Starting phenix.real_space_refine on Sat Mar 16 09:04:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/03_2024/7rb9_24400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/03_2024/7rb9_24400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/03_2024/7rb9_24400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/03_2024/7rb9_24400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/03_2024/7rb9_24400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/03_2024/7rb9_24400_updated.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 91 5.16 5 C 8988 2.51 5 N 2413 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "D TYR 1473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14193 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5358 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 23, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.51, per 1000 atoms: 0.53 Number of scatterers: 14193 At special positions: 0 Unit cell: (112.27, 148.32, 136.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 6 15.00 Mg 3 11.99 O 2692 8.00 N 2413 7.00 C 8988 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: 5.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 15 sheets defined 47.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 92.40 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 removed outlier: 4.040A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.587A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.939A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.013A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.713A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 removed outlier: 3.737A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 5.047A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 261' Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.560A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.726A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 removed outlier: 4.191A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.712A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 removed outlier: 4.816A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.503A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.690A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1232 removed outlier: 4.421A pdb=" N GLU D1231 " --> pdb=" O LYS D1227 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG D1232 " --> pdb=" O THR D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1261 removed outlier: 3.524A pdb=" N GLN D1261 " --> pdb=" O PRO D1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1257 through 1261' Processing helix chain 'D' and resid 1265 through 1270 removed outlier: 3.651A pdb=" N LEU D1268 " --> pdb=" O GLY D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1289 removed outlier: 4.002A pdb=" N ALA D1279 " --> pdb=" O LEU D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1305 through 1318 Processing helix chain 'D' and resid 1322 through 1324 No H-bonds generated for 'chain 'D' and resid 1322 through 1324' Processing helix chain 'D' and resid 1326 through 1333 removed outlier: 4.585A pdb=" N ILE D1331 " --> pdb=" O GLN D1328 " (cutoff:3.500A) Processing helix chain 'D' and resid 1336 through 1342 Processing helix chain 'D' and resid 1380 through 1383 Processing helix chain 'D' and resid 1394 through 1402 Processing helix chain 'D' and resid 1405 through 1411 Processing helix chain 'D' and resid 1429 through 1432 removed outlier: 3.586A pdb=" N GLY D1432 " --> pdb=" O GLU D1429 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1429 through 1432' Processing helix chain 'D' and resid 1435 through 1448 Processing helix chain 'D' and resid 1453 through 1471 removed outlier: 3.954A pdb=" N GLY D1470 " --> pdb=" O ILE D1466 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN D1471 " --> pdb=" O LEU D1467 " (cutoff:3.500A) Processing helix chain 'D' and resid 1491 through 1500 Processing helix chain 'D' and resid 1504 through 1512 Processing helix chain 'D' and resid 1529 through 1558 removed outlier: 3.642A pdb=" N ALA D1540 " --> pdb=" O ARG D1536 " (cutoff:3.500A) Processing helix chain 'D' and resid 1584 through 1615 Processing helix chain 'D' and resid 1617 through 1619 No H-bonds generated for 'chain 'D' and resid 1617 through 1619' Processing helix chain 'D' and resid 1628 through 1635 removed outlier: 4.142A pdb=" N ILE D1634 " --> pdb=" O CYS D1630 " (cutoff:3.500A) Processing helix chain 'D' and resid 1641 through 1650 removed outlier: 4.011A pdb=" N CYS D1650 " --> pdb=" O ASP D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1667 removed outlier: 3.534A pdb=" N LEU D1660 " --> pdb=" O ASP D1656 " (cutoff:3.500A) Processing helix chain 'D' and resid 1699 through 1702 No H-bonds generated for 'chain 'D' and resid 1699 through 1702' Processing helix chain 'D' and resid 1709 through 1717 removed outlier: 3.540A pdb=" N PHE D1715 " --> pdb=" O VAL D1711 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D1716 " --> pdb=" O LEU D1712 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS D1717 " --> pdb=" O ASP D1713 " (cutoff:3.500A) Processing helix chain 'D' and resid 1721 through 1733 Processing helix chain 'D' and resid 1754 through 1772 removed outlier: 5.495A pdb=" N ARG D1771 " --> pdb=" O GLU D1767 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS D1772 " --> pdb=" O LYS D1768 " (cutoff:3.500A) Processing helix chain 'D' and resid 1793 through 1803 Processing helix chain 'D' and resid 1805 through 1812 Processing helix chain 'D' and resid 1822 through 1828 Processing helix chain 'D' and resid 1844 through 1854 Processing helix chain 'D' and resid 1858 through 1860 No H-bonds generated for 'chain 'D' and resid 1858 through 1860' Processing helix chain 'D' and resid 1873 through 1888 removed outlier: 4.749A pdb=" N GLU D1879 " --> pdb=" O HIS D1875 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D1880 " --> pdb=" O GLN D1876 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG D1884 " --> pdb=" O SER D1880 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D1885 " --> pdb=" O MET D1881 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D1888 " --> pdb=" O ARG D1884 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 4.040A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.587A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.939A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.014A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.713A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.736A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix removed outlier: 5.047A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 261' Processing helix chain 'A' and resid 264 through 267 removed outlier: 3.560A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 267' Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.726A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.192A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.713A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 4.817A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.504A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.691A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 4.040A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.586A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.939A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 4.014A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.712A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 removed outlier: 3.737A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 5.047A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 261' Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.560A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.726A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 4.191A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.712A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 347 removed outlier: 4.817A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.503A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.689A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.786A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.505A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 149 through 155 Processing sheet with id= D, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'D' and resid 1243 through 1246 removed outlier: 3.908A pdb=" N LEU D1243 " --> pdb=" O PHE D1776 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D1293 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D1361 " --> pdb=" O ILE D1568 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id= G, first strand: chain 'D' and resid 1682 through 1687 Processing sheet with id= H, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.787A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.504A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 149 through 155 Processing sheet with id= K, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= L, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.786A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.504A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 149 through 155 Processing sheet with id= O, first strand: chain 'C' and resid 238 through 241 527 hydrogen bonds defined for protein. 1356 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: 3.82 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4664 1.35 - 1.46: 3246 1.46 - 1.58: 6417 1.58 - 1.70: 9 1.70 - 1.82: 153 Bond restraints: 14489 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.412 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.411 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 14484 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.32: 453 106.32 - 113.71: 7947 113.71 - 121.11: 7300 121.11 - 128.51: 3849 128.51 - 135.91: 85 Bond angle restraints: 19634 Sorted by residual: angle pdb=" N ALA D1253 " pdb=" CA ALA D1253 " pdb=" C ALA D1253 " ideal model delta sigma weight residual 110.10 103.64 6.46 1.49e+00 4.50e-01 1.88e+01 angle pdb=" N LEU D1837 " pdb=" CA LEU D1837 " pdb=" C LEU D1837 " ideal model delta sigma weight residual 113.16 108.28 4.88 1.24e+00 6.50e-01 1.55e+01 angle pdb=" N TYR D1255 " pdb=" CA TYR D1255 " pdb=" C TYR D1255 " ideal model delta sigma weight residual 109.96 104.27 5.69 1.49e+00 4.50e-01 1.46e+01 angle pdb=" N LEU D1835 " pdb=" CA LEU D1835 " pdb=" C LEU D1835 " ideal model delta sigma weight residual 110.50 105.68 4.82 1.41e+00 5.03e-01 1.17e+01 angle pdb=" C ASN D1838 " pdb=" N VAL D1839 " pdb=" CA VAL D1839 " ideal model delta sigma weight residual 122.60 120.62 1.98 6.80e-01 2.16e+00 8.52e+00 ... (remaining 19629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 8514 30.79 - 61.58: 205 61.58 - 92.37: 20 92.37 - 123.17: 0 123.17 - 153.96: 9 Dihedral angle restraints: 8748 sinusoidal: 3550 harmonic: 5198 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 93.96 -153.96 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 93.90 -153.90 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 93.88 -153.88 1 2.00e+01 2.50e-03 4.55e+01 ... (remaining 8745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1998 0.080 - 0.159: 188 0.159 - 0.238: 2 0.238 - 0.318: 0 0.318 - 0.397: 1 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CG LEU D1837 " pdb=" CB LEU D1837 " pdb=" CD1 LEU D1837 " pdb=" CD2 LEU D1837 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA ALA D1834 " pdb=" N ALA D1834 " pdb=" C ALA D1834 " pdb=" CB ALA D1834 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR D1255 " pdb=" N TYR D1255 " pdb=" C TYR D1255 " pdb=" CB TYR D1255 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 2186 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D1857 " 0.041 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D1858 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D1858 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D1858 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D1833 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL D1833 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL D1833 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA D1834 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D1271 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO D1272 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D1272 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1272 " 0.020 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2328 2.76 - 3.30: 13722 3.30 - 3.83: 22874 3.83 - 4.37: 26884 4.37 - 4.90: 46154 Nonbonded interactions: 111962 Sorted by model distance: nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 402 " model vdw 2.228 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.230 2.170 nonbonded pdb=" OE1 GLN B 354 " pdb=" OH TYR D1639 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 177 " model vdw 2.279 2.520 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.279 2.520 ... (remaining 111957 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' selection = chain 'C' } 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: 15.590 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: 0.010 Extract box with map and model: 36.020 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 35.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.003 0.057 14489 Z= 0.166 Angle : 0.574 8.220 19634 Z= 0.306 Chirality : 0.044 0.397 2189 Planarity : 0.003 0.063 2525 Dihedral : 14.694 153.957 5404 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1765 helix: 1.06 (0.21), residues: 705 sheet: -0.03 (0.31), residues: 304 loop : 0.11 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1550 HIS 0.002 0.000 HIS D1666 PHE 0.013 0.001 PHE D1230 TYR 0.015 0.001 TYR D1473 ARG 0.003 0.000 ARG D1620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1211 MET cc_start: 0.8593 (mmp) cc_final: 0.8329 (mmp) REVERT: D 1286 MET cc_start: 0.9012 (mmp) cc_final: 0.8518 (mmp) REVERT: D 1446 MET cc_start: 0.8921 (ppp) cc_final: 0.8369 (ppp) REVERT: D 1514 LYS cc_start: 0.9105 (tttt) cc_final: 0.8358 (tttm) REVERT: D 1596 LEU cc_start: 0.9631 (mm) cc_final: 0.9165 (pp) REVERT: D 1776 PHE cc_start: 0.8216 (m-10) cc_final: 0.7617 (m-10) REVERT: D 1796 MET cc_start: 0.8964 (mmp) cc_final: 0.8749 (mmp) REVERT: D 1881 MET cc_start: 0.8381 (ppp) cc_final: 0.8096 (ttt) REVERT: A 325 MET cc_start: 0.8189 (mtp) cc_final: 0.7388 (mtt) REVERT: A 334 GLU cc_start: 0.8087 (pm20) cc_final: 0.7771 (pm20) REVERT: C 61 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8535 (ttmm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2624 time to fit residues: 86.9083 Evaluate side-chains 111 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 160 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1501 GLN D1784 HIS D1823 GLN D1873 HIS A 92 ASN C 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14489 Z= 0.179 Angle : 0.550 6.228 19634 Z= 0.273 Chirality : 0.043 0.143 2189 Planarity : 0.004 0.056 2525 Dihedral : 10.381 164.383 1985 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.98 % Allowed : 6.87 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.22), residues: 1765 helix: 1.00 (0.21), residues: 716 sheet: -0.01 (0.33), residues: 291 loop : 0.03 (0.25), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.004 0.001 HIS D1784 PHE 0.013 0.001 PHE D1230 TYR 0.014 0.001 TYR D1665 ARG 0.003 0.000 ARG D1620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7640 (tm-30) REVERT: B 325 MET cc_start: 0.8026 (mtp) cc_final: 0.7777 (ttm) REVERT: D 1211 MET cc_start: 0.8600 (mmp) cc_final: 0.8353 (mmp) REVERT: D 1326 MET cc_start: 0.9323 (tpp) cc_final: 0.9002 (tmm) REVERT: D 1446 MET cc_start: 0.8836 (ppp) cc_final: 0.8402 (ppp) REVERT: D 1796 MET cc_start: 0.8994 (mmp) cc_final: 0.8756 (mmp) REVERT: D 1860 MET cc_start: 0.6765 (tpt) cc_final: 0.6339 (tpt) REVERT: A 176 MET cc_start: 0.8055 (mtp) cc_final: 0.7424 (mtt) REVERT: A 325 MET cc_start: 0.8224 (mtp) cc_final: 0.7422 (mtt) REVERT: C 57 GLU cc_start: 0.7553 (tp30) cc_final: 0.7351 (tp30) REVERT: C 184 ASP cc_start: 0.8214 (m-30) cc_final: 0.7832 (m-30) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.2517 time to fit residues: 49.4134 Evaluate side-chains 116 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1511 ILE Chi-restraints excluded: chain D residue 1626 ASP Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 0.0020 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 0.0020 chunk 143 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14489 Z= 0.218 Angle : 0.541 8.197 19634 Z= 0.265 Chirality : 0.043 0.134 2189 Planarity : 0.004 0.049 2525 Dihedral : 10.220 179.323 1985 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.18 % Allowed : 8.25 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1765 helix: 0.88 (0.21), residues: 731 sheet: -0.07 (0.34), residues: 291 loop : -0.06 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1619 HIS 0.003 0.001 HIS D1667 PHE 0.011 0.001 PHE D1699 TYR 0.013 0.001 TYR D1665 ARG 0.008 0.000 ARG D1266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 294 TYR cc_start: 0.9120 (m-10) cc_final: 0.8882 (m-80) REVERT: B 325 MET cc_start: 0.8241 (mtp) cc_final: 0.7940 (ttm) REVERT: B 355 MET cc_start: 0.8152 (tpp) cc_final: 0.7915 (tpp) REVERT: D 1211 MET cc_start: 0.8698 (mmp) cc_final: 0.8420 (mmp) REVERT: D 1326 MET cc_start: 0.9386 (tpp) cc_final: 0.9142 (tmm) REVERT: D 1446 MET cc_start: 0.8954 (ppp) cc_final: 0.8495 (ppp) REVERT: D 1596 LEU cc_start: 0.9491 (mt) cc_final: 0.9065 (pp) REVERT: D 1860 MET cc_start: 0.6586 (tpt) cc_final: 0.6205 (tpt) REVERT: A 325 MET cc_start: 0.8241 (mtp) cc_final: 0.7472 (mtt) REVERT: C 106 THR cc_start: 0.8591 (p) cc_final: 0.8386 (p) REVERT: C 184 ASP cc_start: 0.8224 (m-30) cc_final: 0.7858 (m-30) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 0.2369 time to fit residues: 44.3376 Evaluate side-chains 115 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.0050 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1343 ASN A 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14489 Z= 0.231 Angle : 0.547 8.472 19634 Z= 0.266 Chirality : 0.043 0.161 2189 Planarity : 0.004 0.048 2525 Dihedral : 9.901 176.535 1985 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.51 % Allowed : 10.14 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1765 helix: 0.98 (0.21), residues: 731 sheet: 0.11 (0.35), residues: 276 loop : -0.01 (0.25), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1619 HIS 0.003 0.001 HIS D1667 PHE 0.017 0.001 PHE D1776 TYR 0.013 0.001 TYR B 143 ARG 0.005 0.000 ARG D1266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 294 TYR cc_start: 0.9128 (m-10) cc_final: 0.8819 (m-80) REVERT: B 325 MET cc_start: 0.8299 (mtp) cc_final: 0.7989 (ttm) REVERT: B 360 GLN cc_start: 0.8086 (tm130) cc_final: 0.7675 (tm130) REVERT: D 1211 MET cc_start: 0.8649 (mmp) cc_final: 0.8385 (mmp) REVERT: D 1319 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6780 (ppp) REVERT: D 1446 MET cc_start: 0.9049 (ppp) cc_final: 0.8565 (ppp) REVERT: D 1596 LEU cc_start: 0.9508 (mt) cc_final: 0.9046 (pp) REVERT: D 1617 MET cc_start: 0.8086 (mpp) cc_final: 0.7754 (mmp) REVERT: D 1796 MET cc_start: 0.8959 (mmp) cc_final: 0.8653 (mmp) REVERT: D 1860 MET cc_start: 0.6456 (tpt) cc_final: 0.6132 (tpt) REVERT: A 283 MET cc_start: 0.7370 (mtp) cc_final: 0.7024 (mtt) REVERT: A 325 MET cc_start: 0.8306 (mtp) cc_final: 0.7515 (mtt) REVERT: C 184 ASP cc_start: 0.8293 (m-30) cc_final: 0.8059 (m-30) outliers start: 23 outliers final: 19 residues processed: 121 average time/residue: 0.2345 time to fit residues: 45.4336 Evaluate side-chains 119 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1319 MET Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1626 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1648 GLN D1760 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14489 Z= 0.304 Angle : 0.581 7.627 19634 Z= 0.284 Chirality : 0.045 0.162 2189 Planarity : 0.004 0.047 2525 Dihedral : 9.833 179.175 1985 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.03 % Allowed : 11.78 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1765 helix: 1.04 (0.21), residues: 718 sheet: -0.02 (0.35), residues: 276 loop : -0.14 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D1619 HIS 0.004 0.001 HIS D1667 PHE 0.018 0.001 PHE D1776 TYR 0.017 0.001 TYR B 143 ARG 0.004 0.000 ARG D1266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 325 MET cc_start: 0.8389 (mtp) cc_final: 0.8189 (ttm) REVERT: B 360 GLN cc_start: 0.8133 (tm130) cc_final: 0.7698 (tm130) REVERT: D 1211 MET cc_start: 0.8684 (mmp) cc_final: 0.8417 (mmp) REVERT: D 1319 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6881 (ppp) REVERT: D 1446 MET cc_start: 0.9160 (ppp) cc_final: 0.8698 (ppp) REVERT: D 1596 LEU cc_start: 0.9543 (mt) cc_final: 0.9088 (pp) REVERT: D 1617 MET cc_start: 0.8127 (mpp) cc_final: 0.7772 (mmp) REVERT: D 1796 MET cc_start: 0.9040 (mmp) cc_final: 0.8654 (mmp) REVERT: D 1860 MET cc_start: 0.6543 (tpt) cc_final: 0.6255 (tpt) REVERT: A 283 MET cc_start: 0.7372 (mtp) cc_final: 0.7014 (mtt) REVERT: A 325 MET cc_start: 0.8430 (mtp) cc_final: 0.7624 (mtt) REVERT: C 283 MET cc_start: 0.7511 (mtp) cc_final: 0.7287 (mtt) REVERT: C 299 MET cc_start: 0.8250 (ptp) cc_final: 0.8033 (ptp) outliers start: 31 outliers final: 23 residues processed: 122 average time/residue: 0.2222 time to fit residues: 43.5747 Evaluate side-chains 122 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1278 ILE Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1319 MET Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 171 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14489 Z= 0.150 Angle : 0.523 9.117 19634 Z= 0.252 Chirality : 0.042 0.155 2189 Planarity : 0.004 0.047 2525 Dihedral : 9.593 179.928 1985 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.51 % Allowed : 13.09 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1765 helix: 0.93 (0.20), residues: 732 sheet: 0.16 (0.35), residues: 273 loop : -0.13 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1619 HIS 0.002 0.001 HIS D1667 PHE 0.020 0.001 PHE D1776 TYR 0.013 0.001 TYR B 279 ARG 0.003 0.000 ARG D1266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.931 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 360 GLN cc_start: 0.8117 (tm130) cc_final: 0.7697 (tm130) REVERT: D 1211 MET cc_start: 0.8706 (mmp) cc_final: 0.8444 (mmp) REVERT: D 1446 MET cc_start: 0.9179 (ppp) cc_final: 0.8721 (ppp) REVERT: D 1596 LEU cc_start: 0.9527 (mt) cc_final: 0.9073 (pp) REVERT: D 1617 MET cc_start: 0.8170 (mpp) cc_final: 0.7754 (mmp) REVERT: D 1796 MET cc_start: 0.9065 (mmp) cc_final: 0.8716 (mmp) REVERT: D 1860 MET cc_start: 0.6551 (tpt) cc_final: 0.6334 (tpt) REVERT: A 95 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8688 (ttm-80) REVERT: A 106 THR cc_start: 0.8927 (p) cc_final: 0.8705 (p) REVERT: A 283 MET cc_start: 0.7342 (mtp) cc_final: 0.7028 (mtt) REVERT: A 325 MET cc_start: 0.8373 (mtp) cc_final: 0.7579 (mtt) outliers start: 23 outliers final: 19 residues processed: 117 average time/residue: 0.2214 time to fit residues: 41.3492 Evaluate side-chains 119 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 144 optimal weight: 0.0470 chunk 95 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14489 Z= 0.130 Angle : 0.515 9.394 19634 Z= 0.247 Chirality : 0.042 0.150 2189 Planarity : 0.004 0.046 2525 Dihedral : 9.415 179.388 1985 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.70 % Allowed : 13.55 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1765 helix: 0.87 (0.20), residues: 754 sheet: 0.15 (0.35), residues: 273 loop : 0.06 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1619 HIS 0.002 0.000 HIS A 161 PHE 0.023 0.001 PHE D1776 TYR 0.015 0.001 TYR B 279 ARG 0.004 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 355 MET cc_start: 0.8223 (mpp) cc_final: 0.7479 (mpp) REVERT: D 1211 MET cc_start: 0.8704 (mmp) cc_final: 0.8442 (mmp) REVERT: D 1446 MET cc_start: 0.9183 (ppp) cc_final: 0.8720 (ppp) REVERT: D 1596 LEU cc_start: 0.9537 (mt) cc_final: 0.9075 (pp) REVERT: D 1617 MET cc_start: 0.8225 (mpp) cc_final: 0.7848 (mmp) REVERT: D 1796 MET cc_start: 0.9044 (mmp) cc_final: 0.8669 (mmp) REVERT: D 1860 MET cc_start: 0.6490 (tpt) cc_final: 0.6273 (tpt) REVERT: A 283 MET cc_start: 0.7379 (mtp) cc_final: 0.7048 (mtt) REVERT: A 325 MET cc_start: 0.8360 (mtp) cc_final: 0.7566 (mtt) REVERT: C 205 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: C 283 MET cc_start: 0.7391 (mtp) cc_final: 0.7151 (mtt) outliers start: 26 outliers final: 17 residues processed: 127 average time/residue: 0.2430 time to fit residues: 49.3456 Evaluate side-chains 120 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1626 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.0000 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 overall best weight: 0.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1657 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14489 Z= 0.159 Angle : 0.530 10.257 19634 Z= 0.254 Chirality : 0.042 0.148 2189 Planarity : 0.004 0.046 2525 Dihedral : 9.368 177.978 1985 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.51 % Allowed : 14.33 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1765 helix: 0.89 (0.20), residues: 758 sheet: 0.04 (0.34), residues: 273 loop : 0.17 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D1619 HIS 0.014 0.001 HIS D1657 PHE 0.025 0.001 PHE D1776 TYR 0.013 0.001 TYR B 279 ARG 0.002 0.000 ARG D1266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7610 (tm-30) REVERT: D 1211 MET cc_start: 0.8705 (mmp) cc_final: 0.8444 (mmp) REVERT: D 1286 MET cc_start: 0.9079 (mmp) cc_final: 0.8858 (mmp) REVERT: D 1319 MET cc_start: 0.7339 (ptp) cc_final: 0.6601 (ppp) REVERT: D 1446 MET cc_start: 0.9193 (ppp) cc_final: 0.8727 (ppp) REVERT: D 1596 LEU cc_start: 0.9518 (mt) cc_final: 0.9068 (pp) REVERT: D 1617 MET cc_start: 0.8227 (mpp) cc_final: 0.7880 (mmp) REVERT: D 1796 MET cc_start: 0.9070 (mmp) cc_final: 0.8679 (mmp) REVERT: D 1860 MET cc_start: 0.6406 (tpt) cc_final: 0.6147 (tpt) REVERT: A 283 MET cc_start: 0.7449 (mtp) cc_final: 0.7053 (mtt) REVERT: A 325 MET cc_start: 0.8373 (mtp) cc_final: 0.7574 (mtt) REVERT: C 205 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7793 (mp0) outliers start: 23 outliers final: 18 residues processed: 123 average time/residue: 0.2190 time to fit residues: 43.4814 Evaluate side-chains 119 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 168 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1657 HIS A 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14489 Z= 0.151 Angle : 0.539 10.804 19634 Z= 0.257 Chirality : 0.042 0.146 2189 Planarity : 0.004 0.046 2525 Dihedral : 9.324 177.027 1985 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.51 % Allowed : 14.40 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1765 helix: 0.90 (0.20), residues: 758 sheet: 0.02 (0.34), residues: 273 loop : 0.18 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D1619 HIS 0.016 0.001 HIS D1657 PHE 0.026 0.001 PHE D1776 TYR 0.018 0.001 TYR D1665 ARG 0.003 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 354 GLN cc_start: 0.8359 (pp30) cc_final: 0.7937 (pp30) REVERT: D 1211 MET cc_start: 0.8770 (mmp) cc_final: 0.8500 (mmp) REVERT: D 1286 MET cc_start: 0.9106 (mmp) cc_final: 0.8863 (mmp) REVERT: D 1319 MET cc_start: 0.7479 (ptp) cc_final: 0.7130 (ppp) REVERT: D 1446 MET cc_start: 0.9195 (ppp) cc_final: 0.8724 (ppp) REVERT: D 1596 LEU cc_start: 0.9541 (mt) cc_final: 0.9078 (pp) REVERT: D 1617 MET cc_start: 0.8221 (mpp) cc_final: 0.7886 (mmp) REVERT: D 1796 MET cc_start: 0.9066 (mmp) cc_final: 0.8671 (mmp) REVERT: D 1860 MET cc_start: 0.6648 (tpt) cc_final: 0.6386 (tpt) REVERT: A 283 MET cc_start: 0.7428 (mtp) cc_final: 0.7040 (mtt) REVERT: A 325 MET cc_start: 0.8371 (mtp) cc_final: 0.7567 (mtt) REVERT: C 205 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7780 (mp0) outliers start: 23 outliers final: 20 residues processed: 121 average time/residue: 0.2229 time to fit residues: 43.6927 Evaluate side-chains 124 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1626 ASP Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 108 optimal weight: 0.1980 chunk 86 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1657 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14489 Z= 0.182 Angle : 0.550 11.294 19634 Z= 0.264 Chirality : 0.043 0.144 2189 Planarity : 0.004 0.046 2525 Dihedral : 9.325 176.090 1985 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.64 % Allowed : 14.40 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1765 helix: 0.92 (0.20), residues: 758 sheet: 0.00 (0.34), residues: 273 loop : 0.17 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D1619 HIS 0.024 0.001 HIS D1657 PHE 0.027 0.001 PHE D1776 TYR 0.020 0.001 TYR B 294 ARG 0.002 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 1211 MET cc_start: 0.8774 (mmp) cc_final: 0.8494 (mmp) REVERT: D 1286 MET cc_start: 0.9102 (mmp) cc_final: 0.8856 (mmp) REVERT: D 1319 MET cc_start: 0.7892 (ptp) cc_final: 0.7206 (ppp) REVERT: D 1446 MET cc_start: 0.9199 (ppp) cc_final: 0.8728 (ppp) REVERT: D 1617 MET cc_start: 0.8012 (mpp) cc_final: 0.7756 (mmp) REVERT: D 1796 MET cc_start: 0.9069 (mmp) cc_final: 0.8677 (mmp) REVERT: D 1860 MET cc_start: 0.6726 (tpt) cc_final: 0.6465 (tpt) REVERT: A 132 MET cc_start: 0.8864 (tmm) cc_final: 0.8596 (ppp) REVERT: A 283 MET cc_start: 0.7393 (mtp) cc_final: 0.6993 (mtt) REVERT: A 325 MET cc_start: 0.8386 (mtp) cc_final: 0.7576 (mtt) REVERT: C 205 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7759 (mp0) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.2271 time to fit residues: 44.6712 Evaluate side-chains 124 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1626 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066280 restraints weight = 33360.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.065397 restraints weight = 22026.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066167 restraints weight = 14533.892| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14489 Z= 0.238 Angle : 0.577 11.691 19634 Z= 0.276 Chirality : 0.044 0.144 2189 Planarity : 0.004 0.046 2525 Dihedral : 9.414 174.626 1985 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.51 % Allowed : 14.59 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1765 helix: 0.78 (0.20), residues: 775 sheet: -0.07 (0.34), residues: 273 loop : 0.04 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D1619 HIS 0.004 0.001 HIS D1657 PHE 0.025 0.001 PHE D1776 TYR 0.016 0.001 TYR B 294 ARG 0.002 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.12 seconds wall clock time: 53 minutes 53.96 seconds (3233.96 seconds total)