Starting phenix.real_space_refine on Sun May 18 13:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fls_50538/05_2025/9fls_50538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fls_50538/05_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_50538/05_2025/9fls_50538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fls_50538/05_2025/9fls_50538.map" model { file = "/net/cci-nas-00/data/ceres_data/9fls_50538/05_2025/9fls_50538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fls_50538/05_2025/9fls_50538.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.168 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F Time building chain proxies: 5.73, per 1000 atoms: 0.35 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 C2077 " - pdb=" SG CYS C2214 " distance=2.03 Simple disulfide: pdb=" SG CYS B2077 " - pdb=" SG CYS B2214 " distance=2.03 Simple disulfide: pdb=" SG CYS E2077 " - pdb=" SG CYS E2214 " distance=2.03 Simple disulfide: pdb=" SG CYS D2077 " - pdb=" SG CYS D2214 " distance=2.03 Simple disulfide: pdb=" SG CYS G2077 " - pdb=" SG CYS G2214 " distance=2.03 Simple disulfide: pdb=" SG CYS F2077 " - pdb=" SG CYS F2214 " distance=2.03 Simple disulfide: pdb=" SG CYS C2159 " - pdb=" SG CYS C2298 " distance=2.02 Simple disulfide: pdb=" SG CYS B2159 " - pdb=" SG CYS B2298 " distance=2.02 Simple disulfide: pdb=" SG CYS E2159 " - pdb=" SG CYS E2298 " distance=2.02 Simple disulfide: pdb=" SG CYS D2159 " - pdb=" SG CYS D2298 " distance=2.02 Simple disulfide: pdb=" SG CYS G2159 " - pdb=" SG CYS G2298 " distance=2.02 Simple disulfide: pdb=" SG CYS F2159 " - pdb=" SG CYS F2298 " distance=2.02 Simple disulfide: pdb=" SG CYS C2241 " - pdb=" SG CYS C2381 " distance=2.04 Simple disulfide: pdb=" SG CYS B2241 " - pdb=" SG CYS B2381 " distance=2.04 Simple disulfide: pdb=" SG CYS E2241 " - pdb=" SG CYS E2381 " distance=2.04 Simple disulfide: pdb=" SG CYS D2241 " - pdb=" SG CYS D2381 " distance=2.04 Simple disulfide: pdb=" SG CYS G2241 " - pdb=" SG CYS G2381 " distance=2.04 Simple disulfide: pdb=" SG CYS F2241 " - pdb=" SG CYS F2381 " 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: 4.15 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 3.57 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: 6.19 Time building geometry restraints manager: 4.88 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.830 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- 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 : 6.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (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 TRP 0.024 0.006 TRP B2177 PHE 0.072 0.010 PHE G2156 TYR 0.040 0.006 TYR F2283 ARG 0.001 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.17182 ( 455) hydrogen bonds : angle 9.30572 ( 1155) SS BOND : bond 0.00718 ( 21) SS BOND : angle 2.70664 ( 42) covalent geometry : bond 0.01819 (16947) covalent geometry : angle 1.58765 (23464) *********************** 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 : 1.809 Fit side-chains revert: symmetry clash REVERT: A 2099 ASP cc_start: 0.7563 (t0) cc_final: 0.7182 (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: 0.7100 (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: 0.6820 (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: 0.7412 (t0) REVERT: C 2104 ASN cc_start: 0.6896 (m-40) cc_final: 0.6669 (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: 0.6835 (mt-10) REVERT: E 2099 ASP cc_start: 0.7738 (t0) cc_final: 0.7408 (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: 0.6827 (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: 0.6392 (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: 0.1787 time to fit residues: 123.9973 Evaluate side-chains 226 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B2284 GLN C2062 ASN C2186 ASN D2062 ASN D2186 ASN E2062 ASN E2186 ASN F2062 ASN F2111 ASN F2186 ASN G2062 ASN G2186 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.129249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102718 restraints weight = 18773.864| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.42 r_work: 0.2854 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16968 Z= 0.146 Angle : 0.577 6.287 23506 Z= 0.311 Chirality : 0.046 0.147 2947 Planarity : 0.005 0.038 3073 Dihedral : 5.067 17.209 2443 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.50 % Allowed : 8.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.99 (0.17), residues: 889 loop : 0.13 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A2177 PHE 0.019 0.003 PHE F2106 TYR 0.010 0.001 TYR B2393 ARG 0.001 0.000 ARG C2260 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 455) hydrogen bonds : angle 5.67453 ( 1155) SS BOND : bond 0.00170 ( 21) SS BOND : angle 0.79907 ( 42) covalent geometry : bond 0.00346 (16947) covalent geometry : angle 0.57651 (23464) *********************** 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 290 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.710 Fit side-chains REVERT: A 2085 SER cc_start: 0.8750 (p) cc_final: 0.8451 (t) REVERT: A 2186 ASN cc_start: 0.8346 (m-40) cc_final: 0.7866 (p0) REVERT: A 2309 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 2368 ASN cc_start: 0.8142 (m-40) cc_final: 0.7821 (m-40) REVERT: B 2085 SER cc_start: 0.8593 (p) cc_final: 0.8287 (t) REVERT: B 2151 SER cc_start: 0.8869 (t) cc_final: 0.8594 (m) REVERT: B 2186 ASN cc_start: 0.8282 (m-40) cc_final: 0.7954 (p0) REVERT: B 2248 MET cc_start: 0.8838 (mtp) cc_final: 0.8618 (mtm) REVERT: B 2309 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8212 (mt-10) REVERT: B 2364 ASN cc_start: 0.8688 (m110) cc_final: 0.8417 (m-40) REVERT: C 2116 ASN cc_start: 0.9162 (t0) cc_final: 0.8936 (t0) REVERT: C 2186 ASN cc_start: 0.8271 (m-40) cc_final: 0.7907 (p0) REVERT: C 2309 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8081 (mt-10) REVERT: C 2368 ASN cc_start: 0.7999 (m-40) cc_final: 0.7719 (m-40) REVERT: D 2085 SER cc_start: 0.8462 (p) cc_final: 0.8217 (t) REVERT: D 2116 ASN cc_start: 0.9004 (t0) cc_final: 0.8495 (t0) REVERT: D 2129 VAL cc_start: 0.8084 (t) cc_final: 0.7837 (t) REVERT: D 2176 ASP cc_start: 0.8268 (t0) cc_final: 0.7931 (t70) REVERT: D 2186 ASN cc_start: 0.8150 (m-40) cc_final: 0.7758 (p0) REVERT: D 2248 MET cc_start: 0.8892 (mtp) cc_final: 0.8613 (mtm) REVERT: D 2309 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8221 (mt-10) REVERT: E 2085 SER cc_start: 0.8674 (p) cc_final: 0.8414 (t) REVERT: E 2151 SER cc_start: 0.8822 (t) cc_final: 0.8579 (m) REVERT: E 2186 ASN cc_start: 0.8188 (m-40) cc_final: 0.7771 (p0) REVERT: E 2364 ASN cc_start: 0.8853 (m110) cc_final: 0.8543 (m-40) REVERT: F 2085 SER cc_start: 0.8769 (p) cc_final: 0.8280 (m) REVERT: F 2099 ASP cc_start: 0.7277 (t0) cc_final: 0.7026 (t0) REVERT: F 2186 ASN cc_start: 0.8318 (m-40) cc_final: 0.8049 (p0) REVERT: F 2364 ASN cc_start: 0.8829 (m110) cc_final: 0.8510 (m-40) REVERT: G 2099 ASP cc_start: 0.7174 (t0) cc_final: 0.6936 (t0) REVERT: G 2186 ASN cc_start: 0.8309 (m-40) cc_final: 0.7914 (p0) outliers start: 48 outliers final: 40 residues processed: 284 average time/residue: 0.1745 time to fit residues: 88.1478 Evaluate side-chains 220 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 B residue 2121 SER Chi-restraints excluded: chain B residue 2147 THR Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2327 THR 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 2126 LEU 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 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 2126 LEU Chi-restraints excluded: chain E residue 2147 THR 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 2325 VAL 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 2391 VAL Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2126 LEU Chi-restraints excluded: chain G residue 2147 THR Chi-restraints excluded: chain G residue 2208 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN ** B2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2364 ASN ** E2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.117240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.090513 restraints weight = 18722.757| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.36 r_work: 0.2740 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16968 Z= 0.249 Angle : 0.616 6.369 23506 Z= 0.326 Chirality : 0.048 0.169 2947 Planarity : 0.006 0.049 3073 Dihedral : 5.093 19.517 2443 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.96 % Allowed : 9.28 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.64 (0.16), residues: 952 loop : -0.05 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C2259 PHE 0.021 0.003 PHE A2106 TYR 0.011 0.002 TYR E2097 ARG 0.001 0.001 ARG C2260 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 455) hydrogen bonds : angle 5.46826 ( 1155) SS BOND : bond 0.00157 ( 21) SS BOND : angle 0.74443 ( 42) covalent geometry : bond 0.00625 (16947) covalent geometry : angle 0.61525 (23464) *********************** 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 270 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 194 time to evaluate : 2.037 Fit side-chains REVERT: A 2085 SER cc_start: 0.8751 (p) cc_final: 0.8457 (t) REVERT: A 2186 ASN cc_start: 0.8234 (m-40) cc_final: 0.7982 (p0) REVERT: A 2309 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8098 (mt-10) REVERT: A 2364 ASN cc_start: 0.9006 (m110) cc_final: 0.8754 (m-40) REVERT: A 2368 ASN cc_start: 0.8281 (m-40) cc_final: 0.7962 (m-40) REVERT: A 2375 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9138 (mp) REVERT: B 2085 SER cc_start: 0.8750 (p) cc_final: 0.8213 (m) REVERT: B 2104 ASN cc_start: 0.7200 (m-40) cc_final: 0.6989 (t0) REVERT: B 2175 TYR cc_start: 0.9254 (m-80) cc_final: 0.8971 (m-80) REVERT: B 2186 ASN cc_start: 0.8235 (m-40) cc_final: 0.7976 (p0) REVERT: B 2309 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 2364 ASN cc_start: 0.8886 (m110) cc_final: 0.8533 (m-40) REVERT: B 2374 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8981 (tp) REVERT: C 2116 ASN cc_start: 0.9033 (t0) cc_final: 0.8658 (t0) REVERT: C 2186 ASN cc_start: 0.8290 (m-40) cc_final: 0.8061 (p0) REVERT: C 2309 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8039 (mt-10) REVERT: D 2085 SER cc_start: 0.8498 (p) cc_final: 0.8181 (t) REVERT: D 2116 ASN cc_start: 0.8978 (t0) cc_final: 0.8574 (t0) REVERT: D 2186 ASN cc_start: 0.8159 (m-40) cc_final: 0.7791 (p0) REVERT: D 2248 MET cc_start: 0.9001 (mtp) cc_final: 0.8639 (mtm) REVERT: D 2309 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8143 (mt-10) REVERT: E 2085 SER cc_start: 0.8694 (p) cc_final: 0.8449 (t) REVERT: E 2186 ASN cc_start: 0.8265 (m-40) cc_final: 0.7986 (p0) REVERT: F 2085 SER cc_start: 0.8762 (p) cc_final: 0.8211 (m) REVERT: F 2099 ASP cc_start: 0.7390 (t0) cc_final: 0.7130 (t0) REVERT: F 2325 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7476 (m) REVERT: G 2099 ASP cc_start: 0.7241 (t0) cc_final: 0.7023 (t0) REVERT: G 2116 ASN cc_start: 0.8949 (t0) cc_final: 0.8506 (t0) REVERT: G 2130 ASN cc_start: 0.8929 (t0) cc_final: 0.8661 (t0) REVERT: G 2176 ASP cc_start: 0.8125 (t70) cc_final: 0.7812 (t70) REVERT: G 2186 ASN cc_start: 0.8090 (m-40) cc_final: 0.7841 (p0) REVERT: G 2329 THR cc_start: 0.9180 (t) cc_final: 0.8959 (p) outliers start: 76 outliers final: 53 residues processed: 260 average time/residue: 0.1761 time to fit residues: 81.9099 Evaluate side-chains 234 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2113 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2375 LEU 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 2327 THR 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 2121 SER Chi-restraints excluded: chain C residue 2126 LEU Chi-restraints excluded: chain C residue 2171 VAL Chi-restraints excluded: chain C residue 2207 SER 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 2118 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2207 SER Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain D residue 2334 SER 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 2185 SER Chi-restraints excluded: chain E residue 2207 SER 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 2327 THR Chi-restraints excluded: chain E residue 2334 SER 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 2126 LEU 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 2126 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 2334 SER Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2368 ASN C2322 ASN ** D2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2322 ASN F2368 ASN G2073 ASN ** G2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.122182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.093721 restraints weight = 18677.606| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.60 r_work: 0.2751 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16968 Z= 0.166 Angle : 0.537 6.611 23506 Z= 0.280 Chirality : 0.045 0.154 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.641 18.866 2443 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.39 % Allowed : 10.32 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.57 (0.16), residues: 903 loop : 0.09 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F2177 PHE 0.016 0.003 PHE A2106 TYR 0.008 0.001 TYR B2373 ARG 0.001 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 455) hydrogen bonds : angle 5.11871 ( 1155) SS BOND : bond 0.00084 ( 21) SS BOND : angle 0.50213 ( 42) covalent geometry : bond 0.00413 (16947) covalent geometry : angle 0.53668 (23464) *********************** 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 261 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 2085 SER cc_start: 0.8717 (p) cc_final: 0.8207 (m) REVERT: A 2116 ASN cc_start: 0.8863 (t0) cc_final: 0.8538 (t0) REVERT: A 2309 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 2375 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9094 (mp) REVERT: B 2085 SER cc_start: 0.8729 (p) cc_final: 0.8190 (m) REVERT: B 2186 ASN cc_start: 0.8263 (m-40) cc_final: 0.8009 (p0) REVERT: B 2248 MET cc_start: 0.8963 (mtp) cc_final: 0.8656 (mtm) REVERT: B 2309 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8322 (mt-10) REVERT: C 2309 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 2322 ASN cc_start: 0.7862 (m-40) cc_final: 0.7576 (m110) REVERT: D 2085 SER cc_start: 0.8474 (p) cc_final: 0.8143 (t) REVERT: D 2104 ASN cc_start: 0.7518 (m-40) cc_final: 0.7008 (t0) REVERT: D 2116 ASN cc_start: 0.8923 (t0) cc_final: 0.8493 (t0) REVERT: D 2186 ASN cc_start: 0.8235 (m-40) cc_final: 0.7914 (p0) REVERT: D 2248 MET cc_start: 0.8979 (mtp) cc_final: 0.8608 (mtm) REVERT: D 2309 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 2085 SER cc_start: 0.8656 (p) cc_final: 0.8188 (m) REVERT: E 2186 ASN cc_start: 0.8311 (m-40) cc_final: 0.7944 (p0) REVERT: E 2309 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8220 (mt-10) REVERT: F 2085 SER cc_start: 0.8753 (p) cc_final: 0.8216 (m) REVERT: F 2099 ASP cc_start: 0.7489 (t0) cc_final: 0.7211 (t0) REVERT: F 2186 ASN cc_start: 0.8480 (p0) cc_final: 0.8212 (p0) REVERT: G 2099 ASP cc_start: 0.7286 (t0) cc_final: 0.7072 (t0) REVERT: G 2116 ASN cc_start: 0.8868 (t0) cc_final: 0.8428 (t0) REVERT: G 2263 ASN cc_start: 0.8651 (p0) cc_final: 0.8273 (p0) REVERT: G 2329 THR cc_start: 0.9122 (t) cc_final: 0.8915 (p) outliers start: 65 outliers final: 51 residues processed: 247 average time/residue: 0.1764 time to fit residues: 77.5335 Evaluate side-chains 226 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 2277 VAL Chi-restraints excluded: chain A residue 2375 LEU 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 2289 THR 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 2121 SER Chi-restraints excluded: chain C residue 2126 LEU 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 2118 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2207 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 2391 VAL 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 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 2391 VAL Chi-restraints excluded: chain F residue 2063 SER Chi-restraints excluded: chain F residue 2111 ASN Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2126 LEU 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 2334 SER 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 2126 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 2289 THR Chi-restraints excluded: chain G residue 2334 SER Chi-restraints excluded: chain G residue 2370 SER Chi-restraints excluded: chain G residue 2371 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 212 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 183 optimal weight: 0.1980 chunk 151 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2322 ASN B2368 ASN ** D2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2368 ASN G2073 ASN ** G2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.122328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.094037 restraints weight = 18900.846| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.61 r_work: 0.2762 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16968 Z= 0.152 Angle : 0.516 6.496 23506 Z= 0.268 Chirality : 0.044 0.153 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.431 18.724 2443 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.91 % Allowed : 10.53 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.49 (0.16), residues: 903 loop : 0.18 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2177 PHE 0.015 0.002 PHE A2106 TYR 0.007 0.001 TYR D2373 ARG 0.001 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 455) hydrogen bonds : angle 4.93273 ( 1155) SS BOND : bond 0.00063 ( 21) SS BOND : angle 0.41413 ( 42) covalent geometry : bond 0.00384 (16947) covalent geometry : angle 0.51642 (23464) *********************** 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 260 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 185 time to evaluate : 1.841 Fit side-chains REVERT: A 2085 SER cc_start: 0.8671 (p) cc_final: 0.8164 (m) REVERT: A 2309 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 2375 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9068 (mp) REVERT: B 2085 SER cc_start: 0.8636 (p) cc_final: 0.8132 (m) REVERT: B 2104 ASN cc_start: 0.7247 (m-40) cc_final: 0.6869 (t0) REVERT: B 2186 ASN cc_start: 0.8290 (m-40) cc_final: 0.8064 (p0) REVERT: B 2248 MET cc_start: 0.8936 (mtp) cc_final: 0.8684 (mtm) REVERT: B 2309 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8372 (mt-10) REVERT: C 2309 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8253 (mt-10) REVERT: C 2322 ASN cc_start: 0.7813 (m-40) cc_final: 0.7517 (m110) REVERT: D 2085 SER cc_start: 0.8495 (p) cc_final: 0.8159 (t) REVERT: D 2116 ASN cc_start: 0.8890 (t0) cc_final: 0.8471 (t0) REVERT: D 2186 ASN cc_start: 0.8248 (m-40) cc_final: 0.7962 (p0) REVERT: D 2309 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8349 (mt-10) REVERT: E 2085 SER cc_start: 0.8642 (p) cc_final: 0.8149 (m) REVERT: E 2186 ASN cc_start: 0.8332 (m-40) cc_final: 0.7994 (p0) REVERT: E 2253 THR cc_start: 0.8911 (m) cc_final: 0.8667 (t) REVERT: E 2309 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8310 (mt-10) REVERT: F 2085 SER cc_start: 0.8774 (p) cc_final: 0.8221 (m) REVERT: F 2099 ASP cc_start: 0.7559 (t0) cc_final: 0.7299 (t0) REVERT: F 2186 ASN cc_start: 0.8586 (p0) cc_final: 0.8382 (p0) REVERT: F 2253 THR cc_start: 0.8993 (m) cc_final: 0.8701 (t) REVERT: G 2176 ASP cc_start: 0.8193 (t70) cc_final: 0.7865 (t70) REVERT: G 2186 ASN cc_start: 0.8442 (p0) cc_final: 0.8229 (p0) REVERT: G 2263 ASN cc_start: 0.8655 (p0) cc_final: 0.8241 (p0) REVERT: G 2309 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8276 (mt-10) outliers start: 75 outliers final: 56 residues processed: 247 average time/residue: 0.1837 time to fit residues: 81.0270 Evaluate side-chains 224 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2126 LEU Chi-restraints excluded: chain A residue 2208 ILE Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2334 SER 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 2185 SER Chi-restraints excluded: chain B residue 2207 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2289 THR 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 2121 SER Chi-restraints excluded: chain C residue 2126 LEU Chi-restraints excluded: chain C residue 2207 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 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 2289 THR Chi-restraints excluded: chain D residue 2318 SER 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 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 2391 VAL Chi-restraints excluded: chain F residue 2063 SER Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2080 THR Chi-restraints excluded: chain F residue 2111 ASN Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2126 LEU 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 2334 SER Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2063 SER Chi-restraints excluded: chain G residue 2080 THR Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2126 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 2289 THR Chi-restraints excluded: chain G residue 2334 SER Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 83 optimal weight: 0.0970 chunk 203 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2322 ASN B2368 ASN D2322 ASN F2322 ASN G2073 ASN G2186 ASN G2322 ASN G2368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.142471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.118918 restraints weight = 18248.542| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.28 r_work: 0.2857 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16968 Z= 0.103 Angle : 0.476 6.380 23506 Z= 0.245 Chirality : 0.042 0.144 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.043 17.088 2443 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.55 % Allowed : 11.78 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2345 helix: None (None), residues: 0 sheet: 0.38 (0.16), residues: 938 loop : 0.46 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2177 PHE 0.013 0.002 PHE A2106 TYR 0.006 0.001 TYR C2373 ARG 0.000 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 455) hydrogen bonds : angle 4.65468 ( 1155) SS BOND : bond 0.00026 ( 21) SS BOND : angle 0.29210 ( 42) covalent geometry : bond 0.00257 (16947) covalent geometry : angle 0.47669 (23464) *********************** 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 262 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 1.924 Fit side-chains REVERT: A 2085 SER cc_start: 0.8643 (p) cc_final: 0.8125 (m) REVERT: A 2309 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 2375 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9086 (mp) REVERT: B 2085 SER cc_start: 0.8594 (p) cc_final: 0.8054 (m) REVERT: B 2151 SER cc_start: 0.8871 (t) cc_final: 0.8569 (m) REVERT: B 2248 MET cc_start: 0.8793 (mtp) cc_final: 0.8581 (mtm) REVERT: B 2309 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 2309 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 2322 ASN cc_start: 0.7573 (m-40) cc_final: 0.7334 (m110) REVERT: D 2085 SER cc_start: 0.8455 (p) cc_final: 0.8138 (t) REVERT: D 2116 ASN cc_start: 0.8835 (t0) cc_final: 0.8436 (t0) REVERT: D 2309 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8129 (mt-10) REVERT: E 2085 SER cc_start: 0.8602 (p) cc_final: 0.8096 (m) REVERT: E 2253 THR cc_start: 0.8857 (m) cc_final: 0.8641 (t) REVERT: E 2309 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8020 (mt-10) REVERT: F 2085 SER cc_start: 0.8750 (p) cc_final: 0.8181 (m) REVERT: F 2363 VAL cc_start: 0.8855 (t) cc_final: 0.8648 (m) REVERT: G 2248 MET cc_start: 0.8756 (mtp) cc_final: 0.8545 (mtm) REVERT: G 2263 ASN cc_start: 0.8533 (p0) cc_final: 0.8270 (p0) outliers start: 68 outliers final: 54 residues processed: 252 average time/residue: 0.1864 time to fit residues: 83.5794 Evaluate side-chains 230 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 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 2207 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2367 THR Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2078 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 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 2126 LEU Chi-restraints excluded: chain D residue 2208 ILE Chi-restraints excluded: chain D residue 2289 THR 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 2078 THR Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2146 LEU 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 2371 THR Chi-restraints excluded: chain E residue 2374 LEU Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2063 SER Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2080 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 2370 SER Chi-restraints excluded: chain F residue 2391 VAL Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2080 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 2289 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 138 optimal weight: 0.2980 chunk 161 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2368 ASN D2284 GLN F2322 ASN G2368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.117191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.089161 restraints weight = 18946.751| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.58 r_work: 0.2659 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 16968 Z= 0.277 Angle : 0.606 6.939 23506 Z= 0.319 Chirality : 0.048 0.166 2947 Planarity : 0.005 0.048 3073 Dihedral : 4.724 21.064 2443 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.81 % Allowed : 12.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.25 (0.16), residues: 903 loop : 0.03 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G2259 PHE 0.019 0.003 PHE D2156 TYR 0.012 0.002 TYR A2097 ARG 0.001 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 455) hydrogen bonds : angle 5.13297 ( 1155) SS BOND : bond 0.00104 ( 21) SS BOND : angle 0.49863 ( 42) covalent geometry : bond 0.00707 (16947) covalent geometry : angle 0.60605 (23464) *********************** 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: 73 poor density : 164 time to evaluate : 1.747 Fit side-chains REVERT: A 2085 SER cc_start: 0.8752 (p) cc_final: 0.8191 (m) REVERT: A 2309 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8180 (mt-10) REVERT: A 2375 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9138 (mp) REVERT: B 2085 SER cc_start: 0.8757 (p) cc_final: 0.8236 (m) REVERT: B 2104 ASN cc_start: 0.7908 (t0) cc_final: 0.7427 (t0) REVERT: B 2309 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 2309 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8173 (mt-10) REVERT: D 2085 SER cc_start: 0.8610 (p) cc_final: 0.8274 (t) REVERT: D 2116 ASN cc_start: 0.8881 (t0) cc_final: 0.8468 (t0) REVERT: D 2309 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8243 (mt-10) REVERT: E 2085 SER cc_start: 0.8741 (p) cc_final: 0.8230 (m) REVERT: E 2309 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8156 (mt-10) REVERT: F 2085 SER cc_start: 0.8842 (p) cc_final: 0.8250 (m) REVERT: G 2176 ASP cc_start: 0.8346 (t70) cc_final: 0.8028 (t70) outliers start: 73 outliers final: 62 residues processed: 227 average time/residue: 0.1842 time to fit residues: 74.5904 Evaluate side-chains 218 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 2208 ILE Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2318 SER Chi-restraints excluded: chain A residue 2334 SER 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 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 2121 SER Chi-restraints excluded: chain C residue 2207 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2327 THR 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 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 2184 THR 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 2371 THR Chi-restraints excluded: chain E residue 2374 LEU Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2063 SER Chi-restraints excluded: chain F residue 2078 THR Chi-restraints excluded: chain F residue 2080 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 2334 SER Chi-restraints excluded: chain F residue 2370 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 2080 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 2370 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 138 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2368 ASN ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2186 ASN ** G2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.094553 restraints weight = 18719.530| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.68 r_work: 0.2678 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 16968 Z= 0.193 Angle : 0.551 6.633 23506 Z= 0.289 Chirality : 0.045 0.216 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.488 20.142 2443 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.07 % Allowed : 12.36 % Favored : 83.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.01 (0.16), residues: 931 loop : 0.20 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G2259 PHE 0.015 0.003 PHE A2106 TYR 0.008 0.001 TYR B2373 ARG 0.000 0.000 ARG G2260 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 455) hydrogen bonds : angle 4.94626 ( 1155) SS BOND : bond 0.00062 ( 21) SS BOND : angle 0.37815 ( 42) covalent geometry : bond 0.00506 (16947) covalent geometry : angle 0.55147 (23464) *********************** 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 238 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 160 time to evaluate : 1.621 Fit side-chains REVERT: A 2085 SER cc_start: 0.8714 (p) cc_final: 0.8139 (m) REVERT: A 2309 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 2375 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 2085 SER cc_start: 0.8697 (p) cc_final: 0.8171 (m) REVERT: B 2104 ASN cc_start: 0.7825 (t0) cc_final: 0.7258 (t0) REVERT: B 2130 ASN cc_start: 0.8904 (t0) cc_final: 0.8572 (t0) REVERT: B 2309 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 2309 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8127 (mt-10) REVERT: D 2085 SER cc_start: 0.8561 (p) cc_final: 0.8245 (t) REVERT: D 2116 ASN cc_start: 0.8833 (t0) cc_final: 0.8423 (t0) REVERT: D 2130 ASN cc_start: 0.8915 (t0) cc_final: 0.8546 (t0) REVERT: D 2309 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8175 (mt-10) REVERT: E 2085 SER cc_start: 0.8668 (p) cc_final: 0.8136 (m) REVERT: E 2253 THR cc_start: 0.8913 (m) cc_final: 0.8679 (t) REVERT: E 2309 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8175 (mt-10) REVERT: F 2085 SER cc_start: 0.8795 (p) cc_final: 0.8198 (m) REVERT: G 2176 ASP cc_start: 0.8158 (t70) cc_final: 0.7818 (t70) REVERT: G 2263 ASN cc_start: 0.8603 (p0) cc_final: 0.8250 (p0) REVERT: G 2365 ASN cc_start: 0.8897 (t0) cc_final: 0.8421 (t0) outliers start: 78 outliers final: 72 residues processed: 224 average time/residue: 0.1742 time to fit residues: 69.7883 Evaluate side-chains 228 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 155 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 2208 ILE Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2318 SER Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2370 SER 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 2207 SER 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 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 2207 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2327 THR 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 2143 VAL Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2186 ASN 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 D residue 2375 LEU 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 2143 VAL 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 2370 SER Chi-restraints excluded: chain E residue 2371 THR Chi-restraints excluded: chain E residue 2374 LEU Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2063 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 2334 SER Chi-restraints excluded: chain F residue 2370 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 2118 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2368 ASN ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2186 ASN G2322 ASN G2368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.099156 restraints weight = 18568.688| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.64 r_work: 0.2787 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 16968 Z= 0.133 Angle : 0.507 6.484 23506 Z= 0.265 Chirality : 0.043 0.162 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.149 19.592 2443 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.44 % Allowed : 12.98 % Favored : 83.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.07 (0.15), residues: 931 loop : 0.35 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D2177 PHE 0.013 0.002 PHE B2106 TYR 0.007 0.001 TYR B2373 ARG 0.001 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 455) hydrogen bonds : angle 4.72477 ( 1155) SS BOND : bond 0.00036 ( 21) SS BOND : angle 0.30279 ( 42) covalent geometry : bond 0.00379 (16947) covalent geometry : angle 0.50686 (23464) *********************** 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 235 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 1.861 Fit side-chains REVERT: A 2085 SER cc_start: 0.8691 (p) cc_final: 0.8136 (m) REVERT: A 2309 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 2375 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9047 (mp) REVERT: A 2393 TYR cc_start: 0.9145 (m-10) cc_final: 0.8759 (m-10) REVERT: B 2085 SER cc_start: 0.8661 (p) cc_final: 0.8154 (m) REVERT: B 2104 ASN cc_start: 0.7735 (t0) cc_final: 0.7148 (t0) REVERT: B 2130 ASN cc_start: 0.8846 (t0) cc_final: 0.8503 (t0) REVERT: B 2309 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8272 (mt-10) REVERT: C 2309 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8164 (mt-10) REVERT: D 2085 SER cc_start: 0.8564 (p) cc_final: 0.8004 (m) REVERT: D 2116 ASN cc_start: 0.8768 (t0) cc_final: 0.8320 (t0) REVERT: D 2130 ASN cc_start: 0.8871 (t0) cc_final: 0.8496 (t0) REVERT: D 2309 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 2085 SER cc_start: 0.8645 (p) cc_final: 0.8107 (m) REVERT: E 2253 THR cc_start: 0.8924 (m) cc_final: 0.8714 (t) REVERT: E 2309 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8179 (mt-10) REVERT: E 2318 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8234 (t) REVERT: F 2085 SER cc_start: 0.8805 (p) cc_final: 0.8195 (m) REVERT: G 2263 ASN cc_start: 0.8625 (p0) cc_final: 0.8291 (p0) REVERT: G 2365 ASN cc_start: 0.8844 (t0) cc_final: 0.8561 (t0) outliers start: 66 outliers final: 62 residues processed: 222 average time/residue: 0.1925 time to fit residues: 76.4113 Evaluate side-chains 226 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 2277 VAL Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2370 SER 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 2207 SER 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 2367 THR 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 2207 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2327 THR 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 2186 ASN Chi-restraints excluded: chain D residue 2289 THR Chi-restraints excluded: chain D residue 2375 LEU 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 2143 VAL 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 2370 SER Chi-restraints excluded: chain E residue 2374 LEU Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2063 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 2370 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 2080 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 2329 THR 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 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2368 ASN ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2186 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 = 0.3319 r_free = 0.3319 target = 0.127187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.099007 restraints weight = 18609.746| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.68 r_work: 0.2752 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 16968 Z= 0.138 Angle : 0.511 6.551 23506 Z= 0.267 Chirality : 0.043 0.152 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.079 18.682 2443 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.55 % Allowed : 13.09 % Favored : 83.37 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.08 (0.15), residues: 931 loop : 0.38 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D2177 PHE 0.013 0.002 PHE C2106 TYR 0.007 0.001 TYR E2283 ARG 0.000 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 455) hydrogen bonds : angle 4.68657 ( 1155) SS BOND : bond 0.00031 ( 21) SS BOND : angle 0.31311 ( 42) covalent geometry : bond 0.00398 (16947) covalent geometry : angle 0.51105 (23464) ********************** 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 239 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 1.828 Fit side-chains REVERT: A 2085 SER cc_start: 0.8700 (p) cc_final: 0.8104 (m) REVERT: A 2309 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 2375 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9048 (mp) REVERT: A 2393 TYR cc_start: 0.9135 (m-10) cc_final: 0.8762 (m-10) REVERT: B 2085 SER cc_start: 0.8651 (p) cc_final: 0.8137 (m) REVERT: B 2104 ASN cc_start: 0.7678 (t0) cc_final: 0.7088 (t0) REVERT: B 2130 ASN cc_start: 0.8829 (t0) cc_final: 0.8419 (t0) REVERT: B 2309 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8279 (mt-10) REVERT: C 2309 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8153 (mt-10) REVERT: D 2085 SER cc_start: 0.8569 (p) cc_final: 0.8015 (m) REVERT: D 2116 ASN cc_start: 0.8750 (t0) cc_final: 0.8285 (t0) REVERT: D 2130 ASN cc_start: 0.8877 (t0) cc_final: 0.8501 (t0) REVERT: D 2309 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8218 (mt-10) REVERT: E 2085 SER cc_start: 0.8634 (p) cc_final: 0.8078 (m) REVERT: E 2253 THR cc_start: 0.8934 (m) cc_final: 0.8710 (t) REVERT: E 2309 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8118 (mt-10) REVERT: E 2318 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8221 (t) REVERT: G 2263 ASN cc_start: 0.8608 (p0) cc_final: 0.8246 (p0) REVERT: G 2365 ASN cc_start: 0.8840 (t0) cc_final: 0.8570 (t0) outliers start: 68 outliers final: 63 residues processed: 226 average time/residue: 0.1842 time to fit residues: 74.6052 Evaluate side-chains 232 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 2277 VAL Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2370 SER 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 2248 MET Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2367 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 2207 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2327 THR 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 2289 THR 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 2078 THR Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2143 VAL 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 2370 SER Chi-restraints excluded: chain E residue 2374 LEU Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2063 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 2370 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 2080 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 2329 THR 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 170 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 193 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2368 ASN ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.126406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098275 restraints weight = 18676.481| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.65 r_work: 0.2677 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 16968 Z= 0.159 Angle : 0.524 6.599 23506 Z= 0.273 Chirality : 0.044 0.158 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.150 19.654 2443 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.49 % Allowed : 13.19 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.03 (0.15), residues: 931 loop : 0.36 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2177 PHE 0.013 0.002 PHE C2106 TYR 0.007 0.001 TYR E2283 ARG 0.001 0.000 ARG D2260 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 455) hydrogen bonds : angle 4.74110 ( 1155) SS BOND : bond 0.00039 ( 21) SS BOND : angle 0.31785 ( 42) covalent geometry : bond 0.00443 (16947) covalent geometry : angle 0.52454 (23464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7315.15 seconds wall clock time: 127 minutes 45.20 seconds (7665.20 seconds total)