Starting phenix.real_space_refine on Wed Mar 4 15:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rb9_24400/03_2026/7rb9_24400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rb9_24400/03_2026/7rb9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rb9_24400/03_2026/7rb9_24400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rb9_24400/03_2026/7rb9_24400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rb9_24400/03_2026/7rb9_24400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rb9_24400/03_2026/7rb9_24400.map" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.83, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 559.3 milliseconds 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... Secondary structure from input PDB file: 96 helices and 22 sheets defined 52.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.946A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 61' Processing helix chain 'B' and resid 79 through 95 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 97 through 101 removed outlier: 3.657A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.857A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.653A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.939A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.673A pdb=" N ARG B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) 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 222 through 231 removed outlier: 3.713A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.508A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.560A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.726A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.507A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.712A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.503A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'D' and resid 1218 through 1230 Processing helix chain 'D' and resid 1231 through 1233 No H-bonds generated for 'chain 'D' and resid 1231 through 1233' Processing helix chain 'D' and resid 1256 through 1262 removed outlier: 4.117A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D1261 " --> pdb=" O PRO D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1266 through 1271 removed outlier: 4.161A pdb=" N GLU D1270 " --> pdb=" O ARG D1266 " (cutoff:3.500A) Processing helix chain 'D' and resid 1274 through 1290 removed outlier: 4.223A pdb=" N ILE D1278 " --> pdb=" O HIS D1274 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA D1279 " --> pdb=" O LEU D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1319 Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 4.353A pdb=" N ASP D1324 " --> pdb=" O GLN D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1334 removed outlier: 3.651A pdb=" N ILE D1331 " --> pdb=" O GLN D1327 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D1332 " --> pdb=" O GLN D1328 " (cutoff:3.500A) Processing helix chain 'D' and resid 1335 through 1342 removed outlier: 3.713A pdb=" N GLU D1339 " --> pdb=" O THR D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1384 Processing helix chain 'D' and resid 1393 through 1403 removed outlier: 4.183A pdb=" N TYR D1397 " --> pdb=" O TYR D1393 " (cutoff:3.500A) Processing helix chain 'D' and resid 1404 through 1412 Processing helix chain 'D' and resid 1428 through 1433 removed outlier: 3.586A pdb=" N GLY D1432 " --> pdb=" O GLU D1429 " (cutoff:3.500A) Processing helix chain 'D' and resid 1434 through 1449 Processing helix chain 'D' and resid 1452 through 1470 removed outlier: 3.954A pdb=" N GLY D1470 " --> pdb=" O ILE D1466 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1501 Processing helix chain 'D' and resid 1503 through 1512 Processing helix chain 'D' and resid 1528 through 1559 removed outlier: 3.642A pdb=" N ALA D1540 " --> pdb=" O ARG D1536 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D1559 " --> pdb=" O VAL D1555 " (cutoff:3.500A) Processing helix chain 'D' and resid 1583 through 1616 Processing helix chain 'D' and resid 1617 through 1620 removed outlier: 3.993A pdb=" N ARG D1620 " --> pdb=" O MET D1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1617 through 1620' Processing helix chain 'D' and resid 1627 through 1636 removed outlier: 3.606A pdb=" N ILE D1631 " --> pdb=" O ASN D1627 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE D1634 " --> pdb=" O CYS D1630 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1650 removed outlier: 4.011A pdb=" N CYS D1650 " --> pdb=" O ASP D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1655 through 1668 removed outlier: 3.595A pdb=" N PHE D1659 " --> pdb=" O THR D1655 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D1660 " --> pdb=" O ASP D1656 " (cutoff:3.500A) Processing helix chain 'D' and resid 1698 through 1703 Processing helix chain 'D' and resid 1708 through 1716 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) Processing helix chain 'D' and resid 1720 through 1734 Processing helix chain 'D' and resid 1753 through 1770 Processing helix chain 'D' and resid 1792 through 1804 Processing helix chain 'D' and resid 1805 through 1813 removed outlier: 4.287A pdb=" N VAL D1809 " --> pdb=" O VAL D1805 " (cutoff:3.500A) Processing helix chain 'D' and resid 1821 through 1829 removed outlier: 4.277A pdb=" N PHE D1825 " --> pdb=" O PRO D1821 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D1829 " --> pdb=" O PHE D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1843 through 1855 removed outlier: 4.445A pdb=" N VAL D1847 " --> pdb=" O GLY D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1857 through 1861 Processing helix chain 'D' and resid 1873 through 1887 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) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.946A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 95 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 97 through 101 removed outlier: 3.656A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.857A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.652A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.939A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.673A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) 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 222 through 231 removed outlier: 3.713A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.509A pdb=" N ARG A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.560A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.726A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.508A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.713A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.504A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.947A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 79 through 95 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 97 through 101 removed outlier: 3.657A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.857A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.652A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.939A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.672A pdb=" N ARG C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) 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 222 through 231 removed outlier: 3.712A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.508A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.560A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.726A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.508A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.712A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.503A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.543A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.505A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.513A pdb=" N GLU B 72 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 5.440A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.089A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'D' and resid 1237 through 1238 removed outlier: 3.808A pdb=" N THR D1237 " --> pdb=" O VAL D1244 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D1244 " --> pdb=" O THR D1237 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER D1245 " --> pdb=" O LEU D1780 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS D1294 " --> pdb=" O LEU D1775 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL D1777 " --> pdb=" O CYS D1294 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D1296 " --> pdb=" O VAL D1777 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS D1779 " --> pdb=" O ILE D1296 " (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) removed outlier: 6.258A pdb=" N GLY D1356 " --> pdb=" O TYR D1376 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY D1370 " --> pdb=" O PHE D1362 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU D1364 " --> pdb=" O ILE D1368 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE D1368 " --> pdb=" O GLU D1364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1343 through 1344 removed outlier: 3.611A pdb=" N SER D1352 " --> pdb=" O ALA D1344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id=AB1, first strand: chain 'D' and resid 1673 through 1674 Processing sheet with id=AB2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.544A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.504A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.513A pdb=" N GLU A 72 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.439A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.544A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.504A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.513A pdb=" N GLU C 72 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.440A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 645 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.52 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: 0.00 - 1.64: 19188 1.64 - 3.29: 365 3.29 - 4.93: 56 4.93 - 6.58: 21 6.58 - 8.22: 4 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: 2315 2.76 - 3.30: 13618 3.30 - 3.83: 22778 3.83 - 4.37: 26698 4.37 - 4.90: 46113 Nonbonded interactions: 111522 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 3.040 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 177 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.279 3.120 ... (remaining 111517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 8.980 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- 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= 0.132 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (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 ARG 0.003 0.000 ARG D1620 TYR 0.015 0.001 TYR D1473 PHE 0.013 0.001 PHE D1230 TRP 0.013 0.001 TRP D1550 HIS 0.002 0.000 HIS D1666 Details of bonding type rmsd covalent geometry : bond 0.00256 (14489) covalent geometry : angle 0.57394 (19634) hydrogen bonds : bond 0.18190 ( 637) hydrogen bonds : angle 6.84600 ( 1737) *********************** 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 to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.555 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: 0.1162 time to fit residues: 38.9625 Evaluate side-chains 111 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 49 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN D1225 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 ASN D1697 HIS D1784 HIS ** D1823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1873 HIS A 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.061225 restraints weight = 33551.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.063385 restraints weight = 16485.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.064813 restraints weight = 10093.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.065701 restraints weight = 7245.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066292 restraints weight = 5851.367| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 14489 Z= 0.297 Angle : 0.695 6.610 19634 Z= 0.351 Chirality : 0.048 0.188 2189 Planarity : 0.005 0.047 2525 Dihedral : 10.506 165.985 1985 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.24 % Allowed : 7.46 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1765 helix: 0.94 (0.20), residues: 728 sheet: 0.03 (0.33), residues: 284 loop : -0.12 (0.25), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 335 TYR 0.015 0.002 TYR D1665 PHE 0.014 0.001 PHE D1699 TRP 0.017 0.002 TRP D1619 HIS 0.005 0.001 HIS D1784 Details of bonding type rmsd covalent geometry : bond 0.00688 (14489) covalent geometry : angle 0.69497 (19634) hydrogen bonds : bond 0.04391 ( 637) hydrogen bonds : angle 5.37295 ( 1737) *********************** 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 132 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 325 MET cc_start: 0.8269 (mtp) cc_final: 0.7994 (ttm) REVERT: D 1211 MET cc_start: 0.8525 (mmp) cc_final: 0.8322 (mmp) REVERT: D 1326 MET cc_start: 0.9044 (tpp) cc_final: 0.8759 (tmm) REVERT: D 1446 MET cc_start: 0.8801 (ppp) cc_final: 0.8401 (ppp) REVERT: D 1617 MET cc_start: 0.7779 (mpp) cc_final: 0.7465 (mmp) REVERT: D 1796 MET cc_start: 0.8789 (mmp) cc_final: 0.8580 (mmp) REVERT: A 95 ARG cc_start: 0.8889 (mtt90) cc_final: 0.8656 (mtt-85) REVERT: A 283 MET cc_start: 0.7357 (mtt) cc_final: 0.7035 (mtt) REVERT: A 325 MET cc_start: 0.8244 (mtp) cc_final: 0.7425 (mtt) REVERT: A 334 GLU cc_start: 0.7977 (pm20) cc_final: 0.7743 (pm20) REVERT: C 106 THR cc_start: 0.8917 (p) cc_final: 0.8715 (p) REVERT: C 184 ASP cc_start: 0.8381 (m-30) cc_final: 0.8146 (m-30) outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 0.1152 time to fit residues: 22.0435 Evaluate side-chains 116 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 1560 SER Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 324 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 297 ASN D1225 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1501 GLN D1597 GLN D1823 GLN A 92 ASN C 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066767 restraints weight = 33080.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.067121 restraints weight = 18447.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067542 restraints weight = 12546.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.067993 restraints weight = 10143.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.068162 restraints weight = 8720.742| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14489 Z= 0.131 Angle : 0.566 6.965 19634 Z= 0.282 Chirality : 0.044 0.141 2189 Planarity : 0.004 0.049 2525 Dihedral : 10.252 175.834 1985 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.18 % Allowed : 9.29 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1765 helix: 1.01 (0.20), residues: 735 sheet: 0.07 (0.33), residues: 284 loop : -0.06 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 335 TYR 0.014 0.001 TYR D1665 PHE 0.012 0.001 PHE D1230 TRP 0.014 0.002 TRP D1619 HIS 0.003 0.001 HIS D1687 Details of bonding type rmsd covalent geometry : bond 0.00300 (14489) covalent geometry : angle 0.56623 (19634) hydrogen bonds : bond 0.03435 ( 637) hydrogen bonds : angle 5.07021 ( 1737) *********************** 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 127 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.527 Fit side-chains REVERT: B 121 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 294 TYR cc_start: 0.9178 (m-10) cc_final: 0.8880 (m-80) REVERT: B 325 MET cc_start: 0.8348 (mtp) cc_final: 0.8018 (ttm) REVERT: D 1326 MET cc_start: 0.9212 (tpp) cc_final: 0.8948 (tmm) REVERT: D 1446 MET cc_start: 0.8986 (ppp) cc_final: 0.8518 (ppp) REVERT: D 1596 LEU cc_start: 0.9506 (mt) cc_final: 0.9060 (pp) REVERT: D 1860 MET cc_start: 0.6477 (tpt) cc_final: 0.6164 (tpt) REVERT: A 283 MET cc_start: 0.7354 (mtt) cc_final: 0.7061 (mtt) REVERT: A 305 MET cc_start: 0.8484 (mtt) cc_final: 0.8241 (mtt) REVERT: A 325 MET cc_start: 0.8200 (mtp) cc_final: 0.7433 (mtt) outliers start: 18 outliers final: 12 residues processed: 122 average time/residue: 0.1024 time to fit residues: 19.6801 Evaluate side-chains 113 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 115 ASN 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 12 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1343 ASN D1648 GLN A 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.100465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065920 restraints weight = 33292.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066574 restraints weight = 17864.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067534 restraints weight = 10916.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067716 restraints weight = 8785.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.067892 restraints weight = 8351.043| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2292 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= 0.121 Angle : 0.553 8.166 19634 Z= 0.272 Chirality : 0.043 0.141 2189 Planarity : 0.004 0.043 2525 Dihedral : 9.901 175.097 1985 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.18 % Allowed : 10.86 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1765 helix: 1.12 (0.20), residues: 735 sheet: 0.11 (0.33), residues: 284 loop : -0.00 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 335 TYR 0.014 0.001 TYR B 279 PHE 0.011 0.001 PHE D1230 TRP 0.017 0.001 TRP D1619 HIS 0.002 0.001 HIS D1667 Details of bonding type rmsd covalent geometry : bond 0.00279 (14489) covalent geometry : angle 0.55320 (19634) hydrogen bonds : bond 0.03062 ( 637) hydrogen bonds : angle 4.88483 ( 1737) *********************** 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 122 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.500 Fit side-chains REVERT: B 121 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 246 GLN cc_start: 0.8511 (pt0) cc_final: 0.8139 (pm20) REVERT: B 294 TYR cc_start: 0.9114 (m-10) cc_final: 0.8742 (m-80) REVERT: B 325 MET cc_start: 0.8334 (mtp) cc_final: 0.8003 (ttm) REVERT: D 1319 MET cc_start: 0.7758 (ptp) cc_final: 0.7024 (ppp) REVERT: D 1326 MET cc_start: 0.9298 (tpp) cc_final: 0.9066 (tmm) REVERT: D 1446 MET cc_start: 0.9111 (ppp) cc_final: 0.8615 (ppp) REVERT: D 1596 LEU cc_start: 0.9510 (mt) cc_final: 0.9089 (pp) REVERT: D 1796 MET cc_start: 0.8731 (mmp) cc_final: 0.8343 (mmp) REVERT: D 1860 MET cc_start: 0.6459 (tpt) cc_final: 0.6245 (tpt) REVERT: A 325 MET cc_start: 0.8211 (mtp) cc_final: 0.7460 (mtt) REVERT: C 184 ASP cc_start: 0.8289 (m-30) cc_final: 0.8019 (m-30) outliers start: 18 outliers final: 13 residues processed: 115 average time/residue: 0.0981 time to fit residues: 18.1340 Evaluate side-chains 113 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET 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 1560 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU 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 70 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 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 12 ASN B 360 GLN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1760 GLN A 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.065612 restraints weight = 33448.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.064967 restraints weight = 20665.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.065616 restraints weight = 14120.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.066076 restraints weight = 10491.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.066233 restraints weight = 9134.082| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14489 Z= 0.198 Angle : 0.584 7.474 19634 Z= 0.288 Chirality : 0.045 0.161 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.852 178.524 1985 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.70 % Allowed : 11.85 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1765 helix: 1.15 (0.20), residues: 734 sheet: 0.13 (0.33), residues: 281 loop : -0.06 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1721 TYR 0.014 0.001 TYR B 279 PHE 0.011 0.001 PHE D1699 TRP 0.017 0.002 TRP D1619 HIS 0.004 0.001 HIS D1667 Details of bonding type rmsd covalent geometry : bond 0.00461 (14489) covalent geometry : angle 0.58412 (19634) hydrogen bonds : bond 0.03287 ( 637) hydrogen bonds : angle 4.85012 ( 1737) *********************** 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 127 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.488 Fit side-chains REVERT: B 121 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 325 MET cc_start: 0.8409 (mtp) cc_final: 0.8176 (ttm) REVERT: D 1326 MET cc_start: 0.9352 (tpp) cc_final: 0.9119 (tmm) REVERT: D 1446 MET cc_start: 0.9156 (ppp) cc_final: 0.8726 (ppp) REVERT: D 1596 LEU cc_start: 0.9526 (mt) cc_final: 0.9115 (pp) REVERT: D 1796 MET cc_start: 0.8848 (mmp) cc_final: 0.8434 (mmp) REVERT: A 325 MET cc_start: 0.8329 (mtp) cc_final: 0.7591 (mtt) REVERT: C 305 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8140 (mtt) outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 0.0900 time to fit residues: 17.2907 Evaluate side-chains 117 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR 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 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 305 MET 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 161 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** D1394 HIS D1468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.059980 restraints weight = 34036.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062123 restraints weight = 16615.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.063517 restraints weight = 10078.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064437 restraints weight = 7185.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.064960 restraints weight = 5795.826| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 14489 Z= 0.283 Angle : 0.666 8.821 19634 Z= 0.331 Chirality : 0.047 0.190 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.987 177.767 1985 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.57 % Allowed : 13.22 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1765 helix: 1.08 (0.20), residues: 740 sheet: -0.05 (0.33), residues: 281 loop : -0.23 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.016 0.002 TYR B 143 PHE 0.018 0.001 PHE D1699 TRP 0.029 0.002 TRP D1619 HIS 0.006 0.001 HIS D1667 Details of bonding type rmsd covalent geometry : bond 0.00655 (14489) covalent geometry : angle 0.66562 (19634) hydrogen bonds : bond 0.03704 ( 637) hydrogen bonds : angle 4.97626 ( 1737) *********************** 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 120 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.550 Fit side-chains REVERT: B 121 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8486 (tm-30) REVERT: B 325 MET cc_start: 0.8418 (mtp) cc_final: 0.8171 (ttm) REVERT: D 1446 MET cc_start: 0.9191 (ppp) cc_final: 0.8797 (ppp) REVERT: D 1796 MET cc_start: 0.8863 (mmp) cc_final: 0.8442 (mmp) REVERT: A 283 MET cc_start: 0.7255 (mtt) cc_final: 0.7035 (mtt) REVERT: A 325 MET cc_start: 0.8365 (mtp) cc_final: 0.7645 (mtt) outliers start: 24 outliers final: 20 residues processed: 110 average time/residue: 0.0836 time to fit residues: 15.5121 Evaluate side-chains 115 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR 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 345 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 305 MET 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 47 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 1 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1271 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.099931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.063159 restraints weight = 33043.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065441 restraints weight = 15853.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.066963 restraints weight = 9472.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.067924 restraints weight = 6689.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.068420 restraints weight = 5337.471| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14489 Z= 0.101 Angle : 0.557 9.440 19634 Z= 0.274 Chirality : 0.043 0.147 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.599 175.854 1985 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.92 % Allowed : 14.79 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1765 helix: 1.28 (0.21), residues: 716 sheet: 0.15 (0.33), residues: 279 loop : 0.06 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1721 TYR 0.014 0.001 TYR C 279 PHE 0.013 0.001 PHE D1727 TRP 0.031 0.002 TRP D1619 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00225 (14489) covalent geometry : angle 0.55698 (19634) hydrogen bonds : bond 0.02916 ( 637) hydrogen bonds : angle 4.72810 ( 1737) *********************** 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 125 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 132 MET cc_start: 0.8845 (tmm) cc_final: 0.8622 (tmm) REVERT: D 1446 MET cc_start: 0.9173 (ppp) cc_final: 0.8727 (ppp) REVERT: D 1796 MET cc_start: 0.8877 (mmp) cc_final: 0.8481 (mmp) REVERT: A 325 MET cc_start: 0.8358 (mtp) cc_final: 0.7599 (mtt) outliers start: 14 outliers final: 13 residues processed: 118 average time/residue: 0.1004 time to fit residues: 18.9494 Evaluate side-chains 116 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1770 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE 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 49 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.064053 restraints weight = 33381.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.064085 restraints weight = 19978.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.064426 restraints weight = 13206.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.064940 restraints weight = 10693.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.065160 restraints weight = 9504.438| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14489 Z= 0.199 Angle : 0.610 8.714 19634 Z= 0.299 Chirality : 0.045 0.163 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.676 173.902 1985 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.51 % Allowed : 14.92 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1765 helix: 1.31 (0.21), residues: 716 sheet: 0.05 (0.33), residues: 281 loop : 0.00 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1721 TYR 0.013 0.001 TYR B 279 PHE 0.011 0.001 PHE A 255 TRP 0.031 0.002 TRP D1619 HIS 0.004 0.001 HIS D1667 Details of bonding type rmsd covalent geometry : bond 0.00461 (14489) covalent geometry : angle 0.60999 (19634) hydrogen bonds : bond 0.03239 ( 637) hydrogen bonds : angle 4.76026 ( 1737) *********************** 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 123 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8364 (tm-30) REVERT: B 313 MET cc_start: 0.8906 (ttm) cc_final: 0.8334 (ttt) REVERT: D 1319 MET cc_start: 0.7776 (ptp) cc_final: 0.7307 (ppp) REVERT: D 1446 MET cc_start: 0.9226 (ppp) cc_final: 0.8812 (ppp) REVERT: D 1796 MET cc_start: 0.8858 (mmp) cc_final: 0.8446 (mmp) REVERT: A 325 MET cc_start: 0.8447 (mtp) cc_final: 0.7753 (mtt) outliers start: 23 outliers final: 19 residues processed: 112 average time/residue: 0.0904 time to fit residues: 16.7294 Evaluate side-chains 114 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 123 MET 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 1560 SER Chi-restraints excluded: chain D residue 1770 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE 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 111 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1632 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.063244 restraints weight = 33152.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065455 restraints weight = 15971.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.066900 restraints weight = 9579.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.067808 restraints weight = 6776.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.068416 restraints weight = 5432.760| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14489 Z= 0.110 Angle : 0.567 10.562 19634 Z= 0.276 Chirality : 0.043 0.138 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.504 172.579 1985 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.05 % Allowed : 15.31 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1765 helix: 1.31 (0.21), residues: 716 sheet: 0.14 (0.33), residues: 279 loop : 0.14 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1721 TYR 0.013 0.001 TYR B 279 PHE 0.013 0.001 PHE D1727 TRP 0.033 0.002 TRP D1619 HIS 0.002 0.001 HIS D1667 Details of bonding type rmsd covalent geometry : bond 0.00249 (14489) covalent geometry : angle 0.56666 (19634) hydrogen bonds : bond 0.02890 ( 637) hydrogen bonds : angle 4.64275 ( 1737) *********************** 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 120 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 132 MET cc_start: 0.8847 (tmm) cc_final: 0.8601 (tmm) REVERT: B 313 MET cc_start: 0.8881 (ttm) cc_final: 0.8332 (ttt) REVERT: D 1286 MET cc_start: 0.8827 (mmp) cc_final: 0.8531 (mmt) REVERT: D 1446 MET cc_start: 0.9177 (ppp) cc_final: 0.8733 (ppp) REVERT: D 1796 MET cc_start: 0.8812 (mmp) cc_final: 0.8405 (mmp) REVERT: A 283 MET cc_start: 0.7182 (mtt) cc_final: 0.6969 (mtt) REVERT: A 325 MET cc_start: 0.8412 (mtp) cc_final: 0.7732 (mtt) outliers start: 16 outliers final: 15 residues processed: 112 average time/residue: 0.0850 time to fit residues: 15.8219 Evaluate side-chains 115 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1516 THR Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1770 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE 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 136 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062047 restraints weight = 33546.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064242 restraints weight = 16291.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.065684 restraints weight = 9814.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066610 restraints weight = 6967.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.067126 restraints weight = 5594.012| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14489 Z= 0.150 Angle : 0.587 9.737 19634 Z= 0.285 Chirality : 0.044 0.229 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.502 169.921 1985 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.11 % Allowed : 15.38 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1765 helix: 1.32 (0.21), residues: 716 sheet: 0.10 (0.33), residues: 279 loop : 0.11 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1721 TYR 0.013 0.001 TYR B 279 PHE 0.012 0.001 PHE D1727 TRP 0.040 0.002 TRP D1619 HIS 0.003 0.001 HIS D1667 Details of bonding type rmsd covalent geometry : bond 0.00349 (14489) covalent geometry : angle 0.58678 (19634) hydrogen bonds : bond 0.03013 ( 637) hydrogen bonds : angle 4.66596 ( 1737) ********************** 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 116 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 313 MET cc_start: 0.8864 (ttm) cc_final: 0.8301 (ttt) REVERT: D 1286 MET cc_start: 0.8900 (mmp) cc_final: 0.8620 (mmt) REVERT: D 1319 MET cc_start: 0.7709 (ptp) cc_final: 0.7318 (ppp) REVERT: D 1446 MET cc_start: 0.9204 (ppp) cc_final: 0.8788 (ppp) REVERT: D 1796 MET cc_start: 0.8828 (mmp) cc_final: 0.8414 (mmp) REVERT: A 325 MET cc_start: 0.8422 (mtp) cc_final: 0.7749 (mtt) outliers start: 17 outliers final: 16 residues processed: 108 average time/residue: 0.0975 time to fit residues: 17.0266 Evaluate side-chains 114 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1516 THR Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1770 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE 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 82 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 84 optimal weight: 0.0040 chunk 104 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.064518 restraints weight = 33474.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064927 restraints weight = 18332.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.066080 restraints weight = 11367.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.066643 restraints weight = 8506.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.066741 restraints weight = 8011.775| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14489 Z= 0.147 Angle : 0.584 8.428 19634 Z= 0.284 Chirality : 0.044 0.215 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.453 167.339 1985 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.24 % Allowed : 15.38 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1765 helix: 1.33 (0.21), residues: 716 sheet: 0.10 (0.33), residues: 279 loop : 0.11 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 335 TYR 0.013 0.001 TYR B 279 PHE 0.013 0.001 PHE D1727 TRP 0.039 0.002 TRP D1619 HIS 0.004 0.001 HIS D1725 Details of bonding type rmsd covalent geometry : bond 0.00340 (14489) covalent geometry : angle 0.58391 (19634) hydrogen bonds : bond 0.02973 ( 637) hydrogen bonds : angle 4.64604 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.65 seconds wall clock time: 39 minutes 11.73 seconds (2351.73 seconds total)