Starting phenix.real_space_refine on Sun Aug 24 04:43:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fls_50538/08_2025/9fls_50538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fls_50538/08_2025/9fls_50538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fls_50538/08_2025/9fls_50538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fls_50538/08_2025/9fls_50538.map" model { file = "/net/cci-nas-00/data/ceres_data/9fls_50538/08_2025/9fls_50538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fls_50538/08_2025/9fls_50538.cif" } resolution = 3.4 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= 0.168 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 10192 2.51 5 N 2688 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16604 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2372 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 22, 'TRANS': 314} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.52, per 1000 atoms: 0.15 Number of scatterers: 16604 At special positions: 0 Unit cell: (91.59, 91.59, 197.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3654 8.00 N 2688 7.00 C 10192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A2077 " - pdb=" SG CYS A2214 " distance=2.03 Simple disulfide: pdb=" SG CYS A2159 " - pdb=" SG CYS A2298 " distance=2.02 Simple disulfide: pdb=" SG CYS A2241 " - pdb=" SG CYS A2381 " distance=2.04 Simple disulfide: pdb=" SG CYS B2077 " - pdb=" SG CYS B2214 " distance=2.03 Simple disulfide: pdb=" SG CYS C2077 " - pdb=" SG CYS C2214 " distance=2.03 Simple disulfide: pdb=" SG CYS D2077 " - pdb=" SG CYS D2214 " distance=2.03 Simple disulfide: pdb=" SG CYS E2077 " - pdb=" SG CYS E2214 " distance=2.03 Simple disulfide: pdb=" SG CYS F2077 " - pdb=" SG CYS F2214 " distance=2.03 Simple disulfide: pdb=" SG CYS G2077 " - pdb=" SG CYS G2214 " distance=2.03 Simple disulfide: pdb=" SG CYS B2159 " - pdb=" SG CYS B2298 " distance=2.02 Simple disulfide: pdb=" SG CYS C2159 " - pdb=" SG CYS C2298 " distance=2.02 Simple disulfide: pdb=" SG CYS D2159 " - pdb=" SG CYS D2298 " distance=2.02 Simple disulfide: pdb=" SG CYS E2159 " - pdb=" SG CYS E2298 " distance=2.02 Simple disulfide: pdb=" SG CYS F2159 " - pdb=" SG CYS F2298 " distance=2.02 Simple disulfide: pdb=" SG CYS G2159 " - pdb=" SG CYS G2298 " distance=2.02 Simple disulfide: pdb=" SG CYS B2241 " - pdb=" SG CYS B2381 " distance=2.04 Simple disulfide: pdb=" SG CYS C2241 " - pdb=" SG CYS C2381 " distance=2.04 Simple disulfide: pdb=" SG CYS D2241 " - pdb=" SG CYS D2381 " distance=2.04 Simple disulfide: pdb=" SG CYS E2241 " - pdb=" SG CYS E2381 " distance=2.04 Simple disulfide: pdb=" SG CYS F2241 " - pdb=" SG CYS F2381 " distance=2.04 Simple disulfide: pdb=" SG CYS G2241 " - pdb=" SG CYS G2381 " distance=2.04 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: 1.32 Conformation dependent library (CDL) restraints added in 868.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 77 sheets defined 2.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 2180 through 2182 No H-bonds generated for 'chain 'A' and resid 2180 through 2182' Processing helix chain 'A' and resid 2197 through 2201 Processing helix chain 'B' and resid 2180 through 2182 No H-bonds generated for 'chain 'B' and resid 2180 through 2182' Processing helix chain 'B' and resid 2197 through 2201 Processing helix chain 'C' and resid 2180 through 2182 No H-bonds generated for 'chain 'C' and resid 2180 through 2182' Processing helix chain 'C' and resid 2197 through 2201 Processing helix chain 'D' and resid 2180 through 2182 No H-bonds generated for 'chain 'D' and resid 2180 through 2182' Processing helix chain 'D' and resid 2197 through 2201 Processing helix chain 'E' and resid 2180 through 2182 No H-bonds generated for 'chain 'E' and resid 2180 through 2182' Processing helix chain 'E' and resid 2197 through 2201 Processing helix chain 'F' and resid 2180 through 2182 No H-bonds generated for 'chain 'F' and resid 2180 through 2182' Processing helix chain 'F' and resid 2197 through 2201 Processing helix chain 'G' and resid 2180 through 2182 No H-bonds generated for 'chain 'G' and resid 2180 through 2182' Processing helix chain 'G' and resid 2197 through 2201 Processing sheet with id=AA1, first strand: chain 'A' and resid 2071 through 2072 Processing sheet with id=AA2, first strand: chain 'A' and resid 2076 through 2077 removed outlier: 6.783A pdb=" N VAL A2076 " --> pdb=" O TYR A2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN A2104 " --> pdb=" O THR A2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP A2096 " --> pdb=" O PHE A2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP A2099 " --> pdb=" O THR A2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR A2122 " --> pdb=" O ASP A2099 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A2132 " --> pdb=" O VAL A2129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN A2104 " --> pdb=" O THR A2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP A2096 " --> pdb=" O PHE A2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP A2099 " --> pdb=" O THR A2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR A2122 " --> pdb=" O ASP A2099 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2156 through 2159 removed outlier: 6.895A pdb=" N PHE A2156 " --> pdb=" O THR A2224 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN A2226 " --> pdb=" O PHE A2156 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A2158 " --> pdb=" O ASN A2226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2234 through 2236 Processing sheet with id=AA7, first strand: chain 'A' and resid 2239 through 2241 removed outlier: 7.013A pdb=" N ILE A2240 " --> pdb=" O ASN A2311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2320 through 2321 removed outlier: 3.693A pdb=" N ALA A2331 " --> pdb=" O VAL A2363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2341 through 2342 Processing sheet with id=AB1, first strand: chain 'A' and resid 2345 through 2346 removed outlier: 3.567A pdb=" N SER A2356 " --> pdb=" O TRP A2345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2371 through 2372 Processing sheet with id=AB3, first strand: chain 'B' and resid 2071 through 2072 Processing sheet with id=AB4, first strand: chain 'B' and resid 2076 through 2077 removed outlier: 6.783A pdb=" N VAL B2076 " --> pdb=" O TYR B2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN B2104 " --> pdb=" O THR B2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP B2096 " --> pdb=" O PHE B2106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP B2099 " --> pdb=" O THR B2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR B2122 " --> pdb=" O ASP B2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B2132 " --> pdb=" O VAL B2129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN B2104 " --> pdb=" O THR B2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP B2096 " --> pdb=" O PHE B2106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP B2099 " --> pdb=" O THR B2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR B2122 " --> pdb=" O ASP B2099 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 2156 through 2159 removed outlier: 6.895A pdb=" N PHE B2156 " --> pdb=" O THR B2224 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN B2226 " --> pdb=" O PHE B2156 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B2158 " --> pdb=" O ASN B2226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2234 through 2236 Processing sheet with id=AB9, first strand: chain 'B' and resid 2239 through 2241 removed outlier: 7.013A pdb=" N ILE B2240 " --> pdb=" O ASN B2311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 2320 through 2321 removed outlier: 3.692A pdb=" N ALA B2331 " --> pdb=" O VAL B2363 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 2341 through 2342 Processing sheet with id=AC3, first strand: chain 'B' and resid 2345 through 2346 removed outlier: 3.566A pdb=" N SER B2356 " --> pdb=" O TRP B2345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 2371 through 2372 Processing sheet with id=AC5, first strand: chain 'C' and resid 2071 through 2072 Processing sheet with id=AC6, first strand: chain 'C' and resid 2076 through 2077 removed outlier: 6.783A pdb=" N VAL C2076 " --> pdb=" O TYR C2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 2103 through 2107 removed outlier: 7.122A pdb=" N ASN C2104 " --> pdb=" O THR C2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP C2096 " --> pdb=" O PHE C2106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP C2099 " --> pdb=" O THR C2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR C2122 " --> pdb=" O ASP C2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C2132 " --> pdb=" O VAL C2129 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 2103 through 2107 removed outlier: 7.122A pdb=" N ASN C2104 " --> pdb=" O THR C2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP C2096 " --> pdb=" O PHE C2106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP C2099 " --> pdb=" O THR C2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR C2122 " --> pdb=" O ASP C2099 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 2156 through 2159 removed outlier: 6.895A pdb=" N PHE C2156 " --> pdb=" O THR C2224 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN C2226 " --> pdb=" O PHE C2156 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C2158 " --> pdb=" O ASN C2226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 2234 through 2236 Processing sheet with id=AD2, first strand: chain 'C' and resid 2239 through 2241 removed outlier: 7.012A pdb=" N ILE C2240 " --> pdb=" O ASN C2311 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 2320 through 2321 removed outlier: 3.692A pdb=" N ALA C2331 " --> pdb=" O VAL C2363 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 2341 through 2342 Processing sheet with id=AD5, first strand: chain 'C' and resid 2345 through 2346 removed outlier: 3.567A pdb=" N SER C2356 " --> pdb=" O TRP C2345 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 2371 through 2372 Processing sheet with id=AD7, first strand: chain 'D' and resid 2071 through 2072 Processing sheet with id=AD8, first strand: chain 'D' and resid 2076 through 2077 removed outlier: 6.783A pdb=" N VAL D2076 " --> pdb=" O TYR D2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 2103 through 2107 removed outlier: 7.122A pdb=" N ASN D2104 " --> pdb=" O THR D2098 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP D2096 " --> pdb=" O PHE D2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP D2099 " --> pdb=" O THR D2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR D2122 " --> pdb=" O ASP D2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D2132 " --> pdb=" O VAL D2129 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2103 through 2107 removed outlier: 7.122A pdb=" N ASN D2104 " --> pdb=" O THR D2098 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP D2096 " --> pdb=" O PHE D2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP D2099 " --> pdb=" O THR D2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR D2122 " --> pdb=" O ASP D2099 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 2156 through 2159 removed outlier: 6.894A pdb=" N PHE D2156 " --> pdb=" O THR D2224 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASN D2226 " --> pdb=" O PHE D2156 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D2158 " --> pdb=" O ASN D2226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 2234 through 2236 Processing sheet with id=AE4, first strand: chain 'D' and resid 2239 through 2241 removed outlier: 7.013A pdb=" N ILE D2240 " --> pdb=" O ASN D2311 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 2320 through 2321 removed outlier: 3.693A pdb=" N ALA D2331 " --> pdb=" O VAL D2363 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 2341 through 2342 Processing sheet with id=AE7, first strand: chain 'D' and resid 2345 through 2346 removed outlier: 3.566A pdb=" N SER D2356 " --> pdb=" O TRP D2345 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 2371 through 2372 Processing sheet with id=AE9, first strand: chain 'E' and resid 2071 through 2072 Processing sheet with id=AF1, first strand: chain 'E' and resid 2076 through 2077 removed outlier: 6.783A pdb=" N VAL E2076 " --> pdb=" O TYR E2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN E2104 " --> pdb=" O THR E2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP E2096 " --> pdb=" O PHE E2106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP E2099 " --> pdb=" O THR E2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR E2122 " --> pdb=" O ASP E2099 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS E2132 " --> pdb=" O VAL E2129 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN E2104 " --> pdb=" O THR E2098 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP E2096 " --> pdb=" O PHE E2106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP E2099 " --> pdb=" O THR E2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR E2122 " --> pdb=" O ASP E2099 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 2156 through 2159 removed outlier: 6.895A pdb=" N PHE E2156 " --> pdb=" O THR E2224 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASN E2226 " --> pdb=" O PHE E2156 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL E2158 " --> pdb=" O ASN E2226 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 2234 through 2236 Processing sheet with id=AF6, first strand: chain 'E' and resid 2239 through 2241 removed outlier: 7.012A pdb=" N ILE E2240 " --> pdb=" O ASN E2311 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 2320 through 2321 removed outlier: 3.692A pdb=" N ALA E2331 " --> pdb=" O VAL E2363 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 2341 through 2342 Processing sheet with id=AF9, first strand: chain 'E' and resid 2345 through 2346 removed outlier: 3.566A pdb=" N SER E2356 " --> pdb=" O TRP E2345 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 2371 through 2372 Processing sheet with id=AG2, first strand: chain 'F' and resid 2071 through 2072 Processing sheet with id=AG3, first strand: chain 'F' and resid 2076 through 2077 removed outlier: 6.783A pdb=" N VAL F2076 " --> pdb=" O TYR F2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN F2104 " --> pdb=" O THR F2098 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F2096 " --> pdb=" O PHE F2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP F2099 " --> pdb=" O THR F2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR F2122 " --> pdb=" O ASP F2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS F2132 " --> pdb=" O VAL F2129 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 2103 through 2107 removed outlier: 7.123A pdb=" N ASN F2104 " --> pdb=" O THR F2098 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F2096 " --> pdb=" O PHE F2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP F2099 " --> pdb=" O THR F2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR F2122 " --> pdb=" O ASP F2099 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 2156 through 2159 removed outlier: 6.894A pdb=" N PHE F2156 " --> pdb=" O THR F2224 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN F2226 " --> pdb=" O PHE F2156 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL F2158 " --> pdb=" O ASN F2226 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 2234 through 2236 Processing sheet with id=AG8, first strand: chain 'F' and resid 2239 through 2241 removed outlier: 7.012A pdb=" N ILE F2240 " --> pdb=" O ASN F2311 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 2320 through 2321 removed outlier: 3.692A pdb=" N ALA F2331 " --> pdb=" O VAL F2363 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 2341 through 2342 Processing sheet with id=AH2, first strand: chain 'F' and resid 2345 through 2346 removed outlier: 3.567A pdb=" N SER F2356 " --> pdb=" O TRP F2345 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 2371 through 2372 Processing sheet with id=AH4, first strand: chain 'G' and resid 2071 through 2072 Processing sheet with id=AH5, first strand: chain 'G' and resid 2076 through 2077 removed outlier: 6.782A pdb=" N VAL G2076 " --> pdb=" O TYR G2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'G' and resid 2103 through 2107 removed outlier: 7.122A pdb=" N ASN G2104 " --> pdb=" O THR G2098 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP G2096 " --> pdb=" O PHE G2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP G2099 " --> pdb=" O THR G2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR G2122 " --> pdb=" O ASP G2099 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS G2132 " --> pdb=" O VAL G2129 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 2103 through 2107 removed outlier: 7.122A pdb=" N ASN G2104 " --> pdb=" O THR G2098 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP G2096 " --> pdb=" O PHE G2106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP G2099 " --> pdb=" O THR G2122 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR G2122 " --> pdb=" O ASP G2099 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 2156 through 2159 removed outlier: 6.895A pdb=" N PHE G2156 " --> pdb=" O THR G2224 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN G2226 " --> pdb=" O PHE G2156 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL G2158 " --> pdb=" O ASN G2226 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 2234 through 2236 Processing sheet with id=AI1, first strand: chain 'G' and resid 2239 through 2241 removed outlier: 7.012A pdb=" N ILE G2240 " --> pdb=" O ASN G2311 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 2320 through 2321 removed outlier: 3.693A pdb=" N ALA G2331 " --> pdb=" O VAL G2363 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 2341 through 2342 Processing sheet with id=AI4, first strand: chain 'G' and resid 2345 through 2346 removed outlier: 3.566A pdb=" N SER G2356 " --> pdb=" O TRP G2345 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 2371 through 2372 511 hydrogen bonds defined for protein. 1155 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: 4.05 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3514 1.32 - 1.44: 4238 1.44 - 1.57: 9111 1.57 - 1.69: 7 1.69 - 1.82: 77 Bond restraints: 16947 Sorted by residual: bond pdb=" CB CYS G2132 " pdb=" SG CYS G2132 " ideal model delta sigma weight residual 1.808 1.636 0.172 3.30e-02 9.18e+02 2.70e+01 bond pdb=" CB CYS A2132 " pdb=" SG CYS A2132 " ideal model delta sigma weight residual 1.808 1.636 0.172 3.30e-02 9.18e+02 2.70e+01 bond pdb=" CB CYS F2132 " pdb=" SG CYS F2132 " ideal model delta sigma weight residual 1.808 1.636 0.172 3.30e-02 9.18e+02 2.70e+01 bond pdb=" CB CYS D2132 " pdb=" SG CYS D2132 " ideal model delta sigma weight residual 1.808 1.636 0.172 3.30e-02 9.18e+02 2.70e+01 bond pdb=" CB CYS C2132 " pdb=" SG CYS C2132 " ideal model delta sigma weight residual 1.808 1.636 0.172 3.30e-02 9.18e+02 2.70e+01 ... (remaining 16942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18906 1.84 - 3.67: 3618 3.67 - 5.51: 818 5.51 - 7.35: 101 7.35 - 9.18: 21 Bond angle restraints: 23464 Sorted by residual: angle pdb=" CA PHE B2156 " pdb=" CB PHE B2156 " pdb=" CG PHE B2156 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.01e+01 angle pdb=" CA PHE A2156 " pdb=" CB PHE A2156 " pdb=" CG PHE A2156 " ideal model delta sigma weight residual 113.80 120.83 -7.03 1.00e+00 1.00e+00 4.94e+01 angle pdb=" CA PHE C2156 " pdb=" CB PHE C2156 " pdb=" CG PHE C2156 " ideal model delta sigma weight residual 113.80 120.81 -7.01 1.00e+00 1.00e+00 4.92e+01 angle pdb=" CA PHE G2156 " pdb=" CB PHE G2156 " pdb=" CG PHE G2156 " ideal model delta sigma weight residual 113.80 120.81 -7.01 1.00e+00 1.00e+00 4.92e+01 angle pdb=" CA PHE F2156 " pdb=" CB PHE F2156 " pdb=" CG PHE F2156 " ideal model delta sigma weight residual 113.80 120.80 -7.00 1.00e+00 1.00e+00 4.90e+01 ... (remaining 23459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 9590 16.77 - 33.54: 350 33.54 - 50.30: 21 50.30 - 67.07: 21 67.07 - 83.84: 7 Dihedral angle restraints: 9989 sinusoidal: 3199 harmonic: 6790 Sorted by residual: dihedral pdb=" CB CYS E2077 " pdb=" SG CYS E2077 " pdb=" SG CYS E2214 " pdb=" CB CYS E2214 " ideal model delta sinusoidal sigma weight residual 93.00 149.90 -56.90 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS B2077 " pdb=" SG CYS B2077 " pdb=" SG CYS B2214 " pdb=" CB CYS B2214 " ideal model delta sinusoidal sigma weight residual 93.00 149.86 -56.86 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CB CYS A2077 " pdb=" SG CYS A2077 " pdb=" SG CYS A2214 " pdb=" CB CYS A2214 " ideal model delta sinusoidal sigma weight residual 93.00 149.86 -56.86 1 1.00e+01 1.00e-02 4.35e+01 ... (remaining 9986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1801 0.064 - 0.129: 745 0.129 - 0.193: 306 0.193 - 0.258: 74 0.258 - 0.322: 21 Chirality restraints: 2947 Sorted by residual: chirality pdb=" CB VAL B2158 " pdb=" CA VAL B2158 " pdb=" CG1 VAL B2158 " pdb=" CG2 VAL B2158 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB VAL E2158 " pdb=" CA VAL E2158 " pdb=" CG1 VAL E2158 " pdb=" CG2 VAL E2158 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL D2158 " pdb=" CA VAL D2158 " pdb=" CG1 VAL D2158 " pdb=" CG2 VAL D2158 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2944 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G2156 " 0.039 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE G2156 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE G2156 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE G2156 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G2156 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE G2156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE G2156 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D2156 " 0.040 2.00e-02 2.50e+03 3.16e-02 1.74e+01 pdb=" CG PHE D2156 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE D2156 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D2156 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D2156 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE D2156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D2156 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F2156 " 0.040 2.00e-02 2.50e+03 3.15e-02 1.74e+01 pdb=" CG PHE F2156 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE F2156 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE F2156 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F2156 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE F2156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F2156 " 0.006 2.00e-02 2.50e+03 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4705 2.81 - 3.33: 14988 3.33 - 3.85: 27486 3.85 - 4.38: 30866 4.38 - 4.90: 53391 Nonbonded interactions: 131436 Sorted by model distance: nonbonded pdb=" ND2 ASN F2321 " pdb=" O THR F2389 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN D2321 " pdb=" O THR D2389 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN E2321 " pdb=" O THR E2389 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN B2321 " pdb=" O THR B2389 " model vdw 2.286 3.120 nonbonded pdb=" ND2 ASN A2321 " pdb=" O THR A2389 " model vdw 2.286 3.120 ... (remaining 131431 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.800 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 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 : 0.018 0.172 16968 Z= 0.895 Angle : 1.590 9.181 23506 Z= 1.067 Chirality : 0.084 0.322 2947 Planarity : 0.008 0.037 3073 Dihedral : 9.429 83.838 5572 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.32 % 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: 0.44 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.86 (0.18), residues: 854 loop : 0.01 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D2260 TYR 0.040 0.006 TYR F2283 PHE 0.072 0.010 PHE G2156 TRP 0.024 0.006 TRP B2177 Details of bonding type rmsd covalent geometry : bond 0.01819 (16947) covalent geometry : angle 1.58765 (23464) SS BOND : bond 0.00718 ( 21) SS BOND : angle 2.70664 ( 42) hydrogen bonds : bond 0.17182 ( 455) hydrogen bonds : angle 9.30572 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 2099 ASP cc_start: 0.7563 (t0) cc_final: 0.7183 (t0) REVERT: A 2104 ASN cc_start: 0.6863 (m-40) cc_final: 0.6633 (t0) REVERT: A 2119 ASN cc_start: 0.7473 (t0) cc_final: 0.7099 (p0) REVERT: A 2176 ASP cc_start: 0.7988 (t0) cc_final: 0.7768 (t70) REVERT: A 2186 ASN cc_start: 0.8284 (m110) cc_final: 0.7192 (p0) REVERT: A 2235 THR cc_start: 0.7290 (m) cc_final: 0.6829 (p) REVERT: A 2309 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6821 (mt-10) REVERT: B 2099 ASP cc_start: 0.7660 (t0) cc_final: 0.7337 (t0) REVERT: B 2104 ASN cc_start: 0.6738 (m-40) cc_final: 0.6521 (t0) REVERT: B 2175 TYR cc_start: 0.7591 (m-80) cc_final: 0.7385 (m-80) REVERT: B 2176 ASP cc_start: 0.7870 (t0) cc_final: 0.7620 (t70) REVERT: B 2186 ASN cc_start: 0.8156 (m110) cc_final: 0.6956 (p0) REVERT: B 2235 THR cc_start: 0.7192 (m) cc_final: 0.6737 (p) REVERT: B 2309 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6839 (mt-10) REVERT: B 2368 ASN cc_start: 0.7548 (t0) cc_final: 0.7328 (m-40) REVERT: C 2099 ASP cc_start: 0.7779 (t0) cc_final: 0.7413 (t0) REVERT: C 2104 ASN cc_start: 0.6896 (m-40) cc_final: 0.6668 (t0) REVERT: C 2119 ASN cc_start: 0.7463 (t0) cc_final: 0.7098 (p0) REVERT: C 2176 ASP cc_start: 0.7879 (t0) cc_final: 0.7508 (t70) REVERT: C 2186 ASN cc_start: 0.8193 (m110) cc_final: 0.7177 (p0) REVERT: C 2235 THR cc_start: 0.7426 (m) cc_final: 0.6935 (p) REVERT: C 2248 MET cc_start: 0.7044 (mtp) cc_final: 0.6756 (mtm) REVERT: C 2266 ASP cc_start: 0.7248 (p0) cc_final: 0.7027 (p0) REVERT: C 2309 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6587 (mt-10) REVERT: D 2099 ASP cc_start: 0.7684 (t0) cc_final: 0.7424 (t0) REVERT: D 2104 ASN cc_start: 0.6848 (m-40) cc_final: 0.6374 (t0) REVERT: D 2119 ASN cc_start: 0.7502 (t0) cc_final: 0.7240 (p0) REVERT: D 2176 ASP cc_start: 0.7947 (t0) cc_final: 0.7632 (t70) REVERT: D 2186 ASN cc_start: 0.8148 (m110) cc_final: 0.6888 (p0) REVERT: D 2235 THR cc_start: 0.7224 (m) cc_final: 0.6849 (p) REVERT: D 2309 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6834 (mt-10) REVERT: E 2099 ASP cc_start: 0.7738 (t0) cc_final: 0.7409 (t0) REVERT: E 2119 ASN cc_start: 0.7518 (t0) cc_final: 0.7097 (p0) REVERT: E 2176 ASP cc_start: 0.7831 (t0) cc_final: 0.7391 (t70) REVERT: E 2186 ASN cc_start: 0.8099 (m110) cc_final: 0.7329 (p0) REVERT: E 2235 THR cc_start: 0.7256 (m) cc_final: 0.6902 (p) REVERT: E 2266 ASP cc_start: 0.7330 (p0) cc_final: 0.7127 (p0) REVERT: E 2368 ASN cc_start: 0.7633 (t0) cc_final: 0.7377 (m-40) REVERT: F 2099 ASP cc_start: 0.7683 (t0) cc_final: 0.7350 (t0) REVERT: F 2104 ASN cc_start: 0.6620 (m-40) cc_final: 0.6199 (t0) REVERT: F 2119 ASN cc_start: 0.7403 (t0) cc_final: 0.7119 (p0) REVERT: F 2176 ASP cc_start: 0.7854 (t0) cc_final: 0.7438 (t0) REVERT: F 2186 ASN cc_start: 0.8241 (m110) cc_final: 0.6908 (p0) REVERT: F 2235 THR cc_start: 0.7251 (m) cc_final: 0.6828 (p) REVERT: F 2368 ASN cc_start: 0.7624 (t0) cc_final: 0.7420 (m-40) REVERT: G 2099 ASP cc_start: 0.7504 (t0) cc_final: 0.7158 (t0) REVERT: G 2104 ASN cc_start: 0.6799 (m-40) cc_final: 0.6391 (t0) REVERT: G 2119 ASN cc_start: 0.7498 (t0) cc_final: 0.7221 (p0) REVERT: G 2186 ASN cc_start: 0.8290 (m110) cc_final: 0.7154 (p0) REVERT: G 2235 THR cc_start: 0.7470 (m) cc_final: 0.6969 (p) REVERT: G 2368 ASN cc_start: 0.7633 (t0) cc_final: 0.7431 (m-40) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.0857 time to fit residues: 60.5003 Evaluate side-chains 227 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2062 ASN A2073 ASN A2186 ASN B2062 ASN B2186 ASN C2062 ASN C2186 ASN D2062 ASN D2186 ASN E2062 ASN E2186 ASN F2062 ASN F2186 ASN G2062 ASN G2186 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.128453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.102001 restraints weight = 18856.315| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.42 r_work: 0.2844 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16968 Z= 0.158 Angle : 0.582 6.369 23506 Z= 0.312 Chirality : 0.046 0.155 2947 Planarity : 0.005 0.040 3073 Dihedral : 5.100 17.362 2443 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.97 % Allowed : 7.92 % Favored : 89.10 % 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: 0.58 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.93 (0.17), residues: 896 loop : 0.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C2260 TYR 0.009 0.001 TYR B2393 PHE 0.021 0.003 PHE G2106 TRP 0.012 0.002 TRP A2177 Details of bonding type rmsd covalent geometry : bond 0.00375 (16947) covalent geometry : angle 0.58159 (23464) SS BOND : bond 0.00164 ( 21) SS BOND : angle 0.82767 ( 42) hydrogen bonds : bond 0.03796 ( 455) hydrogen bonds : angle 5.61227 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.647 Fit side-chains REVERT: A 2085 SER cc_start: 0.8761 (p) cc_final: 0.8451 (t) REVERT: A 2186 ASN cc_start: 0.8354 (m-40) cc_final: 0.7885 (p0) REVERT: A 2309 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 2325 VAL cc_start: 0.7467 (t) cc_final: 0.7149 (m) REVERT: A 2368 ASN cc_start: 0.8138 (m-40) cc_final: 0.7787 (m-40) REVERT: B 2085 SER cc_start: 0.8572 (p) cc_final: 0.8265 (t) REVERT: B 2151 SER cc_start: 0.8920 (t) cc_final: 0.8618 (m) REVERT: B 2186 ASN cc_start: 0.8247 (m-40) cc_final: 0.7924 (p0) REVERT: B 2248 MET cc_start: 0.8841 (mtp) cc_final: 0.8614 (mtm) REVERT: B 2309 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 2364 ASN cc_start: 0.8654 (m110) cc_final: 0.8358 (m-40) REVERT: C 2116 ASN cc_start: 0.9099 (t0) cc_final: 0.8852 (t0) REVERT: C 2186 ASN cc_start: 0.8301 (m-40) cc_final: 0.7928 (p0) REVERT: C 2309 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 2368 ASN cc_start: 0.8043 (m-40) cc_final: 0.7733 (m-40) REVERT: D 2085 SER cc_start: 0.8430 (p) cc_final: 0.8177 (t) REVERT: D 2116 ASN cc_start: 0.8987 (t0) cc_final: 0.8462 (t0) REVERT: D 2129 VAL cc_start: 0.7942 (t) cc_final: 0.7682 (t) REVERT: D 2186 ASN cc_start: 0.8140 (m-40) cc_final: 0.7761 (p0) REVERT: D 2248 MET cc_start: 0.8920 (mtp) cc_final: 0.8631 (mtm) REVERT: D 2309 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8199 (mt-10) REVERT: E 2364 ASN cc_start: 0.8802 (m110) cc_final: 0.8577 (m110) REVERT: F 2085 SER cc_start: 0.8752 (p) cc_final: 0.8300 (m) REVERT: F 2099 ASP cc_start: 0.7281 (t0) cc_final: 0.7026 (t0) REVERT: F 2186 ASN cc_start: 0.8269 (m-40) cc_final: 0.8030 (p0) REVERT: F 2364 ASN cc_start: 0.8845 (m110) cc_final: 0.8540 (m-40) REVERT: G 2099 ASP cc_start: 0.7169 (t0) cc_final: 0.6867 (t0) REVERT: G 2116 ASN cc_start: 0.8922 (t0) cc_final: 0.8545 (t0) REVERT: G 2186 ASN cc_start: 0.8316 (m-40) cc_final: 0.7925 (p0) outliers start: 57 outliers final: 44 residues processed: 285 average time/residue: 0.0822 time to fit residues: 42.2173 Evaluate side-chains 226 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2147 THR Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2147 THR Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2147 THR Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2325 VAL Chi-restraints excluded: chain D residue 2334 SER Chi-restraints excluded: chain D residue 2371 THR Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2126 LEU Chi-restraints excluded: chain E residue 2147 THR Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2195 ASN Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2325 VAL Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2126 LEU Chi-restraints excluded: chain F residue 2147 THR Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2325 VAL Chi-restraints excluded: chain F residue 2334 SER Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2147 THR Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 150 optimal weight: 0.3980 chunk 211 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2365 ASN B2073 ASN B2322 ASN C2322 ASN C2365 ASN D2322 ASN E2322 ASN G2322 ASN G2365 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.096595 restraints weight = 18766.691| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.49 r_work: 0.2820 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16968 Z= 0.118 Angle : 0.509 6.108 23506 Z= 0.267 Chirality : 0.044 0.146 2947 Planarity : 0.005 0.043 3073 Dihedral : 4.412 15.583 2443 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.71 % Allowed : 10.06 % Favored : 87.23 % 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: 0.85 (0.17), residues: 2345 helix: None (None), residues: 0 sheet: 0.94 (0.16), residues: 966 loop : 0.39 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D2260 TYR 0.007 0.001 TYR F2124 PHE 0.016 0.002 PHE D2106 TRP 0.009 0.001 TRP A2177 Details of bonding type rmsd covalent geometry : bond 0.00283 (16947) covalent geometry : angle 0.50908 (23464) SS BOND : bond 0.00072 ( 21) SS BOND : angle 0.51391 ( 42) hydrogen bonds : bond 0.03316 ( 455) hydrogen bonds : angle 4.99787 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.611 Fit side-chains REVERT: A 2085 SER cc_start: 0.8642 (p) cc_final: 0.8106 (m) REVERT: A 2099 ASP cc_start: 0.7183 (t0) cc_final: 0.6934 (t0) REVERT: A 2116 ASN cc_start: 0.8910 (t0) cc_final: 0.8568 (t0) REVERT: A 2309 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 2325 VAL cc_start: 0.7431 (t) cc_final: 0.7228 (m) REVERT: A 2368 ASN cc_start: 0.8209 (m-40) cc_final: 0.7855 (m-40) REVERT: B 2085 SER cc_start: 0.8673 (p) cc_final: 0.8121 (m) REVERT: B 2151 SER cc_start: 0.8980 (t) cc_final: 0.8669 (m) REVERT: B 2186 ASN cc_start: 0.8246 (m-40) cc_final: 0.8011 (p0) REVERT: B 2309 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 2374 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9032 (tp) REVERT: C 2309 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8159 (mt-10) REVERT: C 2322 ASN cc_start: 0.7606 (m-40) cc_final: 0.7358 (m110) REVERT: C 2325 VAL cc_start: 0.7629 (t) cc_final: 0.7397 (m) REVERT: D 2085 SER cc_start: 0.8428 (p) cc_final: 0.8099 (t) REVERT: D 2116 ASN cc_start: 0.8961 (t0) cc_final: 0.8562 (t0) REVERT: D 2129 VAL cc_start: 0.7991 (t) cc_final: 0.7745 (t) REVERT: D 2186 ASN cc_start: 0.8162 (m-40) cc_final: 0.7871 (p0) REVERT: D 2309 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8275 (mt-10) REVERT: D 2325 VAL cc_start: 0.7845 (t) cc_final: 0.7529 (m) REVERT: E 2186 ASN cc_start: 0.8260 (p0) cc_final: 0.7872 (p0) REVERT: F 2085 SER cc_start: 0.8812 (p) cc_final: 0.8275 (m) REVERT: F 2099 ASP cc_start: 0.7310 (t0) cc_final: 0.7070 (t0) REVERT: G 2099 ASP cc_start: 0.7056 (t0) cc_final: 0.6851 (t0) REVERT: G 2116 ASN cc_start: 0.8935 (t0) cc_final: 0.8513 (t0) REVERT: G 2309 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8331 (mt-10) outliers start: 52 outliers final: 31 residues processed: 237 average time/residue: 0.0807 time to fit residues: 34.3275 Evaluate side-chains 201 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2207 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2146 LEU Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN ** B2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2368 ASN ** E2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2368 ASN G2186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.089475 restraints weight = 19076.919| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.59 r_work: 0.2633 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 16968 Z= 0.352 Angle : 0.687 7.649 23506 Z= 0.362 Chirality : 0.052 0.194 2947 Planarity : 0.006 0.057 3073 Dihedral : 5.320 22.412 2443 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.13 % Allowed : 11.00 % Favored : 85.87 % 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: 0.05 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.57 (0.16), residues: 875 loop : -0.26 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D2260 TYR 0.015 0.002 TYR A2097 PHE 0.022 0.004 PHE A2106 TRP 0.014 0.002 TRP B2259 Details of bonding type rmsd covalent geometry : bond 0.00886 (16947) covalent geometry : angle 0.68655 (23464) SS BOND : bond 0.00197 ( 21) SS BOND : angle 0.81024 ( 42) hydrogen bonds : bond 0.04902 ( 455) hydrogen bonds : angle 5.53736 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 2085 SER cc_start: 0.8773 (p) cc_final: 0.8503 (t) REVERT: A 2309 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 2085 SER cc_start: 0.8730 (p) cc_final: 0.8472 (t) REVERT: B 2186 ASN cc_start: 0.8338 (m-40) cc_final: 0.8030 (p0) REVERT: B 2248 MET cc_start: 0.9030 (mtp) cc_final: 0.8703 (mtm) REVERT: B 2309 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 2374 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9086 (tp) REVERT: C 2309 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8201 (mt-10) REVERT: D 2085 SER cc_start: 0.8546 (p) cc_final: 0.8224 (t) REVERT: D 2099 ASP cc_start: 0.8780 (p0) cc_final: 0.8560 (p0) REVERT: D 2104 ASN cc_start: 0.7680 (m-40) cc_final: 0.7213 (t0) REVERT: D 2116 ASN cc_start: 0.8923 (t0) cc_final: 0.8489 (t0) REVERT: D 2130 ASN cc_start: 0.8975 (t0) cc_final: 0.8649 (t0) REVERT: D 2186 ASN cc_start: 0.8278 (m-40) cc_final: 0.7931 (p0) REVERT: D 2309 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8256 (mt-10) REVERT: E 2186 ASN cc_start: 0.8667 (p0) cc_final: 0.8319 (p0) REVERT: F 2085 SER cc_start: 0.8792 (p) cc_final: 0.8241 (m) REVERT: F 2099 ASP cc_start: 0.7545 (t0) cc_final: 0.7314 (t0) REVERT: F 2130 ASN cc_start: 0.8876 (t0) cc_final: 0.8641 (t0) REVERT: F 2325 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7610 (m) REVERT: G 2116 ASN cc_start: 0.8866 (t0) cc_final: 0.8445 (t0) outliers start: 60 outliers final: 45 residues processed: 236 average time/residue: 0.0868 time to fit residues: 36.9816 Evaluate side-chains 221 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2207 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2207 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2318 SER Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2318 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2375 LEU Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2111 ASN Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2325 VAL Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 161 optimal weight: 0.0970 chunk 216 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2322 ASN B2364 ASN B2368 ASN C2322 ASN D2368 ASN E2322 ASN F2322 ASN G2368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.121782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.094330 restraints weight = 18639.446| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.48 r_work: 0.2763 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16968 Z= 0.105 Angle : 0.491 6.350 23506 Z= 0.255 Chirality : 0.043 0.147 2947 Planarity : 0.005 0.048 3073 Dihedral : 4.313 18.261 2443 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.87 % Allowed : 12.10 % Favored : 85.04 % 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: 0.39 (0.17), residues: 2345 helix: None (None), residues: 0 sheet: 0.39 (0.16), residues: 938 loop : 0.28 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B2260 TYR 0.008 0.001 TYR B2124 PHE 0.013 0.002 PHE A2106 TRP 0.013 0.001 TRP A2177 Details of bonding type rmsd covalent geometry : bond 0.00257 (16947) covalent geometry : angle 0.49089 (23464) SS BOND : bond 0.00023 ( 21) SS BOND : angle 0.37866 ( 42) hydrogen bonds : bond 0.03130 ( 455) hydrogen bonds : angle 4.83543 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 2085 SER cc_start: 0.8661 (p) cc_final: 0.8142 (m) REVERT: A 2309 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 2085 SER cc_start: 0.8671 (p) cc_final: 0.8146 (m) REVERT: B 2130 ASN cc_start: 0.8799 (t0) cc_final: 0.8581 (t0) REVERT: B 2248 MET cc_start: 0.8850 (mtp) cc_final: 0.8607 (mtm) REVERT: B 2309 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8357 (mt-10) REVERT: C 2309 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 2085 SER cc_start: 0.8498 (p) cc_final: 0.8179 (t) REVERT: D 2116 ASN cc_start: 0.8874 (t0) cc_final: 0.8441 (t0) REVERT: D 2130 ASN cc_start: 0.8890 (t0) cc_final: 0.8533 (t0) REVERT: D 2248 MET cc_start: 0.8880 (mtp) cc_final: 0.8543 (mtm) REVERT: D 2309 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8346 (mt-10) REVERT: E 2186 ASN cc_start: 0.8627 (p0) cc_final: 0.8302 (p0) REVERT: E 2253 THR cc_start: 0.8908 (m) cc_final: 0.8682 (t) REVERT: E 2309 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8310 (mt-10) REVERT: F 2085 SER cc_start: 0.8768 (p) cc_final: 0.8226 (m) REVERT: F 2130 ASN cc_start: 0.8822 (t0) cc_final: 0.8596 (t0) REVERT: F 2253 THR cc_start: 0.8967 (m) cc_final: 0.8765 (t) REVERT: G 2248 MET cc_start: 0.8868 (mtp) cc_final: 0.8667 (mtm) REVERT: G 2263 ASN cc_start: 0.8598 (p0) cc_final: 0.8279 (p0) REVERT: G 2309 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8332 (mt-10) outliers start: 55 outliers final: 43 residues processed: 239 average time/residue: 0.0889 time to fit residues: 38.0161 Evaluate side-chains 213 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2118 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2146 LEU Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2277 VAL Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2277 VAL Chi-restraints excluded: chain G residue 2334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN B2368 ASN G2368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.123757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.094953 restraints weight = 18611.251| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.68 r_work: 0.2656 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16968 Z= 0.196 Angle : 0.555 7.863 23506 Z= 0.288 Chirality : 0.045 0.158 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.480 19.761 2443 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.65 % Allowed : 12.10 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.18 (0.16), residues: 938 loop : 0.22 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D2260 TYR 0.009 0.001 TYR A2097 PHE 0.015 0.003 PHE A2106 TRP 0.009 0.002 TRP G2259 Details of bonding type rmsd covalent geometry : bond 0.00501 (16947) covalent geometry : angle 0.55519 (23464) SS BOND : bond 0.00074 ( 21) SS BOND : angle 0.43723 ( 42) hydrogen bonds : bond 0.03761 ( 455) hydrogen bonds : angle 4.94804 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 0.560 Fit side-chains REVERT: A 2085 SER cc_start: 0.8683 (p) cc_final: 0.8118 (m) REVERT: A 2309 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 2375 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9080 (mp) REVERT: B 2085 SER cc_start: 0.8715 (p) cc_final: 0.8181 (m) REVERT: B 2104 ASN cc_start: 0.7314 (m-40) cc_final: 0.6985 (t0) REVERT: B 2309 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 2365 ASN cc_start: 0.8957 (t0) cc_final: 0.8646 (t0) REVERT: C 2309 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8253 (mt-10) REVERT: D 2085 SER cc_start: 0.8537 (p) cc_final: 0.8211 (t) REVERT: D 2116 ASN cc_start: 0.8867 (t0) cc_final: 0.8422 (t0) REVERT: D 2130 ASN cc_start: 0.8932 (t0) cc_final: 0.8568 (t0) REVERT: D 2309 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8284 (mt-10) REVERT: E 2186 ASN cc_start: 0.8728 (p0) cc_final: 0.8388 (p0) REVERT: E 2253 THR cc_start: 0.8919 (m) cc_final: 0.8676 (t) REVERT: E 2309 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8257 (mt-10) REVERT: F 2085 SER cc_start: 0.8803 (p) cc_final: 0.8240 (m) REVERT: F 2130 ASN cc_start: 0.8854 (t0) cc_final: 0.8648 (t0) REVERT: F 2253 THR cc_start: 0.8944 (m) cc_final: 0.8713 (t) REVERT: G 2248 MET cc_start: 0.8932 (mtp) cc_final: 0.8710 (mtm) REVERT: G 2263 ASN cc_start: 0.8658 (p0) cc_final: 0.8319 (p0) REVERT: G 2309 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8350 (tt0) outliers start: 70 outliers final: 61 residues processed: 228 average time/residue: 0.0855 time to fit residues: 35.1733 Evaluate side-chains 227 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2126 LEU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2194 THR Chi-restraints excluded: chain B residue 2207 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2367 THR Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2078 THR Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2118 THR Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2118 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2277 VAL Chi-restraints excluded: chain D residue 2334 SER Chi-restraints excluded: chain D residue 2375 LEU Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2318 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2069 SER Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2277 VAL Chi-restraints excluded: chain F residue 2334 SER Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2277 VAL Chi-restraints excluded: chain G residue 2334 SER Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 163 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 196 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN B2368 ASN G2368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099570 restraints weight = 18539.156| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.66 r_work: 0.2690 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16968 Z= 0.128 Angle : 0.501 6.546 23506 Z= 0.259 Chirality : 0.043 0.150 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.164 18.190 2443 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.23 % Allowed : 12.41 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.20 (0.15), residues: 938 loop : 0.36 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F2260 TYR 0.007 0.001 TYR A2124 PHE 0.013 0.002 PHE A2106 TRP 0.011 0.001 TRP B2177 Details of bonding type rmsd covalent geometry : bond 0.00335 (16947) covalent geometry : angle 0.50127 (23464) SS BOND : bond 0.00043 ( 21) SS BOND : angle 0.32919 ( 42) hydrogen bonds : bond 0.03177 ( 455) hydrogen bonds : angle 4.72500 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.573 Fit side-chains REVERT: A 2085 SER cc_start: 0.8673 (p) cc_final: 0.8112 (m) REVERT: A 2309 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 2375 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9076 (mp) REVERT: B 2085 SER cc_start: 0.8691 (p) cc_final: 0.8159 (m) REVERT: B 2309 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8360 (mt-10) REVERT: B 2365 ASN cc_start: 0.8934 (t0) cc_final: 0.8551 (t0) REVERT: C 2309 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 2085 SER cc_start: 0.8546 (p) cc_final: 0.8226 (t) REVERT: D 2116 ASN cc_start: 0.8809 (t0) cc_final: 0.8395 (t0) REVERT: D 2130 ASN cc_start: 0.8917 (t0) cc_final: 0.8543 (t0) REVERT: D 2186 ASN cc_start: 0.8539 (p0) cc_final: 0.8330 (p0) REVERT: D 2248 MET cc_start: 0.8902 (mtp) cc_final: 0.8549 (mtm) REVERT: D 2309 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8310 (mt-10) REVERT: E 2186 ASN cc_start: 0.8742 (p0) cc_final: 0.8413 (p0) REVERT: E 2253 THR cc_start: 0.8913 (m) cc_final: 0.8699 (t) REVERT: E 2309 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8301 (mt-10) REVERT: F 2085 SER cc_start: 0.8804 (p) cc_final: 0.8228 (m) REVERT: F 2130 ASN cc_start: 0.8828 (t0) cc_final: 0.8620 (t0) REVERT: G 2248 MET cc_start: 0.8903 (mtp) cc_final: 0.8699 (mtm) REVERT: G 2263 ASN cc_start: 0.8648 (p0) cc_final: 0.8294 (p0) REVERT: G 2309 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8335 (tt0) outliers start: 62 outliers final: 57 residues processed: 222 average time/residue: 0.0757 time to fit residues: 30.0982 Evaluate side-chains 230 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2194 THR Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2367 THR Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 2118 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2277 VAL Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain D residue 2318 SER Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2078 THR Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2146 LEU Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2277 VAL Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2277 VAL Chi-restraints excluded: chain G residue 2334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 189 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 0.0060 overall best weight: 1.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN B2368 ASN D2368 ASN G2368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.096086 restraints weight = 18737.088| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.67 r_work: 0.2686 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16968 Z= 0.161 Angle : 0.525 7.427 23506 Z= 0.271 Chirality : 0.044 0.154 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.227 18.730 2443 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.49 % Allowed : 12.30 % Favored : 84.20 % 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: 0.24 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.13 (0.16), residues: 931 loop : 0.32 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D2260 TYR 0.007 0.001 TYR B2373 PHE 0.014 0.002 PHE A2106 TRP 0.008 0.001 TRP B2177 Details of bonding type rmsd covalent geometry : bond 0.00416 (16947) covalent geometry : angle 0.52536 (23464) SS BOND : bond 0.00049 ( 21) SS BOND : angle 0.35480 ( 42) hydrogen bonds : bond 0.03438 ( 455) hydrogen bonds : angle 4.79723 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 0.519 Fit side-chains REVERT: A 2085 SER cc_start: 0.8668 (p) cc_final: 0.8055 (m) REVERT: A 2309 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 2375 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9050 (mp) REVERT: B 2085 SER cc_start: 0.8665 (p) cc_final: 0.8123 (m) REVERT: B 2104 ASN cc_start: 0.7705 (t0) cc_final: 0.7415 (t0) REVERT: B 2309 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 2365 ASN cc_start: 0.8892 (t0) cc_final: 0.8526 (t0) REVERT: C 2309 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8166 (mt-10) REVERT: D 2085 SER cc_start: 0.8509 (p) cc_final: 0.8189 (t) REVERT: D 2116 ASN cc_start: 0.8791 (t0) cc_final: 0.8371 (t0) REVERT: D 2130 ASN cc_start: 0.8925 (t0) cc_final: 0.8492 (t0) REVERT: D 2186 ASN cc_start: 0.8550 (p0) cc_final: 0.8240 (p0) REVERT: D 2248 MET cc_start: 0.8959 (mtp) cc_final: 0.8692 (mtm) REVERT: D 2309 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8196 (mt-10) REVERT: E 2186 ASN cc_start: 0.8734 (p0) cc_final: 0.8392 (p0) REVERT: E 2253 THR cc_start: 0.8893 (m) cc_final: 0.8667 (t) REVERT: E 2309 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8190 (mt-10) REVERT: E 2318 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8222 (t) REVERT: F 2085 SER cc_start: 0.8772 (p) cc_final: 0.8179 (m) REVERT: F 2130 ASN cc_start: 0.8862 (t0) cc_final: 0.8648 (t0) REVERT: G 2248 MET cc_start: 0.8938 (mtp) cc_final: 0.8720 (mtm) REVERT: G 2263 ASN cc_start: 0.8608 (p0) cc_final: 0.8182 (p0) REVERT: G 2309 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8230 (tt0) outliers start: 67 outliers final: 62 residues processed: 226 average time/residue: 0.0749 time to fit residues: 30.5984 Evaluate side-chains 231 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2126 LEU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2194 THR Chi-restraints excluded: chain B residue 2207 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2367 THR Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2078 THR Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2277 VAL Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain D residue 2318 SER Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2078 THR Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2146 LEU Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2318 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2069 SER Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2277 VAL Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2085 SER Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2277 VAL Chi-restraints excluded: chain G residue 2334 SER Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 44 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN B2368 ASN D2368 ASN G2368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.125067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.096444 restraints weight = 18684.070| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.67 r_work: 0.2745 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 16968 Z= 0.150 Angle : 0.515 6.872 23506 Z= 0.266 Chirality : 0.044 0.153 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.160 18.546 2443 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.44 % Allowed : 12.46 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.08 (0.15), residues: 931 loop : 0.36 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D2260 TYR 0.007 0.001 TYR B2373 PHE 0.014 0.002 PHE A2106 TRP 0.009 0.001 TRP B2177 Details of bonding type rmsd covalent geometry : bond 0.00398 (16947) covalent geometry : angle 0.51503 (23464) SS BOND : bond 0.00041 ( 21) SS BOND : angle 0.33244 ( 42) hydrogen bonds : bond 0.03323 ( 455) hydrogen bonds : angle 4.74282 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 0.440 Fit side-chains REVERT: A 2085 SER cc_start: 0.8651 (p) cc_final: 0.8044 (m) REVERT: A 2309 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8037 (mt-10) REVERT: A 2375 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9067 (mp) REVERT: B 2085 SER cc_start: 0.8654 (p) cc_final: 0.8109 (m) REVERT: B 2104 ASN cc_start: 0.7751 (t0) cc_final: 0.7414 (t0) REVERT: B 2130 ASN cc_start: 0.8796 (t0) cc_final: 0.8330 (t0) REVERT: B 2309 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 2365 ASN cc_start: 0.8873 (t0) cc_final: 0.8477 (t0) REVERT: C 2309 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 2085 SER cc_start: 0.8522 (p) cc_final: 0.8201 (t) REVERT: D 2116 ASN cc_start: 0.8795 (t0) cc_final: 0.8393 (t0) REVERT: D 2130 ASN cc_start: 0.8956 (t0) cc_final: 0.8519 (t0) REVERT: D 2186 ASN cc_start: 0.8545 (p0) cc_final: 0.8286 (p0) REVERT: D 2248 MET cc_start: 0.8920 (mtp) cc_final: 0.8658 (mtm) REVERT: D 2309 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8207 (mt-10) REVERT: E 2186 ASN cc_start: 0.8717 (p0) cc_final: 0.8391 (p0) REVERT: E 2253 THR cc_start: 0.8905 (m) cc_final: 0.8685 (t) REVERT: E 2309 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8176 (mt-10) REVERT: E 2318 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8240 (t) REVERT: G 2248 MET cc_start: 0.8927 (mtp) cc_final: 0.8691 (mtm) REVERT: G 2263 ASN cc_start: 0.8598 (p0) cc_final: 0.8203 (p0) REVERT: G 2309 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8294 (tt0) outliers start: 66 outliers final: 62 residues processed: 231 average time/residue: 0.0728 time to fit residues: 30.2076 Evaluate side-chains 237 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 173 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2126 LEU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2194 THR Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2248 MET Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2367 THR Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2078 THR Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2277 VAL Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain D residue 2318 SER Chi-restraints excluded: chain D residue 2334 SER Chi-restraints excluded: chain E residue 2063 SER Chi-restraints excluded: chain E residue 2078 THR Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2146 LEU Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2312 SER Chi-restraints excluded: chain E residue 2318 SER Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2277 VAL Chi-restraints excluded: chain F residue 2334 SER Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2085 SER Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2277 VAL Chi-restraints excluded: chain G residue 2334 SER Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 122 optimal weight: 2.9990 chunk 187 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 144 optimal weight: 0.0570 chunk 45 optimal weight: 0.0570 chunk 206 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN B2368 ASN E2200 ASN F2200 ASN G2368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.102779 restraints weight = 18443.535| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.65 r_work: 0.2737 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 16968 Z= 0.097 Angle : 0.475 6.851 23506 Z= 0.245 Chirality : 0.042 0.142 2947 Planarity : 0.005 0.045 3073 Dihedral : 3.734 16.295 2443 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.87 % Allowed : 13.45 % Favored : 83.68 % 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: 0.47 (0.17), residues: 2345 helix: None (None), residues: 0 sheet: 0.26 (0.16), residues: 931 loop : 0.50 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F2260 TYR 0.006 0.001 TYR E2373 PHE 0.012 0.002 PHE A2106 TRP 0.012 0.001 TRP F2177 Details of bonding type rmsd covalent geometry : bond 0.00288 (16947) covalent geometry : angle 0.47538 (23464) SS BOND : bond 0.00039 ( 21) SS BOND : angle 0.26058 ( 42) hydrogen bonds : bond 0.02729 ( 455) hydrogen bonds : angle 4.48793 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.541 Fit side-chains REVERT: A 2085 SER cc_start: 0.8571 (p) cc_final: 0.7959 (m) REVERT: A 2253 THR cc_start: 0.8858 (m) cc_final: 0.8628 (t) REVERT: A 2309 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 2375 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9003 (mp) REVERT: A 2393 TYR cc_start: 0.9109 (m-10) cc_final: 0.8736 (m-10) REVERT: B 2085 SER cc_start: 0.8653 (p) cc_final: 0.8090 (m) REVERT: B 2104 ASN cc_start: 0.7669 (t0) cc_final: 0.7379 (t0) REVERT: B 2130 ASN cc_start: 0.8704 (t0) cc_final: 0.8233 (t0) REVERT: B 2151 SER cc_start: 0.8942 (t) cc_final: 0.8649 (m) REVERT: B 2365 ASN cc_start: 0.8798 (t0) cc_final: 0.8430 (t0) REVERT: C 2309 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8166 (mt-10) REVERT: D 2085 SER cc_start: 0.8484 (p) cc_final: 0.7970 (m) REVERT: D 2116 ASN cc_start: 0.8715 (t0) cc_final: 0.8222 (t0) REVERT: D 2130 ASN cc_start: 0.8892 (t0) cc_final: 0.8461 (t0) REVERT: D 2186 ASN cc_start: 0.8523 (p0) cc_final: 0.8264 (p0) REVERT: D 2248 MET cc_start: 0.8864 (mtp) cc_final: 0.8512 (mtm) REVERT: D 2309 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8209 (mt-10) REVERT: E 2186 ASN cc_start: 0.8696 (p0) cc_final: 0.8381 (p0) REVERT: E 2253 THR cc_start: 0.8981 (m) cc_final: 0.8747 (t) REVERT: E 2309 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8209 (mt-10) REVERT: E 2318 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8289 (t) REVERT: G 2263 ASN cc_start: 0.8505 (p0) cc_final: 0.8287 (p0) REVERT: G 2309 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8365 (tt0) outliers start: 55 outliers final: 48 residues processed: 234 average time/residue: 0.0819 time to fit residues: 34.4208 Evaluate side-chains 234 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2367 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2277 VAL Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain E residue 2078 THR Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2146 LEU Chi-restraints excluded: chain E residue 2185 SER Chi-restraints excluded: chain E residue 2208 ILE Chi-restraints excluded: chain E residue 2318 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 2255 ASN Chi-restraints excluded: chain F residue 2277 VAL Chi-restraints excluded: chain F residue 2334 SER Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2146 LEU Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2255 ASN Chi-restraints excluded: chain G residue 2277 VAL Chi-restraints excluded: chain G residue 2334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 78 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2186 ASN B2368 ASN C2186 ASN D2284 GLN G2368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.122301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.093730 restraints weight = 18706.421| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 1.66 r_work: 0.2663 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 16968 Z= 0.249 Angle : 0.587 7.659 23506 Z= 0.307 Chirality : 0.047 0.164 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.475 20.101 2443 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 13.76 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.11 (0.16), residues: 910 loop : 0.21 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D2260 TYR 0.016 0.002 TYR G2283 PHE 0.016 0.003 PHE B2106 TRP 0.012 0.002 TRP B2259 Details of bonding type rmsd covalent geometry : bond 0.00643 (16947) covalent geometry : angle 0.58739 (23464) SS BOND : bond 0.00088 ( 21) SS BOND : angle 0.42118 ( 42) hydrogen bonds : bond 0.03972 ( 455) hydrogen bonds : angle 4.98126 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.07 seconds wall clock time: 61 minutes 55.50 seconds (3715.50 seconds total)