4.083A pdb=" N GLN C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 584 removed outlier: 4.027A pdb=" N MET C 579 " --> pdb=" O ASP C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 596 removed outlier: 3.911A pdb=" N SER C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 614 removed outlier: 3.596A pdb=" N GLY C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 619 removed outlier: 3.736A pdb=" N VAL C 619 " --> pdb=" O LYS C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 638 Processing helix chain 'C' and resid 641 through 659 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.794A pdb=" N HIS C 668 " --> pdb=" O LYS C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 685 removed outlier: 3.534A pdb=" N ILE C 675 " --> pdb=" O PHE C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 704 removed outlier: 3.988A pdb=" N MET C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 719 removed outlier: 3.762A pdb=" N LYS C 709 " --> pdb=" O ASP C 705 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 removed outlier: 3.882A pdb=" N GLU C 726 " --> pdb=" O SER C 722 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS C 727 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.718A pdb=" N VAL C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 783 through 795 removed outlier: 3.915A pdb=" N ARG C 793 " --> pdb=" O LEU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 851 Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.561A pdb=" N SER C1001 " --> pdb=" O ILE C 997 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN C1002 " --> pdb=" O ASP C 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 997 through 1002' Processing helix chain 'C' and resid 1006 through 1010 removed outlier: 3.588A pdb=" N LEU C1010 " --> pdb=" O SER C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1032 removed outlier: 3.935A pdb=" N CYS C1031 " --> pdb=" O PRO C1027 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C1032 " --> pdb=" O GLN C1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1027 through 1032' Processing helix chain 'C' and resid 1053 through 1057 Processing helix chain 'C' and resid 1190 through 1195 removed outlier: 3.589A pdb=" N LEU C1195 " --> pdb=" O ILE C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1213 through 1217 removed outlier: 3.786A pdb=" N TRP C1217 " --> pdb=" O PRO C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1240 through 1245 removed outlier: 3.853A pdb=" N LEU C1243 " --> pdb=" O LYS C1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 1261 through 1267 removed outlier: 3.551A pdb=" N ILE C1264 " --> pdb=" O PRO C1261 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1291 removed outlier: 3.782A pdb=" N MET C1288 " --> pdb=" O PRO C1285 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C1290 " --> pdb=" O GLU C1287 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1328 removed outlier: 3.559A pdb=" N ARG C1320 " --> pdb=" O LYS C1316 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C1328 " --> pdb=" O GLN C1324 " (cutoff:3.500A) Processing helix chain 'C' and resid 1347 through 1355 removed outlier: 3.641A pdb=" N GLN C1352 " --> pdb=" O THR C1348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C1353 " --> pdb=" O THR C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1398 through 1402 Processing helix chain 'C' and resid 1404 through 1408 Processing helix chain 'C' and resid 1420 through 1424 Processing helix chain 'C' and resid 1426 through 1431 removed outlier: 3.693A pdb=" N ALA C1430 " --> pdb=" O ALA C1426 " (cutoff:3.500A) Processing helix chain 'C' and resid 1431 through 1442 Processing helix chain 'C' and resid 1465 through 1473 removed outlier: 4.121A pdb=" N ILE C1469 " --> pdb=" O CYS C1465 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1509 Processing helix chain 'C' and resid 1517 through 1520 Processing helix chain 'C' and resid 1525 through 1538 Processing helix chain 'C' and resid 1550 through 1560 removed outlier: 3.559A pdb=" N ASN C1560 " --> pdb=" O LEU C1556 " (cutoff:3.500A) Processing helix chain 'C' and resid 1568 through 1578 removed outlier: 3.975A pdb=" N HIS C1574 " --> pdb=" O PRO C1570 " (cutoff:3.500A) Processing helix chain 'C' and resid 1599 through 1612 removed outlier: 3.954A pdb=" N LEU C1603 " --> pdb=" O GLU C1599 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C1608 " --> pdb=" O CYS C1604 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C1609 " --> pdb=" O LYS C1605 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C1610 " --> pdb=" O ILE C1606 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C1611 " --> pdb=" O MET C1607 " (cutoff:3.500A) Processing helix chain 'C' and resid 1644 through 1654 removed outlier: 3.578A pdb=" N GLN C1648 " --> pdb=" O ASN C1644 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE C1650 " --> pdb=" O MET C1646 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C1651 " --> pdb=" O THR C1647 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C1652 " --> pdb=" O GLN C1648 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C1654 " --> pdb=" O PHE C1650 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1713 removed outlier: 3.940A pdb=" N ASN C1710 " --> pdb=" O SER C1706 " (cutoff:3.500A) Processing helix chain 'C' and resid 1770 through 1792 removed outlier: 3.525A pdb=" N ILE C1775 " --> pdb=" O ARG C1771 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS C1783 " --> pdb=" O GLN C1779 " (cutoff:3.500A) Processing helix chain 'C' and resid 1829 through 1835 Processing helix chain 'C' and resid 1852 through 1856 Processing helix chain 'C' and resid 1865 through 1869 Processing helix chain 'C' and resid 1913 through 1925 removed outlier: 4.200A pdb=" N VAL C1923 " --> pdb=" O GLN C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1962 removed outlier: 3.565A pdb=" N LEU C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) Processing helix chain 'C' and resid 1969 through 1988 Processing helix chain 'C' and resid 1996 through 1998 No H-bonds generated for 'chain 'C' and resid 1996 through 1998' Processing helix chain 'C' and resid 2017 through 2026 removed outlier: 3.838A pdb=" N ALA C2021 " --> pdb=" O ASP C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2040 through 2046 Processing helix chain 'C' and resid 2051 through 2069 removed outlier: 4.234A pdb=" N ASP C2055 " --> pdb=" O ASN C2051 " (cutoff:3.500A) Processing helix chain 'C' and resid 2070 through 2077 removed outlier: 3.910A pdb=" N VAL C2074 " --> pdb=" O GLY C2070 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2099 Processing helix chain 'C' and resid 2104 through 2106 No H-bonds generated for 'chain 'C' and resid 2104 through 2106' Processing helix chain 'C' and resid 2107 through 2115 Processing helix chain 'C' and resid 2125 through 2126 No H-bonds generated for 'chain 'C' and resid 2125 through 2126' Processing helix chain 'C' and resid 2128 through 2128 No H-bonds generated for 'chain 'C' and resid 2128 through 2128' Processing helix chain 'C' and resid 2129 through 2134 removed outlier: 4.009A pdb=" N SER C2134 " --> pdb=" O ASP C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2139 removed outlier: 3.759A pdb=" N CYS C2139 " --> pdb=" O ALA C2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2135 through 2139' Processing helix chain 'C' and resid 2277 through 2282 removed outlier: 4.080A pdb=" N VAL C2280 " --> pdb=" O ASP C2277 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C2281 " --> pdb=" O LYS C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2351 removed outlier: 4.176A pdb=" N SER C2350 " --> pdb=" O TYR C2346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2389 through 2394 removed outlier: 3.576A pdb=" N ARG C2394 " --> pdb=" O VAL C2390 " (cutoff:3.500A) Processing helix chain 'C' and resid 2499 through 2523 removed outlier: 3.857A pdb=" N GLN C2505 " --> pdb=" O PRO C2501 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C2508 " --> pdb=" O VAL C2504 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C2509 " --> pdb=" O GLN C2505 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C2512 " --> pdb=" O GLU C2508 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C2523 " --> pdb=" O GLU C2519 " (cutoff:3.500A) Processing helix chain 'C' and resid 2524 through 2526 No H-bonds generated for 'chain 'C' and resid 2524 through 2526' Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 28 through 44 Processing helix chain 'E' and resid 57 through 60 Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 92 removed outlier: 3.712A pdb=" N GLN E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 114 through 125 removed outlier: 3.948A pdb=" N HIS E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 removed outlier: 3.653A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 177 through 190 removed outlier: 3.590A pdb=" N HIS E 185 " --> pdb=" O CYS E 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL E 186 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG E 190 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 215 removed outlier: 4.182A pdb=" N SER E 210 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 211 " --> pdb=" O MET E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 233 Processing helix chain 'E' and resid 237 through 243 removed outlier: 4.327A pdb=" N VAL E 241 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 258 Processing helix chain 'E' and resid 263 through 277 Processing helix chain 'E' and resid 284 through 302 Processing helix chain 'E' and resid 308 through 325 removed outlier: 3.763A pdb=" N LEU E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 360 Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.529A pdb=" N GLN E 367 " --> pdb=" O ASN E 363 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E 380 " --> pdb=" O ASN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 386 removed outlier: 4.376A pdb=" N GLU E 386 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 408 removed outlier: 3.817A pdb=" N GLU E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 429 removed outlier: 3.743A pdb=" N PHE E 415 " --> pdb=" O SER E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 440 Processing helix chain 'E' and resid 441 through 452 Processing helix chain 'E' and resid 455 through 471 removed outlier: 3.950A pdb=" N ALA E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 Proline residue: E 485 - end of helix Processing helix chain 'E' and resid 497 through 513 removed outlier: 4.410A pdb=" N VAL E 513 " --> pdb=" O LEU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 540 removed outlier: 3.692A pdb=" N MET E 532 " --> pdb=" O HIS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 553 Processing helix chain 'E' and resid 556 through 572 removed outlier: 4.080A pdb=" N GLN E 560 " --> pdb=" O ASN E 556 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 584 removed outlier: 4.031A pdb=" N MET E 579 " --> pdb=" O ASP E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 596 removed outlier: 3.916A pdb=" N SER E 588 " --> pdb=" O GLY E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 614 removed outlier: 3.597A pdb=" N GLY E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 619 removed outlier: 3.740A pdb=" N VAL E 619 " --> pdb=" O LYS E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 638 Processing helix chain 'E' and resid 641 through 659 Processing helix chain 'E' and resid 663 through 669 removed outlier: 3.796A pdb=" N HIS E 668 " --> pdb=" O LYS E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 685 removed outlier: 3.537A pdb=" N ILE E 675 " --> pdb=" O PHE E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 704 removed outlier: 3.991A pdb=" N MET E 704 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 719 removed outlier: 3.767A pdb=" N LYS E 709 " --> pdb=" O ASP E 705 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 719 " --> pdb=" O ARG E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 732 removed outlier: 3.879A pdb=" N GLU E 726 " --> pdb=" O SER E 722 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS E 727 " --> pdb=" O ILE E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 751 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.716A pdb=" N VAL E 758 " --> pdb=" O SER E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 781 Processing helix chain 'E' and resid 783 through 795 removed outlier: 3.885A pdb=" N ARG E 793 " --> pdb=" O LEU E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 851 Processing helix chain 'E' and resid 997 through 1002 removed outlier: 3.566A pdb=" N SER E1001 " --> pdb=" O ILE E 997 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN E1002 " --> pdb=" O ASP E 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 997 through 1002' Processing helix chain 'E' and resid 1006 through 1010 removed outlier: 3.592A pdb=" N LEU E1010 " --> pdb=" O SER E1007 " (cutoff:3.500A) Processing helix chain 'E' and resid 1027 through 1032 removed outlier: 3.939A pdb=" N CYS E1031 " --> pdb=" O PRO E1027 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU E1032 " --> pdb=" O GLN E1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1027 through 1032' Processing helix chain 'E' and resid 1053 through 1057 Processing helix chain 'E' and resid 1190 through 1195 removed outlier: 3.581A pdb=" N LEU E1195 " --> pdb=" O ILE E1192 " (cutoff:3.500A) Processing helix chain 'E' and resid 1213 through 1217 removed outlier: 3.783A pdb=" N TRP E1217 " --> pdb=" O PRO E1214 " (cutoff:3.500A) Processing helix chain 'E' and resid 1240 through 1245 removed outlier: 3.858A pdb=" N LEU E1243 " --> pdb=" O LYS E1240 " (cutoff:3.500A) Processing helix chain 'E' and resid 1261 through 1267 removed outlier: 3.554A pdb=" N ILE E1264 " --> pdb=" O PRO E1261 " (cutoff:3.500A) Processing helix chain 'E' and resid 1285 through 1291 removed outlier: 3.777A pdb=" N MET E1288 " --> pdb=" O PRO E1285 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E1290 " --> pdb=" O GLU E1287 " (cutoff:3.500A) Processing helix chain 'E' and resid 1316 through 1328 removed outlier: 3.559A pdb=" N ARG E1320 " --> pdb=" O LYS E1316 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS E1328 " --> pdb=" O GLN E1324 " (cutoff:3.500A) Processing helix chain 'E' and resid 1347 through 1355 removed outlier: 3.650A pdb=" N GLN E1352 " --> pdb=" O THR E1348 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN E1353 " --> pdb=" O THR E1349 " (cutoff:3.500A) Processing helix chain 'E' and resid 1398 through 1402 Processing helix chain 'E' and resid 1404 through 1408 Processing helix chain 'E' and resid 1420 through 1424 Processing helix chain 'E' and resid 1426 through 1431 removed outlier: 3.688A pdb=" N ALA E1430 " --> pdb=" O ALA E1426 " (cutoff:3.500A) Processing helix chain 'E' and resid 1431 through 1442 Processing helix chain 'E' and resid 1465 through 1473 removed outlier: 4.120A pdb=" N ILE E1469 " --> pdb=" O CYS E1465 " (cutoff:3.500A) Processing helix chain 'E' and resid 1494 through 1509 Processing helix chain 'E' and resid 1517 through 1520 Processing helix chain 'E' and resid 1525 through 1538 Processing helix chain 'E' and resid 1550 through 1560 removed outlier: 3.557A pdb=" N ASN E1560 " --> pdb=" O LEU E1556 " (cutoff:3.500A) Processing helix chain 'E' and resid 1568 through 1578 removed outlier: 3.973A pdb=" N HIS E1574 " --> pdb=" O PRO E1570 " (cutoff:3.500A) Processing helix chain 'E' and resid 1599 through 1612 removed outlier: 3.956A pdb=" N LEU E1603 " --> pdb=" O GLU E1599 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E1608 " --> pdb=" O CYS E1604 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN E1609 " --> pdb=" O LYS E1605 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE E1610 " --> pdb=" O ILE E1606 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU E1611 " --> pdb=" O MET E1607 " (cutoff:3.500A) Processing helix chain 'E' and resid 1644 through 1654 removed outlier: 3.574A pdb=" N GLN E1648 " --> pdb=" O ASN E1644 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE E1650 " --> pdb=" O MET E1646 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E1651 " --> pdb=" O THR E1647 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E1652 " --> pdb=" O GLN E1648 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E1654 " --> pdb=" O PHE E1650 " (cutoff:3.500A) Processing helix chain 'E' and resid 1704 through 1713 removed outlier: 3.948A pdb=" N ASN E1710 " --> pdb=" O SER E1706 " (cutoff:3.500A) Processing helix chain 'E' and resid 1770 through 1792 removed outlier: 3.513A pdb=" N ILE E1775 " --> pdb=" O ARG E1771 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS E1783 " --> pdb=" O GLN E1779 " (cutoff:3.500A) Processing helix chain 'E' and resid 1829 through 1835 Processing helix chain 'E' and resid 1852 through 1856 Processing helix chain 'E' and resid 1865 through 1869 Processing helix chain 'E' and resid 1913 through 1925 removed outlier: 4.197A pdb=" N VAL E1923 " --> pdb=" O GLN E1919 " (cutoff:3.500A) Processing helix chain 'E' and resid 1954 through 1962 removed outlier: 3.577A pdb=" N LEU E1958 " --> pdb=" O SER E1954 " (cutoff:3.500A) Processing helix chain 'E' and resid 1969 through 1988 Processing helix chain 'E' and resid 1996 through 1998 No H-bonds generated for 'chain 'E' and resid 1996 through 1998' Processing helix chain 'E' and resid 2017 through 2026 removed outlier: 3.838A pdb=" N ALA E2021 " --> pdb=" O ASP E2017 " (cutoff:3.500A) Processing helix chain 'E' and resid 2040 through 2046 Processing helix chain 'E' and resid 2051 through 2069 removed outlier: 4.237A pdb=" N ASP E2055 " --> pdb=" O ASN E2051 " (cutoff:3.500A) Processing helix chain 'E' and resid 2070 through 2077 removed outlier: 3.905A pdb=" N VAL E2074 " --> pdb=" O GLY E2070 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2099 Processing helix chain 'E' and resid 2104 through 2106 No H-bonds generated for 'chain 'E' and resid 2104 through 2106' Processing helix chain 'E' and resid 2107 through 2115 Processing helix chain 'E' and resid 2125 through 2126 No H-bonds generated for 'chain 'E' and resid 2125 through 2126' Processing helix chain 'E' and resid 2128 through 2128 No H-bonds generated for 'chain 'E' and resid 2128 through 2128' Processing helix chain 'E' and resid 2129 through 2133 Processing helix chain 'E' and resid 2135 through 2139 removed outlier: 3.782A pdb=" N CYS E2139 " --> pdb=" O ALA E2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2135 through 2139' Processing helix chain 'E' and resid 2277 through 2282 removed outlier: 4.082A pdb=" N VAL E2280 " --> pdb=" O ASP E2277 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E2281 " --> pdb=" O LYS E2278 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2351 removed outlier: 4.183A pdb=" N SER E2350 " --> pdb=" O TYR E2346 " (cutoff:3.500A) Processing helix chain 'E' and resid 2389 through 2394 removed outlier: 3.582A pdb=" N ARG E2394 " --> pdb=" O VAL E2390 " (cutoff:3.500A) Processing helix chain 'E' and resid 2499 through 2523 removed outlier: 3.850A pdb=" N GLN E2505 " --> pdb=" O PRO E2501 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E2508 " --> pdb=" O VAL E2504 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS E2509 " --> pdb=" O GLN E2505 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU E2512 " --> pdb=" O GLU E2508 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG E2523 " --> pdb=" O GLU E2519 " (cutoff:3.500A) Processing helix chain 'E' and resid 2524 through 2526 No H-bonds generated for 'chain 'E' and resid 2524 through 2526' Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 52 removed outlier: 3.756A pdb=" N ASP A 43 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 51 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 55 " --> pdb=" O TRP A 51 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS A 84 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU A 123 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE A 86 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN A 125 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE A 88 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU A 122 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 52 removed outlier: 3.754A pdb=" N ASP B 43 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP B 51 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU B 55 " --> pdb=" O TRP B 51 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA B 83 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS B 9 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL B 85 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 11 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET B 87 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 13 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP B 89 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N CYS B 84 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N LEU B 123 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 86 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN B 125 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE B 88 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 122 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1016 through 1017 removed outlier: 6.681A pdb=" N LEU C1016 " --> pdb=" O ASP C1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 1063 through 1064 removed outlier: 7.108A pdb=" N LEU C1063 " --> pdb=" O ASN C1089 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C1113 " --> pdb=" O PHE C1088 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1177 through 1179 removed outlier: 6.956A pdb=" N LEU C1201 " --> pdb=" O LEU C1226 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU C1225 " --> pdb=" O HIS C1251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1330 through 1332 removed outlier: 3.745A pdb=" N GLN C1521 " --> pdb=" O TYR C1332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 1373 through 1380 removed outlier: 3.548A pdb=" N LEU C1390 " --> pdb=" O TRP C1376 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET C1335 " --> pdb=" O VAL C1389 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP C1393 " --> pdb=" O LEU C1337 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N LEU C1414 " --> pdb=" O ARG C1334 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS C1336 " --> pdb=" O LEU C1414 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU C1416 " --> pdb=" O LYS C1336 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET C1338 " --> pdb=" O LEU C1416 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL C1418 " --> pdb=" O MET C1338 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE C1448 " --> pdb=" O ALA C1413 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C1415 " --> pdb=" O ILE C1448 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL C1450 " --> pdb=" O TYR C1415 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA C1417 " --> pdb=" O VAL C1450 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1447 " --> pdb=" O ASP C1484 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N HIS C1486 " --> pdb=" O VAL C1447 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C1449 " --> pdb=" O HIS C1486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1547 through 1549 Processing sheet with id=AA9, first strand: chain 'C' and resid 1690 through 1692 removed outlier: 6.696A pdb=" N TYR C1747 " --> pdb=" O PRO C1768 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS C1748 " --> pdb=" O ASN C1741 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN C1741 " --> pdb=" O CYS C1748 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C1731 " --> pdb=" O GLU E1681 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1811 through 1814 Processing sheet with id=AB2, first strand: chain 'C' and resid 1840 through 1841 Processing sheet with id=AB3, first strand: chain 'C' and resid 1893 through 1898 removed outlier: 3.807A pdb=" N LEU C1945 " --> pdb=" O LYS C1906 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C1937 " --> pdb=" O VAL C1946 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU C1948 " --> pdb=" O LEU C1935 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU C1935 " --> pdb=" O GLU C1948 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 2000 through 2002 Processing sheet with id=AB5, first strand: chain 'C' and resid 2140 through 2145 removed outlier: 6.314A pdb=" N LEU C2140 " --> pdb=" O ASP C2497 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C2497 " --> pdb=" O LEU C2140 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C2142 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS C2467 " --> pdb=" O LEU C2463 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU C2463 " --> pdb=" O LYS C2467 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C2457 " --> pdb=" O LEU C2473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2155 through 2157 Processing sheet with id=AB7, first strand: chain 'C' and resid 2199 through 2207 removed outlier: 3.706A pdb=" N GLU C2212 " --> pdb=" O LEU C2207 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C2226 " --> pdb=" O HIS C2236 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS C2236 " --> pdb=" O VAL C2226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 2245 through 2250 removed outlier: 5.809A pdb=" N GLY C2266 " --> pdb=" O THR C2246 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU C2248 " --> pdb=" O LEU C2264 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C2264 " --> pdb=" O LEU C2248 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C2273 " --> pdb=" O VAL C2265 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR C2267 " --> pdb=" O LYS C2271 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS C2271 " --> pdb=" O THR C2267 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 2315 through 2319 Processing sheet with id=AC1, first strand: chain 'C' and resid 2354 through 2359 removed outlier: 6.802A pdb=" N ALA C2366 " --> pdb=" O ILE C2355 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL C2357 " --> pdb=" O TYR C2364 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR C2364 " --> pdb=" O VAL C2357 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS C2367 " --> pdb=" O VAL C2372 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C2372 " --> pdb=" O LYS C2367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 2414 through 2419 removed outlier: 6.677A pdb=" N GLY C2428 " --> pdb=" O LYS C2415 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU C2417 " --> pdb=" O TRP C2426 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TRP C2426 " --> pdb=" O LEU C2417 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C2436 " --> pdb=" O ARG C2446 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG C2446 " --> pdb=" O LEU C2436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1016 through 1017 removed outlier: 6.685A pdb=" N LEU E1016 " --> pdb=" O ASP E1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 1063 through 1064 removed outlier: 7.135A pdb=" N LEU E1063 " --> pdb=" O ASN E1089 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E1113 " --> pdb=" O PHE E1088 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 1177 through 1179 removed outlier: 6.972A pdb=" N LEU E1201 " --> pdb=" O LEU E1226 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU E1225 " --> pdb=" O HIS E1251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1330 through 1332 removed outlier: 3.738A pdb=" N GLN E1521 " --> pdb=" O TYR E1332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1373 through 1380 removed outlier: 3.553A pdb=" N LEU E1390 " --> pdb=" O TRP E1376 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET E1335 " --> pdb=" O VAL E1389 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP E1393 " --> pdb=" O LEU E1337 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU E1414 " --> pdb=" O ARG E1334 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS E1336 " --> pdb=" O LEU E1414 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU E1416 " --> pdb=" O LYS E1336 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET E1338 " --> pdb=" O LEU E1416 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL E1418 " --> pdb=" O MET E1338 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ILE E1448 " --> pdb=" O ALA E1413 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR E1415 " --> pdb=" O ILE E1448 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL E1450 " --> pdb=" O TYR E1415 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA E1417 " --> pdb=" O VAL E1450 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL E1447 " --> pdb=" O ASP E1484 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N HIS E1486 " --> pdb=" O VAL E1447 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E1449 " --> pdb=" O HIS E1486 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1547 through 1549 Processing sheet with id=AC9, first strand: chain 'E' and resid 1690 through 1692 removed outlier: 6.627A pdb=" N TYR E1747 " --> pdb=" O PRO E1768 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N CYS E1748 " --> pdb=" O ASN E1741 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN E1741 " --> pdb=" O CYS E1748 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN E1741 " --> pdb=" O ASN E1730 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1811 through 1814 Processing sheet with id=AD2, first strand: chain 'E' and resid 1840 through 1841 Processing sheet with id=AD3, first strand: chain 'E' and resid 1893 through 1898 removed outlier: 3.812A pdb=" N LEU E1945 " --> pdb=" O LYS E1906 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E1937 " --> pdb=" O VAL E1946 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU E1948 " --> pdb=" O LEU E1935 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU E1935 " --> pdb=" O GLU E1948 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 2000 through 2002 Processing sheet with id=AD5, first strand: chain 'E' and resid 2140 through 2145 removed outlier: 6.308A pdb=" N LEU E2140 " --> pdb=" O ASP E2497 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP E2497 " --> pdb=" O LEU E2140 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E2142 " --> pdb=" O VAL E2495 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS E2467 " --> pdb=" O LEU E2463 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU E2463 " --> pdb=" O LYS E2467 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E2457 " --> pdb=" O LEU E2473 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 2155 through 2157 Processing sheet with id=AD7, first strand: chain 'E' and resid 2199 through 2207 removed outlier: 3.708A pdb=" N GLU E2212 " --> pdb=" O LEU E2207 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL E2226 " --> pdb=" O HIS E2236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS E2236 " --> pdb=" O VAL E2226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 2245 through 2250 removed outlier: 5.806A pdb=" N GLY E2266 " --> pdb=" O THR E2246 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E2248 " --> pdb=" O LEU E2264 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU E2264 " --> pdb=" O LEU E2248 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E2273 " --> pdb=" O VAL E2265 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR E2267 " --> pdb=" O LYS E2271 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS E2271 " --> pdb=" O THR E2267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 2315 through 2319 Processing sheet with id=AE1, first strand: chain 'E' and resid 2354 through 2359 removed outlier: 6.800A pdb=" N ALA E2366 " --> pdb=" O ILE E2355 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL E2357 " --> pdb=" O TYR E2364 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR E2364 " --> pdb=" O VAL E2357 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS E2367 " --> pdb=" O VAL E2372 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL E2372 " --> pdb=" O LYS E2367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 2414 through 2419 removed outlier: 6.673A pdb=" N GLY E2428 " --> pdb=" O LYS E2415 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU E2417 " --> pdb=" O TRP E2426 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TRP E2426 " --> pdb=" O LEU E2417 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E2436 " --> pdb=" O ARG E2446 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG E2446 " --> pdb=" O LEU E2436 " (cutoff:3.500A) 1538 hydrogen bonds defined for protein. 4317 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: 23.31 Time building geometry restraints manager: 15.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7743 1.33 - 1.45: 7880 1.45 - 1.58: 21096 1.58 - 1.70: 16 1.70 - 1.83: 330 Bond restraints: 37065 Sorted by residual: bond pdb=" CB THR A 94 " pdb=" CG2 THR A 94 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.02e+00 bond pdb=" N ASP C2497 " pdb=" CA ASP C2497 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.28e-02 6.10e+03 6.42e+00 bond pdb=" N ASP E2497 " pdb=" CA ASP E2497 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.15e+00 bond pdb=" C SER C 404 " pdb=" N MET C 405 " ideal model delta sigma weight residual 1.334 1.359 -0.025 1.27e-02 6.20e+03 3.75e+00 bond pdb=" SD MET C1732 " pdb=" CE MET C1732 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.72e+00 ... (remaining 37060 not shown) Histogram of bond angle deviations from ideal: 96.46 - 105.16: 640 105.16 - 113.85: 22152 113.85 - 122.55: 23049 122.55 - 131.25: 4470 131.25 - 139.94: 106 Bond angle restraints: 50417 Sorted by residual: angle pdb=" CA ARG E1728 " pdb=" CB ARG E1728 " pdb=" CG ARG E1728 " ideal model delta sigma weight residual 114.10 126.73 -12.63 2.00e+00 2.50e-01 3.99e+01 angle pdb=" CA ARG C1728 " pdb=" CB ARG C1728 " pdb=" CG ARG C1728 " ideal model delta sigma weight residual 114.10 126.55 -12.45 2.00e+00 2.50e-01 3.87e+01 angle pdb=" CA MET E1732 " pdb=" CB MET E1732 " pdb=" CG MET E1732 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 angle pdb=" C ARG C1728 " pdb=" CA ARG C1728 " pdb=" CB ARG C1728 " ideal model delta sigma weight residual 109.27 117.28 -8.01 1.61e+00 3.86e-01 2.48e+01 angle pdb=" C ARG E1728 " pdb=" CA ARG E1728 " pdb=" CB ARG E1728 " ideal model delta sigma weight residual 109.27 116.79 -7.52 1.61e+00 3.86e-01 2.18e+01 ... (remaining 50412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 20498 17.93 - 35.86: 1630 35.86 - 53.80: 216 53.80 - 71.73: 53 71.73 - 89.66: 38 Dihedral angle restraints: 22435 sinusoidal: 8162 harmonic: 14273 Sorted by residual: dihedral pdb=" CA TRP E2104 " pdb=" C TRP E2104 " pdb=" N PRO E2105 " pdb=" CA PRO E2105 " ideal model delta harmonic sigma weight residual 180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TRP C2104 " pdb=" C TRP C2104 " pdb=" N PRO C2105 " pdb=" CA PRO C2105 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLN E1845 " pdb=" C GLN E1845 " pdb=" N PRO E1846 " pdb=" CA PRO E1846 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 22432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 5331 0.077 - 0.154: 727 0.154 - 0.230: 51 0.230 - 0.307: 4 0.307 - 0.384: 3 Chirality restraints: 6116 Sorted by residual: chirality pdb=" CB ILE C1715 " pdb=" CA ILE C1715 " pdb=" CG1 ILE C1715 " pdb=" CG2 ILE C1715 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE E1715 " pdb=" CA ILE E1715 " pdb=" CG1 ILE E1715 " pdb=" CG2 ILE E1715 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ILE C1680 " pdb=" N ILE C1680 " pdb=" C ILE C1680 " pdb=" CB ILE C1680 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 6113 not shown) Planarity restraints: 6352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C1983 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ARG C1983 " -0.070 2.00e-02 2.50e+03 pdb=" O ARG C1983 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR C1984 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E1983 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C ARG E1983 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG E1983 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR E1984 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1784 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C ILE C1784 " 0.064 2.00e-02 2.50e+03 pdb=" O ILE C1784 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP C1785 " -0.022 2.00e-02 2.50e+03 ... (remaining 6349 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 229 2.54 - 3.13: 28564 3.13 - 3.72: 56104 3.72 - 4.31: 73170 4.31 - 4.90: 120622 Nonbonded interactions: 278689 Sorted by model distance: nonbonded pdb=" CG2 THR A 94 " pdb=" CE MET C 402 " model vdw 1.951 3.880 nonbonded pdb=" CB SER A 97 " pdb=" CD1 LEU C 406 " model vdw 1.978 3.860 nonbonded pdb=" NH2 ARG C 792 " pdb=" O PRO C 820 " model vdw 2.205 2.520 nonbonded pdb=" O PHE C1026 " pdb=" OH TYR C1053 " model vdw 2.205 2.440 nonbonded pdb=" OG SER B 28 " pdb=" O LEU B 46 " model vdw 2.215 2.440 ... (remaining 278684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 12 through 1738 or (resid 1739 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1740 or (resid 1741 and (name N or name C \ A or name C or name O or name CB )) or resid 1742 through 2527 or resid 2601 or \ resid 2602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 24.780 Check model and map are aligned: 0.590 Set scattering table: 0.300 Process input model: 105.390 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 37065 Z= 0.309 Angle : 0.898 12.879 50417 Z= 0.463 Chirality : 0.052 0.384 6116 Planarity : 0.005 0.053 6352 Dihedral : 13.746 89.660 13103 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.12), residues: 4800 helix: 0.49 (0.13), residues: 1904 sheet: -1.35 (0.21), residues: 662 loop : -1.79 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP E 349 HIS 0.008 0.001 HIS C 442 PHE 0.030 0.002 PHE B 44 TYR 0.019 0.002 TYR E1739 ARG 0.007 0.001 ARG C 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 4.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.3807 (tmm) cc_final: 0.3352 (ttp) REVERT: C 407 MET cc_start: -0.0848 (mtm) cc_final: -0.1244 (ttm) REVERT: C 1343 THR cc_start: 0.7519 (m) cc_final: 0.7248 (t) REVERT: C 2458 MET cc_start: 0.7219 (ppp) cc_final: 0.6958 (ppp) REVERT: E 395 PHE cc_start: 0.5587 (m-80) cc_final: 0.5118 (m-10) REVERT: E 1343 THR cc_start: 0.7598 (m) cc_final: 0.7351 (t) REVERT: E 1991 ILE cc_start: 0.8445 (pt) cc_final: 0.8208 (pt) REVERT: E 2458 MET cc_start: 0.7060 (ppp) cc_final: 0.6844 (ppp) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.5043 time to fit residues: 475.5422 Evaluate side-chains 299 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.5980 chunk 369 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 249 optimal weight: 10.0000 chunk 197 optimal weight: 0.3980 chunk 382 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 443 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 594 GLN C1323 GLN ** C1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 594 GLN E1323 GLN E1510 ASN ** E1960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37065 Z= 0.193 Angle : 0.637 14.714 50417 Z= 0.319 Chirality : 0.042 0.217 6116 Planarity : 0.004 0.060 6352 Dihedral : 6.042 71.575 5185 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.34 % Allowed : 9.43 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.12), residues: 4800 helix: 0.60 (0.12), residues: 1958 sheet: -1.40 (0.21), residues: 650 loop : -1.75 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C1376 HIS 0.005 0.001 HIS C 185 PHE 0.023 0.001 PHE C 671 TYR 0.023 0.002 TYR E 612 ARG 0.013 0.000 ARG C1558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 313 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.0421 (mptt) cc_final: -0.1336 (tppt) REVERT: B 103 LYS cc_start: 0.0700 (tppt) cc_final: -0.1188 (mptt) REVERT: C 72 MET cc_start: 0.1314 (mmt) cc_final: 0.1051 (tpp) REVERT: C 406 LEU cc_start: -0.1661 (OUTLIER) cc_final: -0.2163 (mt) REVERT: C 2106 MET cc_start: 0.7861 (ppp) cc_final: 0.7557 (tmm) REVERT: C 2419 LEU cc_start: 0.6735 (tp) cc_final: 0.6516 (tp) REVERT: E 395 PHE cc_start: 0.5590 (m-80) cc_final: 0.5128 (m-10) REVERT: E 787 ILE cc_start: 0.7541 (pt) cc_final: 0.7171 (mt) REVERT: E 2106 MET cc_start: 0.7617 (ppp) cc_final: 0.7321 (tmm) outliers start: 50 outliers final: 25 residues processed: 350 average time/residue: 0.4658 time to fit residues: 277.0937 Evaluate side-chains 292 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1388 LEU Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1131 LEU Chi-restraints excluded: chain E residue 1388 LEU Chi-restraints excluded: chain E residue 1443 SER Chi-restraints excluded: chain E residue 1706 SER Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2200 LEU Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 368 optimal weight: 0.4980 chunk 301 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 443 optimal weight: 0.9990 chunk 479 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 440 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 356 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 GLN C1254 HIS C1510 ASN ** C1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2053 GLN C2113 GLN ** C2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN E1094 GLN E1254 HIS ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2053 GLN ** E2081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2113 GLN ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37065 Z= 0.355 Angle : 0.699 11.128 50417 Z= 0.352 Chirality : 0.045 0.241 6116 Planarity : 0.004 0.073 6352 Dihedral : 6.252 79.593 5185 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.20 % Allowed : 12.11 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.12), residues: 4800 helix: 0.66 (0.12), residues: 1944 sheet: -1.64 (0.20), residues: 654 loop : -1.86 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E1376 HIS 0.009 0.001 HIS C2510 PHE 0.029 0.002 PHE C 511 TYR 0.031 0.002 TYR C1419 ARG 0.008 0.001 ARG E1728 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 304 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: -0.0667 (tpt) cc_final: -0.3496 (mpp) REVERT: A 174 MET cc_start: 0.3326 (mtt) cc_final: 0.3003 (mtt) REVERT: B 21 THR cc_start: 0.5407 (p) cc_final: 0.5137 (p) REVERT: B 103 LYS cc_start: 0.0822 (tppt) cc_final: -0.1055 (mptt) REVERT: C 72 MET cc_start: 0.1188 (mmt) cc_final: 0.0960 (tpp) REVERT: C 443 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6132 (pp) REVERT: C 1118 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6753 (ptpt) REVERT: C 1455 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6990 (p0) REVERT: C 1947 MET cc_start: 0.8443 (ptp) cc_final: 0.8150 (ptp) REVERT: C 2419 LEU cc_start: 0.7116 (tp) cc_final: 0.6768 (pp) REVERT: E 72 MET cc_start: 0.1052 (mmt) cc_final: 0.0712 (tpp) REVERT: E 395 PHE cc_start: 0.5816 (m-80) cc_final: 0.5321 (m-10) REVERT: E 1730 ASN cc_start: 0.7893 (m-40) cc_final: 0.7222 (t0) REVERT: E 1947 MET cc_start: 0.8410 (ptp) cc_final: 0.8047 (ptp) REVERT: E 1967 THR cc_start: 0.7434 (p) cc_final: 0.7185 (t) outliers start: 82 outliers final: 46 residues processed: 366 average time/residue: 0.4438 time to fit residues: 277.4083 Evaluate side-chains 312 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 263 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1118 LYS Chi-restraints excluded: chain C residue 1308 PHE Chi-restraints excluded: chain C residue 1310 HIS Chi-restraints excluded: chain C residue 1455 ASP Chi-restraints excluded: chain C residue 1504 ILE Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2073 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2241 MET Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1308 PHE Chi-restraints excluded: chain E residue 1310 HIS Chi-restraints excluded: chain E residue 1388 LEU Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1706 SER Chi-restraints excluded: chain E residue 1745 GLU Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2196 ASP Chi-restraints excluded: chain E residue 2241 MET Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 298 optimal weight: 20.0000 chunk 445 optimal weight: 0.5980 chunk 471 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 422 optimal weight: 0.0030 chunk 127 optimal weight: 6.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 HIS ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1216 HIS C1510 ASN C1516 GLN ** C2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN E1216 HIS E1516 GLN ** E1960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37065 Z= 0.220 Angle : 0.615 13.379 50417 Z= 0.305 Chirality : 0.042 0.269 6116 Planarity : 0.004 0.068 6352 Dihedral : 5.979 82.495 5185 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.12 % Allowed : 15.27 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 4800 helix: 0.75 (0.12), residues: 1958 sheet: -1.58 (0.21), residues: 650 loop : -1.82 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E1376 HIS 0.005 0.001 HIS C1929 PHE 0.016 0.001 PHE C 662 TYR 0.011 0.001 TYR E 612 ARG 0.006 0.000 ARG C1866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 274 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: -0.0251 (mmtm) cc_final: -0.1835 (tppt) REVERT: A 166 MET cc_start: -0.0875 (tpt) cc_final: -0.3656 (mpp) REVERT: B 87 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.2136 (mtt) REVERT: B 103 LYS cc_start: 0.0823 (tppt) cc_final: -0.1268 (mptt) REVERT: C 72 MET cc_start: 0.1303 (mmt) cc_final: 0.0980 (tpp) REVERT: C 1118 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6784 (ptpt) REVERT: C 1171 LEU cc_start: 0.7642 (mt) cc_final: 0.7432 (mt) REVERT: C 1730 ASN cc_start: 0.7838 (m-40) cc_final: 0.7507 (m-40) REVERT: C 1832 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8146 (tptm) REVERT: C 2419 LEU cc_start: 0.7412 (tp) cc_final: 0.7060 (pp) REVERT: E 72 MET cc_start: 0.1229 (mmt) cc_final: 0.0871 (tpp) REVERT: E 395 PHE cc_start: 0.5804 (m-80) cc_final: 0.5342 (m-10) REVERT: E 449 MET cc_start: 0.4336 (tpt) cc_final: 0.3624 (tpp) REVERT: E 1730 ASN cc_start: 0.8044 (m-40) cc_final: 0.7804 (m-40) REVERT: E 1810 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8239 (ptpp) REVERT: E 1832 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8181 (tptm) REVERT: E 1967 THR cc_start: 0.7395 (p) cc_final: 0.7146 (t) outliers start: 79 outliers final: 50 residues processed: 332 average time/residue: 0.4388 time to fit residues: 249.4169 Evaluate side-chains 316 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 261 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1118 LYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1310 HIS Chi-restraints excluded: chain C residue 1625 ILE Chi-restraints excluded: chain C residue 1697 MET Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1832 LYS Chi-restraints excluded: chain C residue 1893 VAL Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2196 ASP Chi-restraints excluded: chain C residue 2241 MET Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1131 LEU Chi-restraints excluded: chain E residue 1310 HIS Chi-restraints excluded: chain E residue 1388 LEU Chi-restraints excluded: chain E residue 1706 SER Chi-restraints excluded: chain E residue 1738 ILE Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1810 LYS Chi-restraints excluded: chain E residue 1832 LYS Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1944 MET Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2196 ASP Chi-restraints excluded: chain E residue 2241 MET Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 0.1980 chunk 267 optimal weight: 50.0000 chunk 6 optimal weight: 40.0000 chunk 351 optimal weight: 6.9990 chunk 194 optimal weight: 0.0980 chunk 402 optimal weight: 0.0060 chunk 326 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 240 optimal weight: 9.9990 chunk 423 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN C1045 ASN C1510 ASN C1516 GLN E 251 ASN E 360 HIS E1269 ASN E1510 ASN E1516 GLN E1960 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37065 Z= 0.153 Angle : 0.586 11.753 50417 Z= 0.287 Chirality : 0.040 0.249 6116 Planarity : 0.004 0.064 6352 Dihedral : 5.756 86.369 5185 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.12 % Allowed : 16.21 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4800 helix: 0.90 (0.12), residues: 1946 sheet: -1.25 (0.22), residues: 604 loop : -1.82 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1376 HIS 0.006 0.001 HIS C1929 PHE 0.013 0.001 PHE E1650 TYR 0.012 0.001 TYR E 612 ARG 0.004 0.000 ARG C2312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 276 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.0002 (OUTLIER) cc_final: -0.0301 (m-30) REVERT: A 166 MET cc_start: -0.0750 (tpt) cc_final: -0.3503 (mpp) REVERT: A 174 MET cc_start: 0.3481 (mtt) cc_final: 0.1923 (ptp) REVERT: B 87 MET cc_start: 0.2252 (mtt) cc_final: 0.1907 (mtt) REVERT: B 103 LYS cc_start: 0.0721 (tppt) cc_final: -0.1045 (mptt) REVERT: C 72 MET cc_start: 0.1237 (mmt) cc_final: 0.0944 (tpp) REVERT: C 443 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6147 (pp) REVERT: C 449 MET cc_start: 0.4816 (tpt) cc_final: 0.3205 (ttm) REVERT: C 1118 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6748 (ptpt) REVERT: C 1305 ASN cc_start: 0.6567 (OUTLIER) cc_final: 0.5152 (p0) REVERT: C 1730 ASN cc_start: 0.7945 (m-40) cc_final: 0.7658 (m-40) REVERT: C 2419 LEU cc_start: 0.7264 (tp) cc_final: 0.6888 (pp) REVERT: E 72 MET cc_start: 0.1280 (mmt) cc_final: 0.0942 (tpp) REVERT: E 395 PHE cc_start: 0.5758 (m-80) cc_final: 0.5287 (m-10) REVERT: E 1305 ASN cc_start: 0.6476 (OUTLIER) cc_final: 0.5067 (p0) REVERT: E 1376 TRP cc_start: 0.7912 (p-90) cc_final: 0.7706 (p-90) REVERT: E 1730 ASN cc_start: 0.7948 (m-40) cc_final: 0.7736 (m-40) REVERT: E 1867 ASN cc_start: 0.6293 (OUTLIER) cc_final: 0.6014 (p0) outliers start: 79 outliers final: 50 residues processed: 337 average time/residue: 0.4283 time to fit residues: 245.9525 Evaluate side-chains 316 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1118 LYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1305 ASN Chi-restraints excluded: chain C residue 1388 LEU Chi-restraints excluded: chain C residue 1697 MET Chi-restraints excluded: chain C residue 1765 ILE Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1944 MET Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1131 LEU Chi-restraints excluded: chain E residue 1305 ASN Chi-restraints excluded: chain E residue 1388 LEU Chi-restraints excluded: chain E residue 1455 ASP Chi-restraints excluded: chain E residue 1697 MET Chi-restraints excluded: chain E residue 1728 ARG Chi-restraints excluded: chain E residue 1745 GLU Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 1867 ASN Chi-restraints excluded: chain E residue 1944 MET Chi-restraints excluded: chain E residue 1993 ARG Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2241 MET Chi-restraints excluded: chain E residue 2312 ARG Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 0.6980 chunk 424 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 472 optimal weight: 6.9990 chunk 391 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 156 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN C1510 ASN ** C1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1510 ASN ** E1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37065 Z= 0.181 Angle : 0.587 11.035 50417 Z= 0.289 Chirality : 0.041 0.248 6116 Planarity : 0.004 0.064 6352 Dihedral : 5.716 89.515 5185 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.63 % Allowed : 16.24 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 4800 helix: 0.97 (0.12), residues: 1948 sheet: -1.38 (0.22), residues: 620 loop : -1.81 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C1376 HIS 0.006 0.001 HIS E1929 PHE 0.012 0.001 PHE C1883 TYR 0.012 0.001 TYR E 612 ARG 0.002 0.000 ARG E1993 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 275 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: -0.0067 (OUTLIER) cc_final: -0.0269 (m-30) REVERT: A 166 MET cc_start: -0.0954 (tpt) cc_final: -0.3626 (mpp) REVERT: A 174 MET cc_start: 0.3405 (mtt) cc_final: 0.1807 (ptp) REVERT: B 87 MET cc_start: 0.2231 (mtt) cc_final: 0.1921 (mtt) REVERT: B 103 LYS cc_start: 0.0798 (tppt) cc_final: -0.1179 (mptt) REVERT: C 72 MET cc_start: 0.1217 (mmt) cc_final: 0.0921 (tpp) REVERT: C 443 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6236 (pp) REVERT: C 465 MET cc_start: 0.3437 (mmt) cc_final: 0.3178 (mmt) REVERT: C 1118 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6731 (ptpt) REVERT: C 1305 ASN cc_start: 0.6252 (OUTLIER) cc_final: 0.5325 (p0) REVERT: C 1376 TRP cc_start: 0.8041 (p-90) cc_final: 0.7705 (p-90) REVERT: C 1730 ASN cc_start: 0.8079 (m-40) cc_final: 0.7749 (m-40) REVERT: C 1788 MET cc_start: 0.9313 (tpp) cc_final: 0.8960 (tpp) REVERT: C 1832 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8092 (tptm) REVERT: C 1993 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7420 (ptp-110) REVERT: E 72 MET cc_start: 0.1165 (mmt) cc_final: 0.0839 (tpp) REVERT: E 100 MET cc_start: 0.1461 (tpp) cc_final: -0.1450 (mmt) REVERT: E 395 PHE cc_start: 0.5787 (m-80) cc_final: 0.5316 (m-10) REVERT: E 1305 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5177 (p0) REVERT: E 1810 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8308 (ptpp) REVERT: E 1832 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8144 (tptm) outliers start: 98 outliers final: 62 residues processed: 352 average time/residue: 0.4593 time to fit residues: 275.4634 Evaluate side-chains 333 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 262 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1118 LYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1305 ASN Chi-restraints excluded: chain C residue 1310 HIS Chi-restraints excluded: chain C residue 1504 ILE Chi-restraints excluded: chain C residue 1625 ILE Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1765 ILE Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1832 LYS Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1893 VAL Chi-restraints excluded: chain C residue 1944 MET Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 1993 ARG Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2196 ASP Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1131 LEU Chi-restraints excluded: chain E residue 1305 ASN Chi-restraints excluded: chain E residue 1455 ASP Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1697 MET Chi-restraints excluded: chain E residue 1728 ARG Chi-restraints excluded: chain E residue 1745 GLU Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1810 LYS Chi-restraints excluded: chain E residue 1832 LYS Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 1868 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1944 MET Chi-restraints excluded: chain E residue 1958 LEU Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2312 ARG Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 269 optimal weight: 0.0040 chunk 344 optimal weight: 0.0670 chunk 267 optimal weight: 50.0000 chunk 397 optimal weight: 0.7980 chunk 263 optimal weight: 20.0000 chunk 470 optimal weight: 0.0870 chunk 294 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 217 optimal weight: 1.9990 overall best weight: 0.5910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1510 ASN ** C1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37065 Z= 0.167 Angle : 0.585 11.446 50417 Z= 0.287 Chirality : 0.041 0.263 6116 Planarity : 0.003 0.061 6352 Dihedral : 5.633 88.377 5185 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.44 % Allowed : 16.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4800 helix: 1.02 (0.12), residues: 1950 sheet: -1.26 (0.22), residues: 618 loop : -1.78 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 51 HIS 0.005 0.001 HIS E1929 PHE 0.036 0.001 PHE C 511 TYR 0.020 0.001 TYR E 612 ARG 0.006 0.000 ARG C2026 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 268 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: -0.0039 (OUTLIER) cc_final: -0.0288 (m-30) REVERT: A 166 MET cc_start: -0.0963 (tpt) cc_final: -0.3644 (mpp) REVERT: A 174 MET cc_start: 0.3568 (mtt) cc_final: 0.2014 (ptp) REVERT: B 103 LYS cc_start: 0.0695 (tppt) cc_final: -0.1213 (mptt) REVERT: B 174 MET cc_start: 0.2223 (mmm) cc_final: 0.1850 (ttm) REVERT: C 72 MET cc_start: 0.1198 (mmt) cc_final: 0.0916 (tpp) REVERT: C 443 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6163 (pp) REVERT: C 449 MET cc_start: 0.4301 (tpt) cc_final: 0.4062 (tpt) REVERT: C 465 MET cc_start: 0.3568 (mmt) cc_final: 0.3298 (mmt) REVERT: C 1118 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6734 (ptpt) REVERT: C 1305 ASN cc_start: 0.6091 (OUTLIER) cc_final: 0.5422 (p0) REVERT: C 1376 TRP cc_start: 0.8015 (p-90) cc_final: 0.7678 (p-90) REVERT: C 1730 ASN cc_start: 0.8094 (m-40) cc_final: 0.7789 (m-40) REVERT: C 1788 MET cc_start: 0.9287 (tpp) cc_final: 0.8964 (tpp) REVERT: C 1832 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8079 (tptm) REVERT: C 1993 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7420 (ptp-110) REVERT: C 2521 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7247 (tmm) REVERT: E 72 MET cc_start: 0.1122 (mmt) cc_final: 0.0804 (tpp) REVERT: E 100 MET cc_start: 0.1415 (tpp) cc_final: -0.1394 (mmt) REVERT: E 395 PHE cc_start: 0.5794 (m-80) cc_final: 0.5372 (m-10) REVERT: E 1305 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.5373 (p0) REVERT: E 1788 MET cc_start: 0.9126 (tpp) cc_final: 0.8767 (tpp) REVERT: E 1810 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8218 (ptpp) REVERT: E 1832 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8143 (tptm) REVERT: E 1993 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7439 (ptp-110) outliers start: 91 outliers final: 60 residues processed: 337 average time/residue: 0.4588 time to fit residues: 263.3974 Evaluate side-chains 327 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 256 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1118 LYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1305 ASN Chi-restraints excluded: chain C residue 1455 ASP Chi-restraints excluded: chain C residue 1697 MET Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1765 ILE Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1832 LYS Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1893 VAL Chi-restraints excluded: chain C residue 1944 MET Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 1993 ARG Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2196 ASP Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain C residue 2521 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1131 LEU Chi-restraints excluded: chain E residue 1305 ASN Chi-restraints excluded: chain E residue 1310 HIS Chi-restraints excluded: chain E residue 1388 LEU Chi-restraints excluded: chain E residue 1455 ASP Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1697 MET Chi-restraints excluded: chain E residue 1728 ARG Chi-restraints excluded: chain E residue 1745 GLU Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1810 LYS Chi-restraints excluded: chain E residue 1832 LYS Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1944 MET Chi-restraints excluded: chain E residue 1967 THR Chi-restraints excluded: chain E residue 1993 ARG Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2312 ARG Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 280 optimal weight: 40.0000 chunk 141 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 43 optimal weight: 40.0000 chunk 369 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN C1045 ASN ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1303 HIS ** C1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1986 HIS C2502 HIS ** C2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E 572 HIS ** E1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 HIS ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1486 HIS ** E1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1986 HIS E2502 HIS ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 37065 Z= 0.584 Angle : 0.857 12.489 50417 Z= 0.429 Chirality : 0.049 0.279 6116 Planarity : 0.005 0.069 6352 Dihedral : 6.593 88.433 5185 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.08 % Favored : 89.90 % Rotamer: Outliers : 2.63 % Allowed : 17.52 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4800 helix: 0.72 (0.12), residues: 1932 sheet: -1.84 (0.20), residues: 648 loop : -2.03 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP E1393 HIS 0.027 0.002 HIS E 591 PHE 0.030 0.003 PHE C2059 TYR 0.038 0.003 TYR E1415 ARG 0.009 0.001 ARG C1728 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 282 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.0182 (OUTLIER) cc_final: -0.0218 (m-30) REVERT: A 166 MET cc_start: -0.0689 (tpt) cc_final: -0.3455 (mpp) REVERT: A 174 MET cc_start: 0.3750 (mtt) cc_final: 0.2202 (ptp) REVERT: B 52 SER cc_start: 0.2926 (p) cc_final: 0.2641 (m) REVERT: B 103 LYS cc_start: 0.0856 (tppt) cc_final: -0.0915 (mptt) REVERT: B 174 MET cc_start: 0.2150 (mmm) cc_final: 0.1867 (ttm) REVERT: C 72 MET cc_start: 0.1259 (mmt) cc_final: 0.0742 (tpp) REVERT: C 443 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6212 (pp) REVERT: C 465 MET cc_start: 0.4159 (mmt) cc_final: 0.3868 (mmt) REVERT: C 1203 MET cc_start: 0.8500 (mtp) cc_final: 0.8196 (mtt) REVERT: C 1730 ASN cc_start: 0.8106 (m-40) cc_final: 0.7518 (m-40) REVERT: C 1832 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8286 (tptm) REVERT: C 1967 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.8017 (p) REVERT: C 2521 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7310 (tmm) REVERT: E 72 MET cc_start: 0.1289 (mmt) cc_final: 0.0950 (tpp) REVERT: E 100 MET cc_start: 0.1618 (tpp) cc_final: -0.1229 (mmt) REVERT: E 1203 MET cc_start: 0.8320 (mtp) cc_final: 0.7884 (mtt) REVERT: E 1733 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8460 (p90) REVERT: E 1832 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8337 (tptm) REVERT: E 2521 MET cc_start: 0.7329 (tmm) cc_final: 0.6908 (tmm) outliers start: 98 outliers final: 60 residues processed: 355 average time/residue: 0.4422 time to fit residues: 269.8543 Evaluate side-chains 331 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 264 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1310 HIS Chi-restraints excluded: chain C residue 1455 ASP Chi-restraints excluded: chain C residue 1607 MET Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1745 GLU Chi-restraints excluded: chain C residue 1765 ILE Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1806 THR Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1832 LYS Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1893 VAL Chi-restraints excluded: chain C residue 1944 MET Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2073 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2196 ASP Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain C residue 2521 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1310 HIS Chi-restraints excluded: chain E residue 1455 ASP Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1745 GLU Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1810 LYS Chi-restraints excluded: chain E residue 1832 LYS Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 1883 PHE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1944 MET Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2073 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2196 ASP Chi-restraints excluded: chain E residue 2312 ARG Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 0.8980 chunk 450 optimal weight: 0.9990 chunk 411 optimal weight: 0.7980 chunk 438 optimal weight: 0.6980 chunk 263 optimal weight: 20.0000 chunk 190 optimal weight: 0.6980 chunk 344 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 396 optimal weight: 0.7980 chunk 414 optimal weight: 0.5980 chunk 436 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1093 ASN ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1516 GLN ** C2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN E1365 GLN ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37065 Z= 0.194 Angle : 0.633 12.589 50417 Z= 0.309 Chirality : 0.042 0.263 6116 Planarity : 0.004 0.062 6352 Dihedral : 5.981 84.949 5185 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.28 % Allowed : 18.65 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.12), residues: 4800 helix: 0.96 (0.12), residues: 1934 sheet: -1.60 (0.21), residues: 624 loop : -1.86 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP E1376 HIS 0.005 0.001 HIS C1929 PHE 0.027 0.001 PHE C 511 TYR 0.019 0.001 TYR C 612 ARG 0.014 0.000 ARG C1477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 265 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.0181 (OUTLIER) cc_final: -0.0144 (m-30) REVERT: A 166 MET cc_start: -0.0676 (tpt) cc_final: -0.3427 (mpp) REVERT: A 174 MET cc_start: 0.3685 (mtt) cc_final: 0.2417 (ptp) REVERT: B 52 SER cc_start: 0.2929 (p) cc_final: 0.2715 (m) REVERT: B 103 LYS cc_start: 0.0543 (tppt) cc_final: -0.1294 (mptt) REVERT: B 174 MET cc_start: 0.1886 (mmm) cc_final: 0.1468 (tpp) REVERT: C 72 MET cc_start: 0.1228 (mmt) cc_final: 0.0752 (tpp) REVERT: C 402 MET cc_start: 0.1851 (ppp) cc_final: 0.1253 (ptt) REVERT: C 443 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6042 (pp) REVERT: C 465 MET cc_start: 0.4156 (mmt) cc_final: 0.3880 (mmt) REVERT: C 1646 MET cc_start: 0.6338 (mmt) cc_final: 0.6043 (mmt) REVERT: C 1730 ASN cc_start: 0.7989 (m-40) cc_final: 0.7651 (m-40) REVERT: C 1832 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8157 (tptm) REVERT: C 1993 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7471 (ptp-110) REVERT: C 2521 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7184 (tmm) REVERT: E 100 MET cc_start: 0.1467 (tpp) cc_final: -0.1229 (mmt) REVERT: E 449 MET cc_start: 0.1935 (tpt) cc_final: 0.1644 (tpt) REVERT: E 1431 MET cc_start: 0.8430 (ttp) cc_final: 0.8217 (ttp) REVERT: E 1810 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (ptpp) REVERT: E 1832 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8206 (tptm) REVERT: E 1993 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7479 (ptp-110) REVERT: E 2521 MET cc_start: 0.7468 (tmm) cc_final: 0.6619 (tmm) outliers start: 85 outliers final: 63 residues processed: 327 average time/residue: 0.4416 time to fit residues: 247.7652 Evaluate side-chains 325 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 254 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1305 ASN Chi-restraints excluded: chain C residue 1310 HIS Chi-restraints excluded: chain C residue 1455 ASP Chi-restraints excluded: chain C residue 1504 ILE Chi-restraints excluded: chain C residue 1607 MET Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1765 ILE Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1832 LYS Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1893 VAL Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 1993 ARG Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2073 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2356 THR Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain C residue 2512 GLU Chi-restraints excluded: chain C residue 2521 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 465 MET Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1118 LYS Chi-restraints excluded: chain E residue 1305 ASN Chi-restraints excluded: chain E residue 1310 HIS Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1455 ASP Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1706 SER Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1810 LYS Chi-restraints excluded: chain E residue 1832 LYS Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1993 ARG Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2015 ILE Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2312 ARG Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 40.0000 chunk 463 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 486 optimal weight: 0.8980 chunk 447 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 chunk 299 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1365 GLN ** E1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 37065 Z= 0.522 Angle : 0.773 59.200 50417 Z= 0.407 Chirality : 0.051 1.058 6116 Planarity : 0.004 0.078 6352 Dihedral : 5.986 85.758 5185 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.20 % Allowed : 18.62 % Favored : 79.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4800 helix: 0.91 (0.12), residues: 1932 sheet: -1.60 (0.21), residues: 624 loop : -1.88 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E1376 HIS 0.008 0.001 HIS C2510 PHE 0.132 0.002 PHE C 573 TYR 0.018 0.002 TYR E 612 ARG 0.018 0.001 ARG C1320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9600 Ramachandran restraints generated. 4800 Oldfield, 0 Emsley, 4800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 258 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.0396 (OUTLIER) cc_final: -0.0171 (m-30) REVERT: A 166 MET cc_start: -0.0668 (tpt) cc_final: -0.3422 (mpp) REVERT: A 174 MET cc_start: 0.3696 (mtt) cc_final: 0.2426 (ptp) REVERT: B 103 LYS cc_start: 0.0541 (tppt) cc_final: -0.1113 (mptt) REVERT: B 174 MET cc_start: 0.1880 (mmm) cc_final: 0.1472 (tpp) REVERT: C 72 MET cc_start: 0.1242 (mmt) cc_final: 0.0760 (tpp) REVERT: C 443 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6058 (pp) REVERT: C 465 MET cc_start: 0.4175 (mmt) cc_final: 0.3912 (mmt) REVERT: C 1646 MET cc_start: 0.6386 (mmt) cc_final: 0.6085 (mmt) REVERT: C 1730 ASN cc_start: 0.8071 (m-40) cc_final: 0.7722 (m-40) REVERT: C 1832 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8234 (tptm) REVERT: C 1993 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7506 (ptp-110) REVERT: C 2521 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7180 (tmm) REVERT: E 100 MET cc_start: 0.1486 (tpp) cc_final: -0.1221 (mmt) REVERT: E 395 PHE cc_start: 0.5918 (m-80) cc_final: 0.5599 (m-10) REVERT: E 449 MET cc_start: 0.1950 (tpt) cc_final: 0.1656 (tpt) REVERT: E 1832 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8295 (tptm) REVERT: E 1993 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7560 (ptp-110) REVERT: E 2521 MET cc_start: 0.7484 (tmm) cc_final: 0.6620 (tmm) outliers start: 82 outliers final: 70 residues processed: 319 average time/residue: 0.4466 time to fit residues: 244.6761 Evaluate side-chains 332 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 255 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1021 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1305 ASN Chi-restraints excluded: chain C residue 1310 HIS Chi-restraints excluded: chain C residue 1455 ASP Chi-restraints excluded: chain C residue 1504 ILE Chi-restraints excluded: chain C residue 1697 MET Chi-restraints excluded: chain C residue 1706 SER Chi-restraints excluded: chain C residue 1765 ILE Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1832 LYS Chi-restraints excluded: chain C residue 1842 ASN Chi-restraints excluded: chain C residue 1893 VAL Chi-restraints excluded: chain C residue 1944 MET Chi-restraints excluded: chain C residue 1967 THR Chi-restraints excluded: chain C residue 1993 ARG Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain C residue 2356 THR Chi-restraints excluded: chain C residue 2451 PHE Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2460 THR Chi-restraints excluded: chain C residue 2512 GLU Chi-restraints excluded: chain C residue 2521 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 465 MET Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 833 THR Chi-restraints excluded: chain E residue 1011 GLU Chi-restraints excluded: chain E residue 1012 HIS Chi-restraints excluded: chain E residue 1021 ASN Chi-restraints excluded: chain E residue 1065 VAL Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1106 VAL Chi-restraints excluded: chain E residue 1118 LYS Chi-restraints excluded: chain E residue 1305 ASN Chi-restraints excluded: chain E residue 1310 HIS Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1455 ASP Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1697 MET Chi-restraints excluded: chain E residue 1706 SER Chi-restraints excluded: chain E residue 1713 LEU Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1766 THR Chi-restraints excluded: chain E residue 1810 LYS Chi-restraints excluded: chain E residue 1832 LYS Chi-restraints excluded: chain E residue 1842 ASN Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1944 MET Chi-restraints excluded: chain E residue 1993 ARG Chi-restraints excluded: chain E residue 2004 THR Chi-restraints excluded: chain E residue 2015 ILE Chi-restraints excluded: chain E residue 2020 ILE Chi-restraints excluded: chain E residue 2086 LEU Chi-restraints excluded: chain E residue 2202 LEU Chi-restraints excluded: chain E residue 2312 ARG Chi-restraints excluded: chain E residue 2451 PHE Chi-restraints excluded: chain E residue 2460 THR Chi-restraints excluded: chain E residue 2512 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 0.5980 chunk 412 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 356 optimal weight: 3.9990 chunk 57 optimal weight: 50.0000 chunk 107 optimal weight: 0.7980 chunk 387 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 398 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1365 GLN ** E1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** 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 = 0.4469 r_free = 0.4469 target = 0.145020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.122203 restraints weight = 105116.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.116174 restraints weight = 151125.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.113623 restraints weight = 147418.257| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 37065 Z= 0.523 Angle : 0.770 55.241 50417 Z= 0.408 Chirality : 0.051 1.058 6116 Planarity : 0.004 0.078 6352 Dihedral : 5.986 85.758 5185 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.06 % Allowed : 18.70 % Favored : 79.23 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4800 helix: 0.91 (0.12), residues: 1932 sheet: -1.60 (0.21), residues: 624 loop : -1.88 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E1376 HIS 0.008 0.001 HIS C2510 PHE 0.132 0.002 PHE C 573 TYR 0.018 0.002 TYR E 612 ARG 0.018 0.001 ARG C1320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6686.22 seconds wall clock time: 123 minutes 52.33 seconds (7432.33 seconds total)