Starting phenix.real_space_refine on Tue Dec 31 02:07:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r91_24322/12_2024/7r91_24322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r91_24322/12_2024/7r91_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r91_24322/12_2024/7r91_24322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r91_24322/12_2024/7r91_24322.map" model { file = "/net/cci-nas-00/data/ceres_data/7r91_24322/12_2024/7r91_24322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r91_24322/12_2024/7r91_24322_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 11.33, per 1000 atoms: 0.79 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: 3.88 Conformation dependent library (CDL) restraints added in 3.0 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: 2.07 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: 5.97 Time building geometry restraints manager: 4.32 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 375 or resid 401 through \ 402)) selection = (chain 'B' and (resid 3 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'C' and (resid 3 through 44 or resid 51 through 375 or resid 401 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: 14.010 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: 0.000 Extract box with map and model: 4.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.730 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 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:14.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.370 ------------------------------------------------------------------------------- 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= 0.223 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (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 TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE D1727 TYR 0.009 0.001 TYR D1574 ARG 0.007 0.000 ARG D1852 *********************** 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 : 1.709 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: 1.7635 time to fit residues: 314.7492 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 : 1.739 ------------------------------------------------------------------------------- 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 149 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14619 Z= 0.203 Angle : 0.576 6.939 19808 Z= 0.290 Chirality : 0.044 0.149 2205 Planarity : 0.004 0.047 2550 Dihedral : 9.977 152.107 2010 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.49 % Allowed : 6.23 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1789 helix: 1.16 (0.19), residues: 810 sheet: -0.21 (0.29), residues: 289 loop : 0.06 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.003 0.001 HIS C 161 PHE 0.015 0.001 PHE D1825 TYR 0.008 0.001 TYR B 69 ARG 0.006 0.000 ARG D1852 *********************** 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 135 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.668 Fit side-chains REVERT: A 360 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7312 (tp40) REVERT: B 276 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: B 351 THR cc_start: 0.9108 (p) cc_final: 0.8882 (p) REVERT: B 360 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: B 372 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7664 (ptt90) outliers start: 20 outliers final: 1 residues processed: 128 average time/residue: 1.6111 time to fit residues: 224.0998 Evaluate side-chains 107 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 360 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14619 Z= 0.411 Angle : 0.639 8.328 19808 Z= 0.324 Chirality : 0.048 0.166 2205 Planarity : 0.005 0.045 2550 Dihedral : 9.953 172.162 2006 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.88 % Allowed : 7.72 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1789 helix: 1.03 (0.19), residues: 812 sheet: -0.22 (0.28), residues: 291 loop : -0.11 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.013 0.001 PHE D1252 TYR 0.014 0.001 TYR D1236 ARG 0.006 0.000 ARG D1250 *********************** 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 131 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.610 Fit side-chains REVERT: B 276 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: C 99 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7855 (pm20) outliers start: 26 outliers final: 3 residues processed: 118 average time/residue: 1.5714 time to fit residues: 202.1569 Evaluate side-chains 104 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1541 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= 0.210 Angle : 0.561 9.377 19808 Z= 0.279 Chirality : 0.044 0.138 2205 Planarity : 0.004 0.042 2550 Dihedral : 9.682 173.644 2006 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.43 % Allowed : 8.44 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1789 helix: 1.35 (0.19), residues: 789 sheet: -0.14 (0.29), residues: 291 loop : -0.05 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.016 0.001 PHE D1825 TYR 0.010 0.001 TYR D1236 ARG 0.002 0.000 ARG C 312 *********************** 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 124 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.876 Fit side-chains REVERT: B 351 THR cc_start: 0.9146 (p) cc_final: 0.8914 (p) outliers start: 19 outliers final: 4 residues processed: 116 average time/residue: 1.5977 time to fit residues: 202.1071 Evaluate side-chains 101 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain C residue 178 LEU 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 142 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 D1477 HIS D1875 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1605 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= 0.271 Angle : 0.594 10.424 19808 Z= 0.294 Chirality : 0.045 0.144 2205 Planarity : 0.004 0.042 2550 Dihedral : 9.533 179.650 2006 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.62 % Allowed : 8.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1789 helix: 1.38 (0.19), residues: 792 sheet: -0.08 (0.29), residues: 291 loop : -0.07 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE C 31 TYR 0.010 0.001 TYR D1236 ARG 0.002 0.000 ARG B 116 *********************** 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 128 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.624 Fit side-chains revert: symmetry clash REVERT: B 276 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 314 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: B 351 THR cc_start: 0.9143 (p) cc_final: 0.8912 (p) outliers start: 22 outliers final: 6 residues processed: 120 average time/residue: 1.5537 time to fit residues: 203.3427 Evaluate side-chains 105 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN 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 57 optimal weight: 0.7980 chunk 154 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14619 Z= 0.184 Angle : 0.565 10.379 19808 Z= 0.278 Chirality : 0.043 0.138 2205 Planarity : 0.004 0.041 2550 Dihedral : 8.821 169.784 2006 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.43 % Allowed : 9.09 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1789 helix: 1.48 (0.20), residues: 791 sheet: 0.06 (0.30), residues: 291 loop : -0.02 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.016 0.001 PHE D1283 TYR 0.011 0.001 TYR D1829 ARG 0.002 0.000 ARG C 312 *********************** 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 125 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.644 Fit side-chains REVERT: B 314 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 351 THR cc_start: 0.9085 (p) cc_final: 0.8842 (p) REVERT: C 72 GLU cc_start: 0.7742 (mp0) cc_final: 0.7477 (mm-30) REVERT: C 178 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8199 (tp) REVERT: C 355 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7045 (mpp) outliers start: 19 outliers final: 5 residues processed: 118 average time/residue: 1.5442 time to fit residues: 198.8620 Evaluate side-chains 107 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 355 MET 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 165 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14619 Z= 0.219 Angle : 0.586 10.937 19808 Z= 0.288 Chirality : 0.044 0.150 2205 Planarity : 0.004 0.040 2550 Dihedral : 8.377 155.491 2006 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.23 % Allowed : 9.41 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1789 helix: 1.52 (0.19), residues: 787 sheet: 0.10 (0.30), residues: 291 loop : -0.02 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.037 0.001 PHE D1791 TYR 0.018 0.001 TYR D1829 ARG 0.004 0.000 ARG D1852 *********************** 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 116 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.571 Fit side-chains REVERT: B 314 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: B 351 THR cc_start: 0.9071 (p) cc_final: 0.8831 (p) REVERT: C 72 GLU cc_start: 0.7778 (mp0) cc_final: 0.7528 (mm-30) REVERT: C 178 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8174 (tp) REVERT: C 355 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.6991 (mpp) outliers start: 16 outliers final: 5 residues processed: 110 average time/residue: 1.5510 time to fit residues: 186.1472 Evaluate side-chains 104 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 1722 VAL Chi-restraints excluded: chain D residue 1772 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 155 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1811 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= 0.176 Angle : 0.567 10.592 19808 Z= 0.277 Chirality : 0.043 0.148 2205 Planarity : 0.004 0.041 2550 Dihedral : 7.662 127.224 2006 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.78 % Allowed : 9.86 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1789 helix: 1.59 (0.19), residues: 788 sheet: 0.14 (0.30), residues: 291 loop : 0.00 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.020 0.001 PHE D1791 TYR 0.016 0.001 TYR D1829 ARG 0.002 0.000 ARG D1852 *********************** 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 114 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.681 Fit side-chains REVERT: B 314 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 351 THR cc_start: 0.9064 (p) cc_final: 0.8811 (p) REVERT: C 72 GLU cc_start: 0.7735 (mp0) cc_final: 0.7467 (mm-30) REVERT: C 178 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8214 (tp) outliers start: 9 outliers final: 2 residues processed: 110 average time/residue: 1.7382 time to fit residues: 208.2010 Evaluate side-chains 105 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 1223 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 168 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14619 Z= 0.208 Angle : 0.599 13.796 19808 Z= 0.289 Chirality : 0.044 0.157 2205 Planarity : 0.004 0.041 2550 Dihedral : 7.453 118.672 2006 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.78 % Allowed : 10.25 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1789 helix: 1.57 (0.19), residues: 787 sheet: 0.14 (0.30), residues: 291 loop : -0.01 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE D1283 TYR 0.009 0.001 TYR D1829 ARG 0.009 0.000 ARG D1323 *********************** 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 114 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.828 Fit side-chains REVERT: B 314 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: B 351 THR cc_start: 0.9047 (p) cc_final: 0.8790 (p) REVERT: C 72 GLU cc_start: 0.7755 (mp0) cc_final: 0.7489 (mm-30) REVERT: C 178 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8189 (tp) outliers start: 9 outliers final: 4 residues processed: 110 average time/residue: 1.5817 time to fit residues: 190.2182 Evaluate side-chains 107 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 1223 LEU 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 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1477 HIS D1875 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14619 Z= 0.274 Angle : 0.625 13.738 19808 Z= 0.304 Chirality : 0.045 0.163 2205 Planarity : 0.004 0.042 2550 Dihedral : 7.467 116.087 2006 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.78 % Allowed : 10.25 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1789 helix: 1.53 (0.20), residues: 786 sheet: 0.09 (0.30), residues: 291 loop : -0.07 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.018 0.001 PHE D1825 TYR 0.009 0.001 TYR B 69 ARG 0.006 0.000 ARG D1323 ********************** 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 112 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.651 Fit side-chains REVERT: B 314 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: B 351 THR cc_start: 0.9069 (p) cc_final: 0.8814 (p) REVERT: C 72 GLU cc_start: 0.7765 (mp0) cc_final: 0.7500 (mm-30) REVERT: D 1211 MET cc_start: 0.9173 (mmm) cc_final: 0.8934 (mmt) REVERT: D 1332 LEU cc_start: 0.8693 (tp) cc_final: 0.8411 (tt) REVERT: D 1791 PHE cc_start: 0.7193 (t80) cc_final: 0.6988 (t80) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 1.6408 time to fit residues: 197.5164 Evaluate side-chains 107 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 1223 LEU 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 43 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1477 HIS D1875 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085769 restraints weight = 36612.072| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.44 r_work: 0.2817 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14619 Z= 0.285 Angle : 0.636 17.209 19808 Z= 0.309 Chirality : 0.046 0.208 2205 Planarity : 0.004 0.042 2550 Dihedral : 7.479 114.776 2006 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.78 % Allowed : 10.51 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1789 helix: 1.47 (0.19), residues: 786 sheet: -0.10 (0.31), residues: 273 loop : -0.05 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.014 0.001 PHE C 223 TYR 0.009 0.001 TYR B 69 ARG 0.004 0.000 ARG D1323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.98 seconds wall clock time: 85 minutes 56.95 seconds (5156.95 seconds total)