Starting phenix.real_space_refine on Wed Mar 4 15:23:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r91_24322/03_2026/7r91_24322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r91_24322/03_2026/7r91_24322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r91_24322/03_2026/7r91_24322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r91_24322/03_2026/7r91_24322_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r91_24322/03_2026/7r91_24322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r91_24322/03_2026/7r91_24322.map" } resolution = 2.83 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= 0.004 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 94 5.16 5 C 9065 2.51 5 N 2437 2.21 5 O 2715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 14320 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2958 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 2938 Chain: "B" Number of atoms: 2958 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 2938 Chain: "C" Number of atoms: 2958 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 2938 Chain: "D" Number of atoms: 5362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5362 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 23, 'TRANS': 643} Chain breaks: 2 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: "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: "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} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AVAL A 45 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 45 " occ=0.50 residue: pdb=" N AGLY A 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 46 " occ=0.50 residue: pdb=" N AMET A 47 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AGLN A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 49 " occ=0.50 residue: pdb=" N ALYS A 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 50 " occ=0.50 residue: pdb=" N AVAL B 45 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 45 " occ=0.50 residue: pdb=" N AGLY B 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 46 " occ=0.50 residue: pdb=" N AMET B 47 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 47 " occ=0.50 residue: pdb=" N AGLY B 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 48 " occ=0.50 residue: pdb=" N AGLN B 49 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 49 " occ=0.50 residue: pdb=" N ALYS B 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 50 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 4.94, per 1000 atoms: 0.34 Number of scatterers: 14320 At special positions: 0 Unit cell: (122.57, 144.2, 139.05, 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 94 16.00 P 6 15.00 Mg 3 11.99 O 2715 8.00 N 2437 7.00 C 9065 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: 1.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 23 sheets defined 52.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.521A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.610A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.751A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix 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 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.692A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.130A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 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 355 removed outlier: 3.774A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.206A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.521A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.611A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.751A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix 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 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.692A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.130A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 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 355 removed outlier: 3.773A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.207A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.522A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.612A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.751A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix 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 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.692A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.130A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 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 355 removed outlier: 3.775A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.205A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1214 removed outlier: 3.719A pdb=" N GLN D1213 " --> pdb=" O ASP D1210 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1232 Processing helix chain 'D' and resid 1256 through 1263 Processing helix chain 'D' and resid 1274 through 1290 removed outlier: 3.687A pdb=" N ILE D1278 " --> pdb=" O HIS D1274 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1320 Processing helix chain 'D' and resid 1325 through 1333 Processing helix chain 'D' and resid 1334 through 1342 Processing helix chain 'D' and resid 1393 through 1403 removed outlier: 4.184A 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 1434 through 1449 Processing helix chain 'D' and resid 1452 through 1470 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 Processing helix chain 'D' and resid 1583 through 1615 removed outlier: 3.750A pdb=" N LEU D1599 " --> pdb=" O ASN D1595 " (cutoff:3.500A) Processing helix chain 'D' and resid 1627 through 1636 removed outlier: 3.525A pdb=" N ILE D1631 " --> pdb=" O ASN D1627 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1649 Processing helix chain 'D' and resid 1655 through 1668 Processing helix chain 'D' and resid 1708 through 1717 Processing helix chain 'D' and resid 1720 through 1734 Processing helix chain 'D' and resid 1753 through 1768 Processing helix chain 'D' and resid 1792 through 1803 Processing helix chain 'D' and resid 1805 through 1813 removed outlier: 4.058A pdb=" N VAL D1809 " --> pdb=" O VAL D1805 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D1813 " --> pdb=" O VAL D1809 " (cutoff:3.500A) Processing helix chain 'D' and resid 1821 through 1829 removed outlier: 4.109A pdb=" N PHE D1825 " --> pdb=" O PRO D1821 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D1826 " --> pdb=" O PHE D1822 " (cutoff:3.500A) Processing helix chain 'D' and resid 1830 through 1832 No H-bonds generated for 'chain 'D' and resid 1830 through 1832' Processing helix chain 'D' and resid 1843 through 1853 Processing helix chain 'D' and resid 1857 through 1861 removed outlier: 3.645A pdb=" N MET D1860 " --> pdb=" O THR D1857 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D1861 " --> pdb=" O PRO D1858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1857 through 1861' Processing helix chain 'D' and resid 1873 through 1889 removed outlier: 4.151A pdb=" N ARG D1888 " --> pdb=" O ARG D1884 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA D1889 " --> pdb=" O VAL D1885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.597A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.560A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.560A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.393A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.596A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.597A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.393A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 6.899A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER D1245 " --> pdb=" O LEU D1780 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D1293 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D1566 " --> pdb=" O LEU D1363 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D1362 " --> pdb=" O GLY D1370 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY D1370 " --> pdb=" O PHE D1362 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU D1364 " --> pdb=" O ILE D1368 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D1368 " --> pdb=" O GLU D1364 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1343 through 1344 Processing sheet with id=AC3, first strand: chain 'D' and resid 1474 through 1478 Processing sheet with id=AC4, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id=AC5, first strand: chain 'D' and resid 1673 through 1674 713 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4696 1.34 - 1.46: 2397 1.46 - 1.58: 7358 1.58 - 1.69: 9 1.69 - 1.81: 159 Bond restraints: 14619 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.410 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.410 -0.041 2.00e-02 2.50e+03 4.10e+00 ... (remaining 14614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 19368 1.49 - 2.98: 340 2.98 - 4.48: 69 4.48 - 5.97: 20 5.97 - 7.46: 11 Bond angle restraints: 19808 Sorted by residual: angle pdb=" N ILE C 64 " pdb=" CA ILE C 64 " pdb=" C ILE C 64 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 angle pdb=" N ILE B 64 " pdb=" CA ILE B 64 " pdb=" C ILE B 64 " ideal model delta sigma weight residual 113.20 109.72 3.48 9.60e-01 1.09e+00 1.31e+01 angle pdb=" N ILE A 64 " pdb=" CA ILE A 64 " pdb=" C ILE A 64 " ideal model delta sigma weight residual 113.20 109.74 3.46 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CA ARG D1322 " pdb=" CB ARG D1322 " pdb=" CG ARG D1322 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA ARG D1852 " pdb=" CB ARG D1852 " pdb=" CG ARG D1852 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.29e+00 ... (remaining 19803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 8545 28.91 - 57.82: 228 57.82 - 86.73: 46 86.73 - 115.64: 5 115.64 - 144.55: 6 Dihedral angle restraints: 8830 sinusoidal: 3585 harmonic: 5245 Sorted by residual: dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.55 -144.55 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.53 -144.53 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.48 -144.48 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 8827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1241 0.030 - 0.059: 633 0.059 - 0.089: 177 0.089 - 0.118: 136 0.118 - 0.148: 18 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA PRO D1652 " pdb=" N PRO D1652 " pdb=" C PRO D1652 " pdb=" CB PRO D1652 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE D1239 " pdb=" N ILE D1239 " pdb=" C ILE D1239 " pdb=" CB ILE D1239 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL D1559 " pdb=" N VAL D1559 " pdb=" C VAL D1559 " pdb=" CB VAL D1559 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2202 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D1651 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO D1652 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D1652 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1652 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D1628 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO D1629 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO D1629 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D1629 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 243 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.018 5.00e-02 4.00e+02 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1426 2.75 - 3.28: 13395 3.28 - 3.82: 23492 3.82 - 4.36: 28643 4.36 - 4.90: 49661 Nonbonded interactions: 116617 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.207 2.170 nonbonded pdb=" OD2 ASP A 222 " pdb=" ND2 ASN A 225 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP C 222 " pdb=" ND2 ASN C 225 " model vdw 2.212 3.120 ... (remaining 116612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 44 or resid 51 through 402)) selection = (chain 'B' and (resid 3 through 44 or resid 51 through 402)) selection = (chain 'C' and (resid 3 through 44 or resid 51 through 402)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 0.055 14619 Z= 0.155 Angle : 0.555 7.461 19808 Z= 0.293 Chirality : 0.044 0.148 2205 Planarity : 0.004 0.037 2550 Dihedral : 14.983 144.553 5460 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.19 % Allowed : 0.26 % Favored : 99.55 % 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: 0.49 (0.21), residues: 1789 helix: 1.11 (0.19), residues: 807 sheet: -0.44 (0.30), residues: 274 loop : -0.12 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1852 TYR 0.009 0.001 TYR D1574 PHE 0.010 0.001 PHE D1727 TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00339 (14619) covalent geometry : angle 0.55481 (19808) hydrogen bonds : bond 0.18759 ( 706) hydrogen bonds : angle 6.56280 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.575 Fit side-chains REVERT: B 246 GLN cc_start: 0.8888 (mt0) cc_final: 0.8687 (mt0) REVERT: B 283 MET cc_start: 0.8769 (mmm) cc_final: 0.8556 (mmp) REVERT: B 372 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7644 (ptt90) outliers start: 0 outliers final: 1 residues processed: 165 average time/residue: 0.7704 time to fit residues: 137.1265 Evaluate side-chains 102 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 115 ASN B 353 GLN C 12 ASN D1477 HIS D1590 ASN D1823 GLN D1875 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.081111 restraints weight = 28830.084| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.35 r_work: 0.2716 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14619 Z= 0.207 Angle : 0.615 6.763 19808 Z= 0.311 Chirality : 0.047 0.164 2205 Planarity : 0.005 0.047 2550 Dihedral : 10.097 160.744 2010 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 6.16 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.20), residues: 1789 helix: 0.99 (0.19), residues: 819 sheet: -0.31 (0.29), residues: 274 loop : 0.01 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D1852 TYR 0.012 0.001 TYR B 69 PHE 0.014 0.001 PHE D1825 TRP 0.017 0.002 TRP B 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00502 (14619) covalent geometry : angle 0.61452 (19808) hydrogen bonds : bond 0.04756 ( 706) hydrogen bonds : angle 4.79011 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.397 Fit side-chains REVERT: A 176 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8101 (mmt) REVERT: A 360 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8230 (tp40) REVERT: A 364 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8037 (mp0) REVERT: B 276 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: C 132 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8677 (ttt) REVERT: D 1283 PHE cc_start: 0.9583 (t80) cc_final: 0.9366 (t80) outliers start: 23 outliers final: 2 residues processed: 127 average time/residue: 0.6973 time to fit residues: 96.0152 Evaluate side-chains 109 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.077453 restraints weight = 45952.342| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.02 r_work: 0.2607 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14619 Z= 0.326 Angle : 0.686 7.919 19808 Z= 0.351 Chirality : 0.051 0.181 2205 Planarity : 0.005 0.049 2550 Dihedral : 10.012 178.952 2006 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.82 % Allowed : 7.66 % Favored : 90.53 % 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: 0.25 (0.20), residues: 1789 helix: 0.85 (0.19), residues: 812 sheet: -0.37 (0.28), residues: 291 loop : -0.26 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1250 TYR 0.016 0.002 TYR B 69 PHE 0.010 0.002 PHE B 255 TRP 0.020 0.003 TRP C 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00802 (14619) covalent geometry : angle 0.68567 (19808) hydrogen bonds : bond 0.05171 ( 706) hydrogen bonds : angle 4.68689 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.479 Fit side-chains REVERT: A 205 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8940 (mt-10) REVERT: A 360 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8334 (tp40) REVERT: A 364 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8190 (mp0) REVERT: B 276 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: B 314 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8680 (tt0) REVERT: D 1797 MET cc_start: 0.9289 (mmm) cc_final: 0.8978 (mmm) REVERT: D 1860 MET cc_start: 0.8143 (ppp) cc_final: 0.7834 (ppp) outliers start: 25 outliers final: 6 residues processed: 123 average time/residue: 0.6807 time to fit residues: 91.2891 Evaluate side-chains 108 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1517 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 353 GLN C 12 ASN D1477 HIS D1875 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.081444 restraints weight = 30738.628| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.59 r_work: 0.2712 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14619 Z= 0.134 Angle : 0.566 9.530 19808 Z= 0.283 Chirality : 0.044 0.141 2205 Planarity : 0.004 0.043 2550 Dihedral : 9.225 173.743 2006 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.36 % Allowed : 8.63 % Favored : 90.01 % 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 (0.20), residues: 1789 helix: 1.25 (0.19), residues: 789 sheet: -0.19 (0.29), residues: 289 loop : -0.14 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 312 TYR 0.010 0.001 TYR D1236 PHE 0.016 0.001 PHE D1825 TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00315 (14619) covalent geometry : angle 0.56562 (19808) hydrogen bonds : bond 0.03655 ( 706) hydrogen bonds : angle 4.43971 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.631 Fit side-chains REVERT: D 1797 MET cc_start: 0.9218 (mmm) cc_final: 0.8951 (mmm) REVERT: D 1829 TYR cc_start: 0.8446 (m-80) cc_final: 0.8093 (m-10) REVERT: D 1860 MET cc_start: 0.8201 (ppp) cc_final: 0.7852 (ppp) outliers start: 18 outliers final: 3 residues processed: 120 average time/residue: 0.7393 time to fit residues: 96.2371 Evaluate side-chains 104 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain D residue 1252 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN C 12 ASN D1477 HIS D1875 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.081163 restraints weight = 35105.258| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.51 r_work: 0.2713 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14619 Z= 0.148 Angle : 0.575 10.306 19808 Z= 0.286 Chirality : 0.044 0.141 2205 Planarity : 0.004 0.042 2550 Dihedral : 8.750 161.735 2006 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.10 % Allowed : 9.15 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1789 helix: 1.33 (0.19), residues: 792 sheet: -0.11 (0.29), residues: 289 loop : -0.08 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.009 0.001 TYR D1236 PHE 0.009 0.001 PHE C 31 TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00352 (14619) covalent geometry : angle 0.57461 (19808) hydrogen bonds : bond 0.03684 ( 706) hydrogen bonds : angle 4.38918 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: D 1705 ASP cc_start: 0.9063 (t0) cc_final: 0.8803 (t70) REVERT: D 1797 MET cc_start: 0.9267 (mmm) cc_final: 0.8973 (mmm) REVERT: D 1829 TYR cc_start: 0.8594 (m-80) cc_final: 0.8297 (m-10) REVERT: D 1860 MET cc_start: 0.8270 (ppp) cc_final: 0.7895 (ppp) outliers start: 14 outliers final: 5 residues processed: 118 average time/residue: 0.6851 time to fit residues: 87.9047 Evaluate side-chains 106 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1252 PHE Chi-restraints excluded: chain D residue 1722 VAL Chi-restraints excluded: chain D residue 1852 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 151 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 138 optimal weight: 0.0030 chunk 162 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085819 restraints weight = 29192.377| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.55 r_work: 0.2828 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14619 Z= 0.122 Angle : 0.565 10.528 19808 Z= 0.281 Chirality : 0.044 0.144 2205 Planarity : 0.004 0.042 2550 Dihedral : 7.920 135.833 2006 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.36 % Allowed : 9.47 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.20), residues: 1789 helix: 1.43 (0.19), residues: 792 sheet: -0.01 (0.29), residues: 291 loop : -0.01 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.009 0.001 TYR D1236 PHE 0.017 0.001 PHE D1825 TRP 0.012 0.001 TRP C 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00287 (14619) covalent geometry : angle 0.56514 (19808) hydrogen bonds : bond 0.03360 ( 706) hydrogen bonds : angle 4.32598 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.558 Fit side-chains REVERT: A 99 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8282 (pp20) REVERT: C 72 GLU cc_start: 0.8298 (mp0) cc_final: 0.7992 (mm-30) REVERT: C 178 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8411 (tp) REVERT: D 1705 ASP cc_start: 0.9073 (t0) cc_final: 0.8832 (t70) REVERT: D 1797 MET cc_start: 0.9267 (mmm) cc_final: 0.8978 (mmm) REVERT: D 1829 TYR cc_start: 0.8628 (m-80) cc_final: 0.8238 (m-10) REVERT: D 1860 MET cc_start: 0.8370 (ppp) cc_final: 0.8039 (ppp) outliers start: 18 outliers final: 5 residues processed: 117 average time/residue: 0.7317 time to fit residues: 93.0478 Evaluate side-chains 108 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1252 PHE Chi-restraints excluded: chain D residue 1722 VAL Chi-restraints excluded: chain D residue 1772 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 114 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 159 optimal weight: 0.0980 chunk 175 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 80 optimal weight: 0.0980 overall best weight: 0.1178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089533 restraints weight = 35752.930| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.44 r_work: 0.2871 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 14619 Z= 0.092 Angle : 0.553 11.192 19808 Z= 0.270 Chirality : 0.042 0.195 2205 Planarity : 0.004 0.038 2550 Dihedral : 7.239 111.758 2006 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.10 % Allowed : 9.86 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.21), residues: 1789 helix: 1.63 (0.20), residues: 788 sheet: 0.18 (0.30), residues: 291 loop : 0.08 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1852 TYR 0.009 0.001 TYR B 306 PHE 0.014 0.001 PHE D1283 TRP 0.010 0.001 TRP B 79 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00200 (14619) covalent geometry : angle 0.55285 (19808) hydrogen bonds : bond 0.02824 ( 706) hydrogen bonds : angle 4.24802 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.631 Fit side-chains REVERT: A 99 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: A 100 GLU cc_start: 0.9190 (pt0) cc_final: 0.8966 (pt0) REVERT: B 353 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7806 (mm110) REVERT: C 72 GLU cc_start: 0.8276 (mp0) cc_final: 0.7978 (mm-30) REVERT: C 178 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (tp) REVERT: C 364 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: D 1313 LEU cc_start: 0.9243 (mt) cc_final: 0.8991 (pp) REVERT: D 1617 MET cc_start: 0.6560 (ptm) cc_final: 0.4948 (pp-130) REVERT: D 1796 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8367 (mmm) REVERT: D 1797 MET cc_start: 0.9216 (mmm) cc_final: 0.8978 (mmm) REVERT: D 1829 TYR cc_start: 0.8644 (m-80) cc_final: 0.8293 (m-10) REVERT: D 1860 MET cc_start: 0.8377 (ppp) cc_final: 0.8050 (ppp) outliers start: 14 outliers final: 2 residues processed: 125 average time/residue: 0.6718 time to fit residues: 91.7030 Evaluate side-chains 112 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1796 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 111 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN D1477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088405 restraints weight = 24586.843| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.29 r_work: 0.2859 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14619 Z= 0.143 Angle : 0.583 10.936 19808 Z= 0.288 Chirality : 0.045 0.170 2205 Planarity : 0.004 0.041 2550 Dihedral : 7.336 112.456 2006 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.97 % Allowed : 10.58 % Favored : 88.45 % 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: 1.04 (0.21), residues: 1789 helix: 1.52 (0.19), residues: 794 sheet: 0.16 (0.30), residues: 291 loop : 0.09 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1852 TYR 0.008 0.001 TYR B 69 PHE 0.017 0.001 PHE D1825 TRP 0.012 0.002 TRP B 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00342 (14619) covalent geometry : angle 0.58304 (19808) hydrogen bonds : bond 0.03308 ( 706) hydrogen bonds : angle 4.26505 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.500 Fit side-chains REVERT: A 99 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8255 (pp20) REVERT: C 178 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 364 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: D 1278 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9173 (pp) REVERT: D 1313 LEU cc_start: 0.9230 (mt) cc_final: 0.8983 (pp) REVERT: D 1796 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8435 (mmm) REVERT: D 1860 MET cc_start: 0.8390 (ppp) cc_final: 0.8088 (ppp) REVERT: D 1873 HIS cc_start: 0.9321 (m90) cc_final: 0.9060 (m90) outliers start: 12 outliers final: 2 residues processed: 105 average time/residue: 0.6902 time to fit residues: 78.8287 Evaluate side-chains 108 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 1278 ILE Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1796 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.081820 restraints weight = 27482.953| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.08 r_work: 0.2727 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14619 Z= 0.190 Angle : 0.616 11.423 19808 Z= 0.304 Chirality : 0.046 0.175 2205 Planarity : 0.004 0.043 2550 Dihedral : 7.512 115.216 2006 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.97 % Allowed : 10.51 % Favored : 88.51 % 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: 0.89 (0.21), residues: 1789 helix: 1.41 (0.20), residues: 792 sheet: 0.09 (0.30), residues: 291 loop : 0.01 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1852 TYR 0.010 0.001 TYR B 69 PHE 0.009 0.001 PHE B 255 TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00464 (14619) covalent geometry : angle 0.61609 (19808) hydrogen bonds : bond 0.03767 ( 706) hydrogen bonds : angle 4.35114 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.592 Fit side-chains REVERT: A 99 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: A 100 GLU cc_start: 0.9166 (pt0) cc_final: 0.8901 (pt0) REVERT: C 72 GLU cc_start: 0.8328 (mp0) cc_final: 0.8049 (mm-30) REVERT: C 364 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: D 1278 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9203 (pp) REVERT: D 1313 LEU cc_start: 0.9232 (mt) cc_final: 0.8990 (pp) REVERT: D 1617 MET cc_start: 0.6524 (ptm) cc_final: 0.4988 (pp-130) REVERT: D 1860 MET cc_start: 0.8375 (ppp) cc_final: 0.8084 (ppp) REVERT: D 1873 HIS cc_start: 0.9324 (m90) cc_final: 0.9074 (m90) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 0.6816 time to fit residues: 84.6300 Evaluate side-chains 109 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 1278 ILE Chi-restraints excluded: chain D residue 1720 THR Chi-restraints excluded: chain D residue 1722 VAL Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1796 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN C 12 ASN D1477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082444 restraints weight = 25606.125| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.19 r_work: 0.2750 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14619 Z= 0.128 Angle : 0.603 12.210 19808 Z= 0.294 Chirality : 0.044 0.164 2205 Planarity : 0.004 0.041 2550 Dihedral : 7.307 111.318 2006 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.91 % Allowed : 10.84 % Favored : 88.25 % 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: 0.94 (0.20), residues: 1789 helix: 1.47 (0.19), residues: 792 sheet: -0.04 (0.31), residues: 271 loop : 0.07 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1323 TYR 0.007 0.001 TYR D1236 PHE 0.018 0.001 PHE D1825 TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00304 (14619) covalent geometry : angle 0.60324 (19808) hydrogen bonds : bond 0.03314 ( 706) hydrogen bonds : angle 4.30410 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.573 Fit side-chains REVERT: A 99 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8193 (pp20) REVERT: A 100 GLU cc_start: 0.9151 (pt0) cc_final: 0.8876 (pt0) REVERT: C 72 GLU cc_start: 0.8311 (mp0) cc_final: 0.8004 (mm-30) REVERT: C 178 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8391 (tp) REVERT: C 364 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: D 1278 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9234 (pp) REVERT: D 1313 LEU cc_start: 0.9223 (mt) cc_final: 0.8994 (pp) REVERT: D 1617 MET cc_start: 0.6469 (ptm) cc_final: 0.4503 (pp-130) REVERT: D 1860 MET cc_start: 0.8332 (ppp) cc_final: 0.8042 (ppp) REVERT: D 1873 HIS cc_start: 0.9336 (m90) cc_final: 0.9087 (m90) outliers start: 11 outliers final: 4 residues processed: 113 average time/residue: 0.6944 time to fit residues: 85.2002 Evaluate side-chains 108 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 1278 ILE Chi-restraints excluded: chain D residue 1722 VAL Chi-restraints excluded: chain D residue 1772 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 125 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082456 restraints weight = 34847.900| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.53 r_work: 0.2740 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14619 Z= 0.116 Angle : 0.584 12.221 19808 Z= 0.284 Chirality : 0.044 0.158 2205 Planarity : 0.004 0.040 2550 Dihedral : 7.154 108.616 2006 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.78 % Allowed : 10.77 % Favored : 88.45 % 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: 0.93 (0.21), residues: 1789 helix: 1.39 (0.19), residues: 810 sheet: 0.02 (0.31), residues: 271 loop : 0.09 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1323 TYR 0.007 0.001 TYR D1236 PHE 0.008 0.001 PHE B 255 TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00271 (14619) covalent geometry : angle 0.58403 (19808) hydrogen bonds : bond 0.03198 ( 706) hydrogen bonds : angle 4.26597 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.76 seconds wall clock time: 110 minutes 43.13 seconds (6643.13 seconds total)