Starting phenix.real_space_refine on Thu Sep 18 11:02:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7udt_26459/09_2025/7udt_26459.cif Found real_map, /net/cci-nas-00/data/ceres_data/7udt_26459/09_2025/7udt_26459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7udt_26459/09_2025/7udt_26459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7udt_26459/09_2025/7udt_26459.map" model { file = "/net/cci-nas-00/data/ceres_data/7udt_26459/09_2025/7udt_26459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7udt_26459/09_2025/7udt_26459.cif" } resolution = 3.17 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= 0.003 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 103 5.16 5 C 10009 2.51 5 N 2690 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15806 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1187 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} 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: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5661 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 23, 'TRANS': 677} 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: 4.52, per 1000 atoms: 0.29 Number of scatterers: 15806 At special positions: 0 Unit cell: (114.33, 166.86, 166.86, 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 103 16.00 P 6 15.00 Mg 3 11.99 O 2995 8.00 N 2690 7.00 C 10009 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: 1.30 Conformation dependent library (CDL) restraints added in 849.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3708 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 24 sheets defined 53.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'G' and resid 27 through 42 removed outlier: 4.484A pdb=" N GLN G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU G 33 " --> pdb=" O SER G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 59 removed outlier: 4.530A pdb=" N LEU G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 99 through 110 removed outlier: 3.939A pdb=" N PHE G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 135 through 144 Processing helix chain 'G' and resid 156 through 166 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: 3.609A 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: 3.752A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.775A 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: 4.207A 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: 3.752A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.693A 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: 3.523A 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: 3.972A 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: 3.751A pdb=" N LEU D1599 " --> pdb=" O ASN D1595 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU D1615 " --> pdb=" O GLU D1611 " (cutoff:3.500A) Processing helix chain 'D' and resid 1627 through 1636 removed outlier: 3.524A 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 1822 through 1829 removed outlier: 3.828A pdb=" N TYR D1829 " --> pdb=" O PHE D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1846 through 1855 removed outlier: 3.528A pdb=" N LEU D1850 " --> pdb=" O CYS D1846 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D1855 " --> pdb=" O SER D1851 " (cutoff:3.500A) Processing helix chain 'D' and resid 1871 through 1910 Processing helix chain 'D' and resid 1913 through 1922 Processing sheet with id=AA1, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AA2, 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: 8.425A 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: 7.884A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.561A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.561A 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=AA6, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA8, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.392A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB1, 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: 7.882A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB5, 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=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.392A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC2, 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: 3.570A 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: 5.820A pdb=" N ILE D1368 " --> pdb=" O GLU D1364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1343 through 1344 Processing sheet with id=AC4, first strand: chain 'D' and resid 1474 through 1478 Processing sheet with id=AC5, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id=AC6, first strand: chain 'D' and resid 1673 through 1674 792 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2938 1.33 - 1.45: 3975 1.45 - 1.57: 9037 1.57 - 1.69: 9 1.69 - 1.81: 176 Bond restraints: 16135 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 7.65e+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 7.50e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" N GLU G 92 " pdb=" CA GLU G 92 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.25e-02 6.40e+03 5.46e+00 bond pdb=" C ASP D1618 " pdb=" O ASP D1618 " ideal model delta sigma weight residual 1.232 1.203 0.029 1.37e-02 5.33e+03 4.40e+00 ... (remaining 16130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21523 2.07 - 4.13: 277 4.13 - 6.20: 26 6.20 - 8.26: 14 8.26 - 10.33: 3 Bond angle restraints: 21843 Sorted by residual: angle pdb=" N GLU G 92 " pdb=" CA GLU G 92 " pdb=" C GLU G 92 " ideal model delta sigma weight residual 112.93 123.25 -10.32 1.33e+00 5.65e-01 6.03e+01 angle pdb=" C VAL D1833 " pdb=" N ALA D1834 " pdb=" CA ALA D1834 " ideal model delta sigma weight residual 122.93 133.26 -10.33 1.51e+00 4.39e-01 4.68e+01 angle pdb=" N LYS G 93 " pdb=" CA LYS G 93 " pdb=" C LYS G 93 " ideal model delta sigma weight residual 110.80 119.47 -8.67 2.13e+00 2.20e-01 1.66e+01 angle pdb=" C GLU G 92 " pdb=" CA GLU G 92 " pdb=" CB GLU G 92 " ideal model delta sigma weight residual 110.08 104.13 5.95 1.57e+00 4.06e-01 1.44e+01 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 ... (remaining 21838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 9425 28.91 - 57.83: 259 57.83 - 86.74: 47 86.74 - 115.65: 6 115.65 - 144.56: 6 Dihedral angle restraints: 9743 sinusoidal: 3976 harmonic: 5767 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 84.56 -144.56 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 84.56 -144.56 1 2.00e+01 2.50e-03 4.36e+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 84.49 -144.50 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 9740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2170 0.071 - 0.143: 243 0.143 - 0.214: 1 0.214 - 0.285: 0 0.285 - 0.356: 2 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CA LEU D1837 " pdb=" N LEU D1837 " pdb=" C LEU D1837 " pdb=" CB LEU D1837 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LYS G 93 " pdb=" N LYS G 93 " pdb=" C LYS G 93 " pdb=" CB LYS G 93 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 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 5.67e-01 ... (remaining 2413 not shown) Planarity restraints: 2823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D1612 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C TYR D1612 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR D1612 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE D1613 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1884 " 0.097 9.50e-02 1.11e+02 4.47e-02 2.42e+00 pdb=" NE ARG D1884 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D1884 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D1884 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D1884 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D1651 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+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 " -0.020 5.00e-02 4.00e+02 ... (remaining 2820 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1612 2.75 - 3.28: 15096 3.28 - 3.82: 25964 3.82 - 4.36: 31389 4.36 - 4.90: 54102 Nonbonded interactions: 128163 Sorted by model distance: nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.208 2.170 nonbonded pdb=" OD2 ASP C 222 " pdb=" ND2 ASN C 225 " model vdw 2.211 3.120 nonbonded pdb=" OD2 ASP A 222 " pdb=" ND2 ASN A 225 " model vdw 2.212 3.120 ... (remaining 128158 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: 13.320 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.440 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 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 16135 Z= 0.161 Angle : 0.594 10.331 21843 Z= 0.321 Chirality : 0.044 0.356 2416 Planarity : 0.004 0.046 2823 Dihedral : 14.888 144.565 6035 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.24 % Allowed : 0.41 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1967 helix: 1.13 (0.18), residues: 912 sheet: -0.44 (0.30), residues: 274 loop : -0.41 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D1884 TYR 0.012 0.001 TYR D1896 PHE 0.021 0.001 PHE D1822 TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00342 (16135) covalent geometry : angle 0.59355 (21843) hydrogen bonds : bond 0.18249 ( 785) hydrogen bonds : angle 6.51484 ( 2145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7609 (mttm) cc_final: 0.7189 (mmtm) REVERT: A 82 MET cc_start: 0.8060 (tpt) cc_final: 0.7698 (tpp) REVERT: A 246 GLN cc_start: 0.7096 (mt0) cc_final: 0.6590 (mt0) REVERT: A 355 MET cc_start: 0.7970 (mtt) cc_final: 0.7543 (mtt) REVERT: A 360 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8501 (mp10) REVERT: B 68 LYS cc_start: 0.7514 (mttm) cc_final: 0.6622 (mtmm) REVERT: B 95 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.6692 (mmt180) REVERT: B 211 ASP cc_start: 0.6957 (t0) cc_final: 0.6659 (t0) REVERT: B 286 ASP cc_start: 0.7540 (m-30) cc_final: 0.7295 (m-30) REVERT: B 314 GLN cc_start: 0.6672 (tt0) cc_final: 0.6390 (mt0) REVERT: B 328 LYS cc_start: 0.6802 (mttp) cc_final: 0.6500 (ttmt) REVERT: C 118 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6612 (mtpt) REVERT: C 244 ASP cc_start: 0.7889 (p0) cc_final: 0.7677 (m-30) REVERT: C 269 MET cc_start: 0.7825 (mtp) cc_final: 0.7564 (mtm) REVERT: C 283 MET cc_start: 0.8061 (mmm) cc_final: 0.7830 (mmm) REVERT: C 359 LYS cc_start: 0.7249 (tptp) cc_final: 0.7005 (mtpp) REVERT: D 1276 PHE cc_start: 0.5884 (m-10) cc_final: 0.5354 (m-80) REVERT: D 1390 GLU cc_start: 0.6959 (pt0) cc_final: 0.6582 (mt-10) REVERT: D 1397 TYR cc_start: 0.7286 (m-80) cc_final: 0.6614 (m-80) REVERT: D 1427 ASN cc_start: 0.8319 (t0) cc_final: 0.7388 (p0) REVERT: D 1428 CYS cc_start: 0.7267 (m) cc_final: 0.6192 (m) REVERT: D 1429 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6912 (tp30) REVERT: D 1559 VAL cc_start: 0.6704 (t) cc_final: 0.6440 (m) REVERT: D 1566 LEU cc_start: 0.7961 (mt) cc_final: 0.7651 (mt) REVERT: D 1860 MET cc_start: 0.7235 (pmm) cc_final: 0.6762 (pmm) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.1193 time to fit residues: 71.1050 Evaluate side-chains 223 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 225 ASN A 353 GLN B 12 ASN B 121 GLN B 360 GLN C 40 HIS C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1687 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106983 restraints weight = 41926.211| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.38 r_work: 0.3126 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16135 Z= 0.160 Angle : 0.659 8.868 21843 Z= 0.332 Chirality : 0.046 0.250 2416 Planarity : 0.005 0.080 2823 Dihedral : 9.470 141.752 2204 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.65 % Allowed : 9.13 % Favored : 89.22 % 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 aren not related in a simple way. whole: 0.50 (0.19), residues: 1967 helix: 1.11 (0.18), residues: 914 sheet: -0.24 (0.28), residues: 289 loop : -0.25 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1819 TYR 0.025 0.002 TYR C 294 PHE 0.024 0.002 PHE D1548 TRP 0.011 0.002 TRP B 340 HIS 0.010 0.001 HIS D1477 Details of bonding type rmsd covalent geometry : bond 0.00358 (16135) covalent geometry : angle 0.65909 (21843) hydrogen bonds : bond 0.03898 ( 785) hydrogen bonds : angle 4.85660 ( 2145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8654 (mtt) cc_final: 0.8402 (mtt) REVERT: A 176 MET cc_start: 0.7194 (mmm) cc_final: 0.6742 (mmt) REVERT: A 246 GLN cc_start: 0.7956 (mt0) cc_final: 0.7570 (mt0) REVERT: A 355 MET cc_start: 0.8237 (mtt) cc_final: 0.7924 (mtt) REVERT: A 360 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8655 (mp10) REVERT: B 95 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7422 (mmt180) REVERT: B 314 GLN cc_start: 0.7464 (tt0) cc_final: 0.7188 (mt0) REVERT: B 353 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8261 (tt0) REVERT: C 176 MET cc_start: 0.8639 (mmt) cc_final: 0.8394 (mmm) REVERT: C 244 ASP cc_start: 0.7940 (p0) cc_final: 0.7540 (m-30) REVERT: C 253 GLU cc_start: 0.7892 (mp0) cc_final: 0.7654 (mp0) REVERT: C 325 MET cc_start: 0.6426 (mmt) cc_final: 0.6140 (mmm) REVERT: C 359 LYS cc_start: 0.7453 (tptp) cc_final: 0.7220 (mttm) REVERT: D 1283 PHE cc_start: 0.7256 (t80) cc_final: 0.7049 (t80) REVERT: D 1397 TYR cc_start: 0.7592 (m-80) cc_final: 0.6957 (m-80) REVERT: D 1427 ASN cc_start: 0.8216 (t0) cc_final: 0.7406 (p0) REVERT: D 1428 CYS cc_start: 0.7211 (m) cc_final: 0.6486 (m) REVERT: D 1429 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6965 (tp30) REVERT: D 1442 LEU cc_start: 0.9194 (tp) cc_final: 0.8919 (tp) REVERT: D 1559 VAL cc_start: 0.6502 (t) cc_final: 0.6129 (m) REVERT: D 1617 MET cc_start: 0.4549 (ppp) cc_final: 0.3882 (tmm) REVERT: D 1800 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7856 (tt) REVERT: D 1868 LEU cc_start: 0.4937 (OUTLIER) cc_final: 0.4626 (pt) outliers start: 25 outliers final: 15 residues processed: 263 average time/residue: 0.1066 time to fit residues: 41.9142 Evaluate side-chains 224 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1486 SER Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1603 ILE Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1769 MET Chi-restraints excluded: chain D residue 1800 LEU Chi-restraints excluded: chain D residue 1868 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 121 optimal weight: 0.0010 chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 162 ASN B 12 ASN B 162 ASN C 87 HIS C 225 ASN C 297 ASN ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106870 restraints weight = 49078.179| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.54 r_work: 0.3096 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16135 Z= 0.132 Angle : 0.601 7.280 21843 Z= 0.302 Chirality : 0.045 0.307 2416 Planarity : 0.004 0.054 2823 Dihedral : 9.235 139.450 2204 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.12 % Allowed : 10.66 % Favored : 87.22 % 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 aren not related in a simple way. whole: 0.51 (0.19), residues: 1967 helix: 1.12 (0.18), residues: 920 sheet: -0.21 (0.28), residues: 291 loop : -0.28 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1884 TYR 0.019 0.001 TYR C 294 PHE 0.020 0.001 PHE D1822 TRP 0.009 0.001 TRP B 340 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00299 (16135) covalent geometry : angle 0.60129 (21843) hydrogen bonds : bond 0.03586 ( 785) hydrogen bonds : angle 4.63659 ( 2145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8674 (mtt) cc_final: 0.8438 (mtt) REVERT: A 176 MET cc_start: 0.7322 (mmm) cc_final: 0.6882 (mmt) REVERT: A 313 MET cc_start: 0.8170 (tpp) cc_final: 0.7967 (tpp) REVERT: A 355 MET cc_start: 0.8321 (mtt) cc_final: 0.7994 (mtt) REVERT: A 360 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8662 (mp10) REVERT: B 44 MET cc_start: 0.5065 (ptp) cc_final: 0.4774 (ptp) REVERT: B 95 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7465 (mmt180) REVERT: B 306 TYR cc_start: 0.8298 (m-80) cc_final: 0.8050 (m-80) REVERT: B 314 GLN cc_start: 0.7463 (tt0) cc_final: 0.7194 (mt0) REVERT: B 326 LYS cc_start: 0.8267 (pttm) cc_final: 0.8022 (pttt) REVERT: C 176 MET cc_start: 0.8683 (mmt) cc_final: 0.8437 (mmm) REVERT: C 244 ASP cc_start: 0.7798 (p0) cc_final: 0.7319 (m-30) REVERT: C 253 GLU cc_start: 0.7877 (mp0) cc_final: 0.7539 (mp0) REVERT: C 325 MET cc_start: 0.6400 (mmt) cc_final: 0.6108 (mmm) REVERT: C 359 LYS cc_start: 0.7540 (tptp) cc_final: 0.7021 (mttt) REVERT: D 1390 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7254 (mt-10) REVERT: D 1397 TYR cc_start: 0.7539 (m-80) cc_final: 0.6910 (m-80) REVERT: D 1427 ASN cc_start: 0.8191 (t0) cc_final: 0.7346 (p0) REVERT: D 1428 CYS cc_start: 0.7305 (m) cc_final: 0.6596 (m) REVERT: D 1429 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6993 (tp30) REVERT: D 1442 LEU cc_start: 0.9223 (tp) cc_final: 0.8999 (tp) REVERT: D 1517 GLU cc_start: 0.7636 (tp30) cc_final: 0.7390 (tp30) REVERT: D 1610 GLU cc_start: 0.7681 (tp30) cc_final: 0.7015 (tm-30) REVERT: D 1617 MET cc_start: 0.4479 (ppp) cc_final: 0.3579 (tmm) REVERT: D 1767 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8040 (mm-30) REVERT: D 1800 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7894 (tt) REVERT: D 1884 ARG cc_start: 0.8954 (mtm-85) cc_final: 0.8670 (ptt-90) outliers start: 33 outliers final: 25 residues processed: 244 average time/residue: 0.1084 time to fit residues: 40.2180 Evaluate side-chains 227 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1471 ASN Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1603 ILE Chi-restraints excluded: chain D residue 1701 ASP Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Chi-restraints excluded: chain D residue 1800 LEU Chi-restraints excluded: chain D residue 1813 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 40.0000 chunk 166 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 353 GLN C 49 GLN B C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 ASN D1687 HIS D1823 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103457 restraints weight = 37518.412| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.07 r_work: 0.3098 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16135 Z= 0.215 Angle : 0.675 8.618 21843 Z= 0.342 Chirality : 0.047 0.198 2416 Planarity : 0.005 0.048 2823 Dihedral : 9.147 143.299 2204 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.36 % Allowed : 11.54 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 1967 helix: 0.97 (0.18), residues: 922 sheet: -0.25 (0.28), residues: 303 loop : -0.44 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.019 0.002 TYR C 294 PHE 0.023 0.002 PHE D1822 TRP 0.013 0.002 TRP B 340 HIS 0.008 0.002 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00510 (16135) covalent geometry : angle 0.67527 (21843) hydrogen bonds : bond 0.04067 ( 785) hydrogen bonds : angle 4.64743 ( 2145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8884 (mtt) cc_final: 0.8596 (mtt) REVERT: A 176 MET cc_start: 0.7503 (mmm) cc_final: 0.7059 (mmt) REVERT: A 355 MET cc_start: 0.8515 (mtt) cc_final: 0.8242 (mtt) REVERT: A 360 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8681 (mp10) REVERT: B 44 MET cc_start: 0.5268 (ptp) cc_final: 0.4804 (ptp) REVERT: B 95 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7674 (mmt180) REVERT: B 306 TYR cc_start: 0.8438 (m-80) cc_final: 0.8221 (m-80) REVERT: C 68 LYS cc_start: 0.7968 (mttm) cc_final: 0.7523 (ptpp) REVERT: C 244 ASP cc_start: 0.7563 (p0) cc_final: 0.7225 (m-30) REVERT: C 325 MET cc_start: 0.6296 (mmt) cc_final: 0.5673 (mmm) REVERT: C 359 LYS cc_start: 0.7779 (tptp) cc_final: 0.7457 (mttm) REVERT: D 1427 ASN cc_start: 0.8042 (t0) cc_final: 0.7300 (p0) REVERT: D 1517 GLU cc_start: 0.7610 (tp30) cc_final: 0.7363 (tp30) REVERT: D 1610 GLU cc_start: 0.7783 (tp30) cc_final: 0.7219 (tm-30) REVERT: D 1617 MET cc_start: 0.3883 (ppp) cc_final: 0.3642 (ppp) REVERT: D 1800 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7965 (tt) outliers start: 37 outliers final: 27 residues processed: 229 average time/residue: 0.1085 time to fit residues: 38.0383 Evaluate side-chains 205 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1471 ASN Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1511 ILE Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1769 MET Chi-restraints excluded: chain D residue 1800 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 141 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 83 optimal weight: 0.0050 chunk 72 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 ASN A 162 ASN A 353 GLN B 353 GLN C 87 HIS C 297 ASN ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1471 ASN ** D1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105145 restraints weight = 40289.491| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.24 r_work: 0.3114 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16135 Z= 0.135 Angle : 0.614 10.294 21843 Z= 0.304 Chirality : 0.044 0.318 2416 Planarity : 0.004 0.044 2823 Dihedral : 8.908 143.017 2204 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.53 % Allowed : 12.78 % Favored : 84.69 % 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 aren not related in a simple way. whole: 0.46 (0.19), residues: 1967 helix: 1.08 (0.18), residues: 925 sheet: -0.11 (0.29), residues: 297 loop : -0.38 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1461 TYR 0.020 0.001 TYR C 294 PHE 0.020 0.001 PHE D1822 TRP 0.010 0.002 TRP B 79 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00313 (16135) covalent geometry : angle 0.61378 (21843) hydrogen bonds : bond 0.03471 ( 785) hydrogen bonds : angle 4.51716 ( 2145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8846 (mtt) cc_final: 0.8619 (mtt) REVERT: A 176 MET cc_start: 0.7463 (mmm) cc_final: 0.7000 (mmt) REVERT: A 246 GLN cc_start: 0.8105 (mt0) cc_final: 0.7862 (mp10) REVERT: A 355 MET cc_start: 0.8544 (mtt) cc_final: 0.8299 (mtt) REVERT: A 360 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8715 (mp10) REVERT: B 44 MET cc_start: 0.5376 (ptp) cc_final: 0.4935 (ptp) REVERT: B 95 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7582 (mmt180) REVERT: B 306 TYR cc_start: 0.8406 (m-80) cc_final: 0.8183 (m-80) REVERT: C 244 ASP cc_start: 0.7416 (p0) cc_final: 0.7112 (m-30) REVERT: C 325 MET cc_start: 0.6273 (mmt) cc_final: 0.5680 (mmm) REVERT: C 359 LYS cc_start: 0.7697 (tptp) cc_final: 0.7292 (mttm) REVERT: C 372 ARG cc_start: 0.7816 (ptp-170) cc_final: 0.7590 (ptp-170) REVERT: D 1397 TYR cc_start: 0.7525 (m-80) cc_final: 0.6991 (m-80) REVERT: D 1427 ASN cc_start: 0.8022 (t0) cc_final: 0.7304 (p0) REVERT: D 1517 GLU cc_start: 0.7510 (tp30) cc_final: 0.7226 (tp30) REVERT: D 1563 GLN cc_start: 0.6072 (pp30) cc_final: 0.5862 (pp30) REVERT: D 1610 GLU cc_start: 0.7787 (tp30) cc_final: 0.7243 (tm-30) REVERT: D 1617 MET cc_start: 0.3904 (ppp) cc_final: 0.3617 (ppp) REVERT: D 1800 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8062 (tt) outliers start: 40 outliers final: 30 residues processed: 222 average time/residue: 0.1091 time to fit residues: 36.7554 Evaluate side-chains 218 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1295 VAL Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1399 LEU Chi-restraints excluded: chain D residue 1471 ASN Chi-restraints excluded: chain D residue 1486 SER Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Chi-restraints excluded: chain D residue 1800 LEU Chi-restraints excluded: chain D residue 1813 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 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 162 ASN A 353 GLN C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1471 ASN ** D1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103792 restraints weight = 51311.530| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.64 r_work: 0.3072 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16135 Z= 0.150 Angle : 0.627 10.853 21843 Z= 0.309 Chirality : 0.045 0.352 2416 Planarity : 0.004 0.044 2823 Dihedral : 8.793 142.618 2204 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.47 % Allowed : 13.02 % Favored : 84.51 % 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 aren not related in a simple way. whole: 0.45 (0.19), residues: 1967 helix: 1.08 (0.18), residues: 926 sheet: -0.07 (0.29), residues: 295 loop : -0.41 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D1884 TYR 0.013 0.001 TYR A 279 PHE 0.018 0.001 PHE D1822 TRP 0.009 0.002 TRP B 79 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00354 (16135) covalent geometry : angle 0.62680 (21843) hydrogen bonds : bond 0.03487 ( 785) hydrogen bonds : angle 4.48105 ( 2145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8897 (mtt) cc_final: 0.8657 (mtt) REVERT: A 176 MET cc_start: 0.7540 (mmm) cc_final: 0.7069 (mmt) REVERT: A 246 GLN cc_start: 0.8148 (mt0) cc_final: 0.7710 (mt0) REVERT: A 360 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8720 (mp10) REVERT: B 95 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7599 (mmt180) REVERT: B 306 TYR cc_start: 0.8465 (m-80) cc_final: 0.8201 (m-80) REVERT: B 325 MET cc_start: 0.7933 (mmp) cc_final: 0.7488 (mmt) REVERT: C 244 ASP cc_start: 0.7397 (p0) cc_final: 0.7163 (m-30) REVERT: C 325 MET cc_start: 0.6247 (mmt) cc_final: 0.5648 (mmm) REVERT: C 359 LYS cc_start: 0.7681 (tptp) cc_final: 0.7285 (mttm) REVERT: C 372 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.7657 (ptp-170) REVERT: D 1427 ASN cc_start: 0.8051 (t0) cc_final: 0.7306 (p0) REVERT: D 1517 GLU cc_start: 0.7570 (tp30) cc_final: 0.7247 (tp30) REVERT: D 1610 GLU cc_start: 0.7786 (tp30) cc_final: 0.7244 (tm-30) REVERT: D 1617 MET cc_start: 0.3998 (ppp) cc_final: 0.3685 (ppp) outliers start: 39 outliers final: 27 residues processed: 218 average time/residue: 0.1072 time to fit residues: 35.3371 Evaluate side-chains 209 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1295 VAL Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1399 LEU Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Chi-restraints excluded: chain D residue 1813 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 353 GLN C 87 HIS C 162 ASN C 297 ASN ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103846 restraints weight = 45099.309| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.38 r_work: 0.3069 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16135 Z= 0.177 Angle : 0.653 11.001 21843 Z= 0.322 Chirality : 0.046 0.336 2416 Planarity : 0.004 0.045 2823 Dihedral : 8.722 142.999 2204 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.18 % Allowed : 13.84 % Favored : 83.98 % 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 aren not related in a simple way. whole: 0.41 (0.19), residues: 1967 helix: 1.04 (0.18), residues: 925 sheet: -0.05 (0.29), residues: 295 loop : -0.45 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D1884 TYR 0.012 0.001 TYR A 279 PHE 0.019 0.001 PHE D1822 TRP 0.010 0.002 TRP B 340 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00419 (16135) covalent geometry : angle 0.65324 (21843) hydrogen bonds : bond 0.03675 ( 785) hydrogen bonds : angle 4.48556 ( 2145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8899 (mtt) cc_final: 0.8616 (mtt) REVERT: A 176 MET cc_start: 0.7521 (mmm) cc_final: 0.7039 (mmt) REVERT: A 246 GLN cc_start: 0.8144 (mt0) cc_final: 0.7534 (mt0) REVERT: A 360 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8698 (mp10) REVERT: B 95 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7586 (mmt180) REVERT: B 306 TYR cc_start: 0.8479 (m-80) cc_final: 0.8075 (m-80) REVERT: C 118 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7567 (mtpt) REVERT: C 244 ASP cc_start: 0.7580 (p0) cc_final: 0.7349 (m-30) REVERT: C 325 MET cc_start: 0.6016 (mmt) cc_final: 0.5486 (mmm) REVERT: C 372 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7605 (ptp-170) REVERT: D 1427 ASN cc_start: 0.8083 (t0) cc_final: 0.7304 (p0) REVERT: D 1517 GLU cc_start: 0.7585 (tp30) cc_final: 0.7254 (tp30) REVERT: D 1610 GLU cc_start: 0.7788 (tp30) cc_final: 0.7263 (tm-30) outliers start: 34 outliers final: 27 residues processed: 209 average time/residue: 0.1133 time to fit residues: 35.8726 Evaluate side-chains 204 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1295 VAL Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1399 LEU Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 184 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 162 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 354 GLN C 87 HIS C 297 ASN ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104838 restraints weight = 45799.930| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.44 r_work: 0.3088 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16135 Z= 0.123 Angle : 0.623 12.473 21843 Z= 0.304 Chirality : 0.044 0.373 2416 Planarity : 0.004 0.043 2823 Dihedral : 8.549 140.962 2204 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.88 % Allowed : 14.25 % Favored : 83.86 % 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 aren not related in a simple way. whole: 0.60 (0.19), residues: 1967 helix: 1.17 (0.18), residues: 924 sheet: 0.11 (0.29), residues: 290 loop : -0.34 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1884 TYR 0.010 0.001 TYR A 279 PHE 0.019 0.001 PHE D1822 TRP 0.009 0.001 TRP A 340 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00281 (16135) covalent geometry : angle 0.62325 (21843) hydrogen bonds : bond 0.03239 ( 785) hydrogen bonds : angle 4.37743 ( 2145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8900 (mtt) cc_final: 0.8648 (mtt) REVERT: A 157 ASP cc_start: 0.7901 (p0) cc_final: 0.7580 (p0) REVERT: A 166 TYR cc_start: 0.8270 (t80) cc_final: 0.7893 (t80) REVERT: A 176 MET cc_start: 0.7598 (mmm) cc_final: 0.7170 (mmt) REVERT: A 246 GLN cc_start: 0.8132 (mt0) cc_final: 0.7555 (mt0) REVERT: A 360 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8719 (mp10) REVERT: B 95 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7555 (mmt180) REVERT: B 306 TYR cc_start: 0.8466 (m-80) cc_final: 0.8137 (m-80) REVERT: B 325 MET cc_start: 0.7896 (mmp) cc_final: 0.7415 (mmt) REVERT: C 81 ASP cc_start: 0.7732 (m-30) cc_final: 0.7160 (m-30) REVERT: C 118 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7550 (mtpt) REVERT: C 325 MET cc_start: 0.5993 (mmt) cc_final: 0.5463 (mmm) REVERT: C 372 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7580 (ptp-170) REVERT: D 1332 LEU cc_start: 0.8478 (pp) cc_final: 0.8246 (pp) REVERT: D 1427 ASN cc_start: 0.8060 (t0) cc_final: 0.7304 (p0) REVERT: D 1517 GLU cc_start: 0.7557 (tp30) cc_final: 0.7246 (tp30) REVERT: D 1610 GLU cc_start: 0.7775 (tp30) cc_final: 0.7228 (tm-30) REVERT: D 1617 MET cc_start: 0.3613 (ppp) cc_final: 0.3350 (ppp) outliers start: 29 outliers final: 24 residues processed: 212 average time/residue: 0.1054 time to fit residues: 33.9529 Evaluate side-chains 206 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1295 VAL Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN B 354 GLN C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1876 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104182 restraints weight = 49295.648| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.54 r_work: 0.3081 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16135 Z= 0.135 Angle : 0.632 12.376 21843 Z= 0.309 Chirality : 0.045 0.363 2416 Planarity : 0.004 0.043 2823 Dihedral : 8.497 141.659 2204 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.83 % Allowed : 14.72 % Favored : 83.45 % 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 aren not related in a simple way. whole: 0.62 (0.20), residues: 1967 helix: 1.19 (0.18), residues: 922 sheet: 0.14 (0.29), residues: 290 loop : -0.34 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1884 TYR 0.011 0.001 TYR C 294 PHE 0.019 0.001 PHE D1822 TRP 0.009 0.002 TRP A 340 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00316 (16135) covalent geometry : angle 0.63235 (21843) hydrogen bonds : bond 0.03307 ( 785) hydrogen bonds : angle 4.36824 ( 2145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 74 MET cc_start: 0.0673 (tmm) cc_final: 0.0421 (tmm) REVERT: A 44 MET cc_start: 0.8913 (mtt) cc_final: 0.8645 (mtt) REVERT: A 157 ASP cc_start: 0.7910 (p0) cc_final: 0.7588 (p0) REVERT: A 166 TYR cc_start: 0.8256 (t80) cc_final: 0.7858 (t80) REVERT: A 176 MET cc_start: 0.7631 (mmm) cc_final: 0.7193 (mmt) REVERT: A 246 GLN cc_start: 0.8141 (mt0) cc_final: 0.7520 (mt0) REVERT: A 360 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8757 (mp10) REVERT: B 95 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7542 (mmt180) REVERT: B 306 TYR cc_start: 0.8479 (m-80) cc_final: 0.8079 (m-80) REVERT: B 325 MET cc_start: 0.7886 (mmp) cc_final: 0.7395 (mmt) REVERT: C 325 MET cc_start: 0.5977 (mmt) cc_final: 0.5435 (mmm) REVERT: D 1332 LEU cc_start: 0.8450 (pp) cc_final: 0.8219 (pp) REVERT: D 1397 TYR cc_start: 0.7608 (m-80) cc_final: 0.6988 (m-80) REVERT: D 1427 ASN cc_start: 0.8034 (t0) cc_final: 0.7286 (p0) REVERT: D 1517 GLU cc_start: 0.7562 (tp30) cc_final: 0.7239 (tp30) REVERT: D 1610 GLU cc_start: 0.7753 (tp30) cc_final: 0.7221 (tm-30) outliers start: 28 outliers final: 25 residues processed: 204 average time/residue: 0.1089 time to fit residues: 34.3168 Evaluate side-chains 204 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1295 VAL Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 174 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 78 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112162 restraints weight = 42344.341| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.14 r_work: 0.3140 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16135 Z= 0.132 Angle : 0.639 13.481 21843 Z= 0.312 Chirality : 0.045 0.393 2416 Planarity : 0.004 0.043 2823 Dihedral : 8.436 141.586 2204 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.83 % Allowed : 14.84 % Favored : 83.33 % 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 aren not related in a simple way. whole: 0.69 (0.20), residues: 1967 helix: 1.29 (0.18), residues: 902 sheet: 0.19 (0.30), residues: 290 loop : -0.33 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1884 TYR 0.012 0.001 TYR C 294 PHE 0.018 0.001 PHE D1825 TRP 0.009 0.001 TRP A 340 HIS 0.008 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00309 (16135) covalent geometry : angle 0.63937 (21843) hydrogen bonds : bond 0.03259 ( 785) hydrogen bonds : angle 4.36177 ( 2145) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 74 MET cc_start: 0.0685 (tmm) cc_final: 0.0427 (tmm) REVERT: A 44 MET cc_start: 0.8897 (mtt) cc_final: 0.8636 (mtt) REVERT: A 157 ASP cc_start: 0.7869 (p0) cc_final: 0.7519 (p0) REVERT: A 166 TYR cc_start: 0.8212 (t80) cc_final: 0.7809 (t80) REVERT: A 176 MET cc_start: 0.7545 (mmm) cc_final: 0.7080 (mmt) REVERT: A 246 GLN cc_start: 0.8101 (mt0) cc_final: 0.7528 (mt0) REVERT: B 95 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7438 (mmt180) REVERT: B 306 TYR cc_start: 0.8437 (m-80) cc_final: 0.8032 (m-80) REVERT: B 325 MET cc_start: 0.7822 (mmp) cc_final: 0.7318 (mmt) REVERT: C 81 ASP cc_start: 0.7644 (m-30) cc_final: 0.7020 (m-30) REVERT: C 325 MET cc_start: 0.5937 (mmt) cc_final: 0.5382 (mmm) REVERT: D 1332 LEU cc_start: 0.8445 (pp) cc_final: 0.8212 (pp) REVERT: D 1397 TYR cc_start: 0.7582 (m-80) cc_final: 0.6993 (m-80) REVERT: D 1427 ASN cc_start: 0.8086 (t0) cc_final: 0.7301 (p0) REVERT: D 1517 GLU cc_start: 0.7506 (tp30) cc_final: 0.7175 (tp30) REVERT: D 1610 GLU cc_start: 0.7785 (tp30) cc_final: 0.7261 (tm-30) REVERT: D 1881 MET cc_start: 0.8801 (tmm) cc_final: 0.8478 (ppp) outliers start: 28 outliers final: 26 residues processed: 208 average time/residue: 0.1096 time to fit residues: 34.8229 Evaluate side-chains 210 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 1225 ASN Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1295 VAL Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1338 LEU Chi-restraints excluded: chain D residue 1386 GLN Chi-restraints excluded: chain D residue 1488 VAL Chi-restraints excluded: chain D residue 1552 ILE Chi-restraints excluded: chain D residue 1574 TYR Chi-restraints excluded: chain D residue 1707 VAL Chi-restraints excluded: chain D residue 1763 LEU Chi-restraints excluded: chain D residue 1769 MET Chi-restraints excluded: chain D residue 1813 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 189 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.152618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106268 restraints weight = 50018.454| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.59 r_work: 0.3114 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16135 Z= 0.117 Angle : 0.638 13.193 21843 Z= 0.309 Chirality : 0.045 0.361 2416 Planarity : 0.004 0.042 2823 Dihedral : 8.332 139.891 2204 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 14.78 % Favored : 83.27 % 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 aren not related in a simple way. whole: 0.71 (0.20), residues: 1967 helix: 1.21 (0.18), residues: 926 sheet: 0.14 (0.32), residues: 266 loop : -0.19 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1852 TYR 0.019 0.001 TYR C 294 PHE 0.019 0.001 PHE D1869 TRP 0.010 0.001 TRP A 340 HIS 0.007 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00268 (16135) covalent geometry : angle 0.63849 (21843) hydrogen bonds : bond 0.03065 ( 785) hydrogen bonds : angle 4.29622 ( 2145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4409.20 seconds wall clock time: 75 minutes 57.83 seconds (4557.83 seconds total)