Starting phenix.real_space_refine on Mon Nov 18 17:39:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fls_50538/11_2024/9fls_50538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fls_50538/11_2024/9fls_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fls_50538/11_2024/9fls_50538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fls_50538/11_2024/9fls_50538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fls_50538/11_2024/9fls_50538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fls_50538/11_2024/9fls_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.30, per 1000 atoms: 0.38 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=3, 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 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: 4.35 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: 3.41 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: 6.87 Time building geometry restraints manager: 4.98 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: 9560 16.77 - 33.54: 338 33.54 - 50.30: 21 50.30 - 67.07: 9 67.07 - 83.84: 7 Dihedral angle restraints: 9935 sinusoidal: 3145 harmonic: 6790 Sorted by residual: 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 dihedral pdb=" CB CYS A2159 " pdb=" SG CYS A2159 " pdb=" SG CYS A2298 " pdb=" CB CYS A2298 " ideal model delta sinusoidal sigma weight residual 93.00 144.14 -51.14 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" C PHE E2156 " pdb=" N PHE E2156 " pdb=" CA PHE E2156 " pdb=" CB PHE E2156 " ideal model delta harmonic sigma weight residual -122.60 -132.41 9.81 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 9932 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: 2.02 - 2.60: 193 2.60 - 3.17: 14684 3.17 - 3.75: 24723 3.75 - 4.32: 34498 4.32 - 4.90: 57392 Nonbonded interactions: 131490 Sorted by model distance: nonbonded pdb=" SG CYS B2159 " pdb=" SG CYS B2298 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS F2159 " pdb=" SG CYS F2298 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS D2159 " pdb=" SG CYS D2298 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS C2159 " pdb=" SG CYS C2298 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS E2159 " pdb=" SG CYS E2298 " model vdw 2.022 3.760 ... (remaining 131485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.050 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.980 ------------------------------------------------------------------------------- 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 16947 Z= 1.218 Angle : 1.588 9.181 23464 Z= 1.067 Chirality : 0.084 0.322 2947 Planarity : 0.008 0.037 3073 Dihedral : 9.429 83.838 5572 Min Nonbonded Distance : 2.021 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 *********************** 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 : 1.718 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: 0.1879 time to fit residues: 130.7353 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 : 1.839 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F2186 ASN G2062 ASN G2186 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16947 Z= 0.233 Angle : 0.578 6.268 23464 Z= 0.314 Chirality : 0.046 0.146 2947 Planarity : 0.005 0.038 3073 Dihedral : 5.142 17.550 2443 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.45 % Allowed : 8.45 % 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: 0.66 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.97 (0.17), residues: 889 loop : 0.16 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2177 PHE 0.021 0.003 PHE G2106 TYR 0.010 0.001 TYR B2393 ARG 0.002 0.001 ARG C2260 *********************** 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 286 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 1.790 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7274 (t0) cc_final: 0.7022 (p0) REVERT: A 2186 ASN cc_start: 0.8022 (m-40) cc_final: 0.7200 (p0) REVERT: A 2309 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6928 (mt-10) REVERT: A 2368 ASN cc_start: 0.7893 (m-40) cc_final: 0.7546 (m-40) REVERT: B 2099 ASP cc_start: 0.7604 (t0) cc_final: 0.7302 (t0) REVERT: B 2151 SER cc_start: 0.7854 (t) cc_final: 0.7570 (m) REVERT: B 2186 ASN cc_start: 0.8053 (m-40) cc_final: 0.7294 (p0) REVERT: B 2248 MET cc_start: 0.7250 (mtp) cc_final: 0.7048 (mtm) REVERT: B 2309 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6893 (mt-10) REVERT: B 2368 ASN cc_start: 0.7752 (t0) cc_final: 0.7510 (m-40) REVERT: C 2099 ASP cc_start: 0.7738 (t0) cc_final: 0.7411 (t0) REVERT: C 2116 ASN cc_start: 0.8517 (t0) cc_final: 0.8307 (t0) REVERT: C 2119 ASN cc_start: 0.7456 (t0) cc_final: 0.7109 (p0) REVERT: C 2151 SER cc_start: 0.7842 (t) cc_final: 0.7630 (m) REVERT: C 2186 ASN cc_start: 0.8012 (m-40) cc_final: 0.7370 (p0) REVERT: C 2266 ASP cc_start: 0.7495 (p0) cc_final: 0.7290 (p0) REVERT: C 2309 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6857 (mt-10) REVERT: D 2099 ASP cc_start: 0.7691 (t0) cc_final: 0.7407 (t0) REVERT: D 2116 ASN cc_start: 0.8373 (t0) cc_final: 0.7933 (t0) REVERT: D 2119 ASN cc_start: 0.7495 (t0) cc_final: 0.7142 (p0) REVERT: D 2176 ASP cc_start: 0.7355 (t0) cc_final: 0.6898 (t70) REVERT: D 2186 ASN cc_start: 0.7831 (m-40) cc_final: 0.7105 (p0) REVERT: D 2309 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6800 (mt-10) REVERT: E 2099 ASP cc_start: 0.7769 (t0) cc_final: 0.7481 (t0) REVERT: E 2119 ASN cc_start: 0.7519 (t0) cc_final: 0.7059 (p0) REVERT: E 2151 SER cc_start: 0.7798 (t) cc_final: 0.7562 (m) REVERT: E 2186 ASN cc_start: 0.7838 (m-40) cc_final: 0.7285 (p0) REVERT: E 2368 ASN cc_start: 0.7741 (t0) cc_final: 0.7481 (m-40) REVERT: F 2085 SER cc_start: 0.7696 (p) cc_final: 0.7488 (m) REVERT: F 2099 ASP cc_start: 0.7671 (t0) cc_final: 0.7320 (t0) REVERT: F 2119 ASN cc_start: 0.7363 (t0) cc_final: 0.7132 (p0) REVERT: F 2176 ASP cc_start: 0.7394 (t0) cc_final: 0.7131 (t70) REVERT: F 2186 ASN cc_start: 0.7985 (m-40) cc_final: 0.7285 (p0) REVERT: F 2309 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6999 (mt-10) REVERT: G 2099 ASP cc_start: 0.7545 (t0) cc_final: 0.7193 (t0) REVERT: G 2119 ASN cc_start: 0.7465 (t0) cc_final: 0.7115 (p0) REVERT: G 2186 ASN cc_start: 0.7911 (m-40) cc_final: 0.7149 (p0) REVERT: G 2368 ASN cc_start: 0.7734 (t0) cc_final: 0.7500 (m-40) outliers start: 47 outliers final: 38 residues processed: 279 average time/residue: 0.1882 time to fit residues: 93.0511 Evaluate side-chains 222 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 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 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 116 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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** B2364 ASN ** 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** E2364 ASN ** F2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16947 Z= 0.351 Angle : 0.587 6.331 23464 Z= 0.310 Chirality : 0.047 0.160 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.973 19.336 2443 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.75 % Allowed : 9.33 % Favored : 86.91 % 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: 0.48 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.66 (0.16), residues: 966 loop : 0.16 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C2259 PHE 0.020 0.003 PHE A2106 TYR 0.010 0.002 TYR B2097 ARG 0.001 0.000 ARG C2260 *********************** 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 271 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 1.821 Fit side-chains REVERT: A 2099 ASP cc_start: 0.7527 (t0) cc_final: 0.7222 (t0) REVERT: A 2119 ASN cc_start: 0.7370 (t0) cc_final: 0.7044 (p0) REVERT: A 2186 ASN cc_start: 0.7821 (m-40) cc_final: 0.7307 (p0) REVERT: A 2309 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 2368 ASN cc_start: 0.8052 (m-40) cc_final: 0.7746 (m-40) REVERT: A 2375 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7120 (mp) REVERT: B 2099 ASP cc_start: 0.7702 (t0) cc_final: 0.7419 (t0) REVERT: B 2186 ASN cc_start: 0.7927 (m-40) cc_final: 0.7341 (p0) REVERT: B 2309 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 2368 ASN cc_start: 0.7786 (t0) cc_final: 0.7563 (m-40) REVERT: B 2374 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7306 (tp) REVERT: C 2099 ASP cc_start: 0.7714 (t0) cc_final: 0.7412 (t0) REVERT: C 2116 ASN cc_start: 0.8289 (t0) cc_final: 0.7989 (t0) REVERT: C 2119 ASN cc_start: 0.7500 (t0) cc_final: 0.7057 (p0) REVERT: C 2186 ASN cc_start: 0.7960 (m-40) cc_final: 0.7484 (p0) REVERT: C 2309 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6761 (mt-10) REVERT: C 2322 ASN cc_start: 0.8177 (m110) cc_final: 0.7973 (m110) REVERT: D 2099 ASP cc_start: 0.7704 (t0) cc_final: 0.7470 (t0) REVERT: D 2116 ASN cc_start: 0.8371 (t0) cc_final: 0.8034 (t0) REVERT: D 2119 ASN cc_start: 0.7455 (t0) cc_final: 0.7003 (p0) REVERT: D 2176 ASP cc_start: 0.7584 (t0) cc_final: 0.7382 (t70) REVERT: D 2186 ASN cc_start: 0.7894 (m-40) cc_final: 0.7205 (p0) REVERT: D 2309 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6739 (mt-10) REVERT: E 2099 ASP cc_start: 0.7858 (t0) cc_final: 0.7592 (t0) REVERT: E 2119 ASN cc_start: 0.7416 (t0) cc_final: 0.6864 (p0) REVERT: E 2186 ASN cc_start: 0.7849 (m-40) cc_final: 0.7230 (p0) REVERT: E 2368 ASN cc_start: 0.7621 (t0) cc_final: 0.7408 (m-40) REVERT: F 2085 SER cc_start: 0.7833 (p) cc_final: 0.7580 (m) REVERT: F 2099 ASP cc_start: 0.7691 (t0) cc_final: 0.7357 (t70) REVERT: F 2119 ASN cc_start: 0.7304 (t0) cc_final: 0.6973 (p0) REVERT: F 2186 ASN cc_start: 0.7890 (m-40) cc_final: 0.7381 (p0) REVERT: F 2309 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6736 (mt-10) REVERT: G 2099 ASP cc_start: 0.7616 (t0) cc_final: 0.7262 (t0) REVERT: G 2116 ASN cc_start: 0.8308 (t0) cc_final: 0.7942 (t0) REVERT: G 2119 ASN cc_start: 0.7379 (t0) cc_final: 0.6898 (p0) REVERT: G 2130 ASN cc_start: 0.8984 (t0) cc_final: 0.8656 (t0) REVERT: G 2186 ASN cc_start: 0.7797 (m-40) cc_final: 0.7314 (p0) REVERT: G 2368 ASN cc_start: 0.7793 (t0) cc_final: 0.7449 (m-40) outliers start: 72 outliers final: 48 residues processed: 260 average time/residue: 0.1844 time to fit residues: 85.0973 Evaluate side-chains 230 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 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 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 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE 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 2325 VAL Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2375 LEU Chi-restraints excluded: chain E residue 2391 VAL 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 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 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 207 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 223 optimal weight: 0.0370 chunk 110 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2364 ASN B2322 ASN C2322 ASN D2322 ASN F2322 ASN F2368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16947 Z= 0.259 Angle : 0.518 6.396 23464 Z= 0.269 Chirality : 0.044 0.154 2947 Planarity : 0.005 0.045 3073 Dihedral : 4.546 18.884 2443 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.34 % Allowed : 10.27 % Favored : 86.39 % 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: 0.53 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.64 (0.16), residues: 903 loop : 0.26 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2177 PHE 0.016 0.002 PHE A2106 TYR 0.008 0.001 TYR D2373 ARG 0.001 0.000 ARG C2260 *********************** 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: 64 poor density : 197 time to evaluate : 1.708 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7347 (t0) cc_final: 0.7047 (p0) REVERT: A 2186 ASN cc_start: 0.7728 (m-40) cc_final: 0.7366 (p0) REVERT: A 2309 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6796 (mt-10) REVERT: A 2375 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7093 (mp) REVERT: B 2099 ASP cc_start: 0.7592 (t0) cc_final: 0.7310 (t0) REVERT: B 2186 ASN cc_start: 0.7823 (m-40) cc_final: 0.7380 (p0) REVERT: B 2248 MET cc_start: 0.7333 (mtp) cc_final: 0.7118 (mtm) REVERT: B 2309 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 2368 ASN cc_start: 0.7781 (t0) cc_final: 0.7530 (m-40) REVERT: C 2099 ASP cc_start: 0.7637 (t0) cc_final: 0.7380 (t0) REVERT: C 2119 ASN cc_start: 0.7500 (t0) cc_final: 0.7054 (p0) REVERT: C 2186 ASN cc_start: 0.7830 (m-40) cc_final: 0.7471 (p0) REVERT: C 2309 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6774 (mt-10) REVERT: C 2322 ASN cc_start: 0.7902 (m-40) cc_final: 0.7670 (m110) REVERT: D 2099 ASP cc_start: 0.7683 (t0) cc_final: 0.7427 (t0) REVERT: D 2116 ASN cc_start: 0.8342 (t0) cc_final: 0.7983 (t0) REVERT: D 2119 ASN cc_start: 0.7474 (t0) cc_final: 0.7024 (p0) REVERT: D 2176 ASP cc_start: 0.7359 (t0) cc_final: 0.7142 (t70) REVERT: D 2186 ASN cc_start: 0.7819 (m-40) cc_final: 0.7257 (p0) REVERT: D 2248 MET cc_start: 0.7147 (mtp) cc_final: 0.6900 (mtm) REVERT: D 2309 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6779 (mt-10) REVERT: E 2099 ASP cc_start: 0.7868 (t0) cc_final: 0.7586 (t0) REVERT: E 2119 ASN cc_start: 0.7494 (t0) cc_final: 0.7000 (p0) REVERT: E 2186 ASN cc_start: 0.7855 (m-40) cc_final: 0.7266 (p0) REVERT: E 2309 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7027 (mt-10) REVERT: E 2368 ASN cc_start: 0.7635 (t0) cc_final: 0.7433 (m-40) REVERT: F 2085 SER cc_start: 0.7839 (p) cc_final: 0.7577 (m) REVERT: F 2099 ASP cc_start: 0.7674 (t0) cc_final: 0.7352 (t0) REVERT: F 2119 ASN cc_start: 0.7359 (t0) cc_final: 0.7038 (p0) REVERT: F 2130 ASN cc_start: 0.8901 (t0) cc_final: 0.8644 (t0) REVERT: F 2186 ASN cc_start: 0.7767 (m-40) cc_final: 0.7415 (p0) REVERT: F 2309 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6836 (mt-10) REVERT: G 2099 ASP cc_start: 0.7652 (t0) cc_final: 0.7365 (t0) REVERT: G 2116 ASN cc_start: 0.8308 (t0) cc_final: 0.7957 (t0) REVERT: G 2119 ASN cc_start: 0.7426 (t0) cc_final: 0.6869 (p0) REVERT: G 2186 ASN cc_start: 0.7706 (m-40) cc_final: 0.7344 (p0) REVERT: G 2309 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6793 (mt-10) REVERT: G 2368 ASN cc_start: 0.7739 (t0) cc_final: 0.7499 (m-40) outliers start: 64 outliers final: 48 residues processed: 250 average time/residue: 0.1949 time to fit residues: 86.3539 Evaluate side-chains 227 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2118 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 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 2208 ILE Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2126 LEU 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 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2208 ILE 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 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 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 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 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 2289 THR Chi-restraints excluded: chain G residue 2329 THR Chi-restraints excluded: chain G residue 2334 SER Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** D2368 ASN F2322 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16947 Z= 0.334 Angle : 0.546 6.516 23464 Z= 0.283 Chirality : 0.046 0.157 2947 Planarity : 0.005 0.046 3073 Dihedral : 4.638 20.002 2443 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.86 % Allowed : 11.16 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.42 (0.16), residues: 903 loop : 0.23 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B2259 PHE 0.016 0.003 PHE A2106 TYR 0.010 0.001 TYR A2097 ARG 0.001 0.000 ARG D2260 *********************** 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 259 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 1.625 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7456 (t0) cc_final: 0.7012 (p0) REVERT: A 2186 ASN cc_start: 0.7739 (m-40) cc_final: 0.7373 (p0) REVERT: A 2309 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 2375 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7074 (mp) REVERT: B 2099 ASP cc_start: 0.7580 (t0) cc_final: 0.7303 (t0) REVERT: B 2186 ASN cc_start: 0.7864 (m-40) cc_final: 0.7411 (p0) REVERT: B 2309 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 2365 ASN cc_start: 0.8747 (t0) cc_final: 0.8268 (t0) REVERT: B 2368 ASN cc_start: 0.7766 (t0) cc_final: 0.7494 (m-40) REVERT: C 2099 ASP cc_start: 0.7659 (t0) cc_final: 0.7422 (t0) REVERT: C 2119 ASN cc_start: 0.7502 (t0) cc_final: 0.6962 (p0) REVERT: C 2186 ASN cc_start: 0.7825 (m-40) cc_final: 0.7495 (p0) REVERT: C 2309 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6732 (mt-10) REVERT: C 2322 ASN cc_start: 0.7963 (m-40) cc_final: 0.7658 (m110) REVERT: D 2099 ASP cc_start: 0.7588 (t0) cc_final: 0.7310 (t0) REVERT: D 2116 ASN cc_start: 0.8304 (t0) cc_final: 0.7951 (t0) REVERT: D 2119 ASN cc_start: 0.7440 (t0) cc_final: 0.6916 (p0) REVERT: D 2176 ASP cc_start: 0.7507 (t0) cc_final: 0.7264 (t70) REVERT: D 2186 ASN cc_start: 0.7861 (m-40) cc_final: 0.7304 (p0) REVERT: D 2309 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6692 (mt-10) REVERT: D 2365 ASN cc_start: 0.8634 (t0) cc_final: 0.8209 (t0) REVERT: E 2099 ASP cc_start: 0.7861 (t0) cc_final: 0.7600 (t0) REVERT: E 2119 ASN cc_start: 0.7478 (t0) cc_final: 0.6899 (p0) REVERT: E 2186 ASN cc_start: 0.7826 (m-40) cc_final: 0.7268 (p0) REVERT: E 2309 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6986 (mt-10) REVERT: E 2368 ASN cc_start: 0.7733 (t0) cc_final: 0.7499 (m-40) REVERT: F 2085 SER cc_start: 0.7845 (p) cc_final: 0.7573 (m) REVERT: F 2099 ASP cc_start: 0.7747 (t0) cc_final: 0.7455 (t0) REVERT: F 2119 ASN cc_start: 0.7485 (t0) cc_final: 0.6985 (p0) REVERT: F 2130 ASN cc_start: 0.9007 (t0) cc_final: 0.8735 (t0) REVERT: F 2186 ASN cc_start: 0.7775 (m-40) cc_final: 0.7425 (p0) REVERT: F 2309 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6642 (mt-10) REVERT: G 2099 ASP cc_start: 0.7687 (t0) cc_final: 0.7422 (t0) REVERT: G 2116 ASN cc_start: 0.8248 (t0) cc_final: 0.7906 (t0) REVERT: G 2119 ASN cc_start: 0.7310 (t0) cc_final: 0.6828 (p0) REVERT: G 2176 ASP cc_start: 0.7037 (t70) cc_final: 0.6707 (t70) REVERT: G 2186 ASN cc_start: 0.7689 (m-40) cc_final: 0.7437 (p0) REVERT: G 2309 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6511 (tt0) REVERT: G 2368 ASN cc_start: 0.7753 (t0) cc_final: 0.7491 (m-40) outliers start: 74 outliers final: 64 residues processed: 250 average time/residue: 0.1908 time to fit residues: 84.8784 Evaluate side-chains 242 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2063 SER Chi-restraints excluded: chain A residue 2118 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 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 2185 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 2078 THR 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 2334 SER Chi-restraints excluded: chain C residue 2375 LEU Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2207 SER Chi-restraints excluded: chain D residue 2208 ILE 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 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 2318 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 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 2334 SER Chi-restraints excluded: chain F residue 2370 SER Chi-restraints excluded: chain F residue 2375 LEU 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 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 75 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 223 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2322 ASN D2368 ASN F2322 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16947 Z= 0.236 Angle : 0.500 6.426 23464 Z= 0.258 Chirality : 0.044 0.151 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.331 18.651 2443 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.55 % Allowed : 11.84 % Favored : 84.62 % 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: 0.41 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.37 (0.16), residues: 903 loop : 0.33 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2177 PHE 0.014 0.002 PHE A2106 TYR 0.007 0.001 TYR D2124 ARG 0.001 0.000 ARG D2260 *********************** 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 246 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 2.186 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7338 (t0) cc_final: 0.6885 (p0) REVERT: A 2186 ASN cc_start: 0.7722 (m-40) cc_final: 0.7409 (p0) REVERT: A 2309 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6822 (mt-10) REVERT: A 2375 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7027 (mp) REVERT: B 2099 ASP cc_start: 0.7587 (t0) cc_final: 0.7295 (t0) REVERT: B 2186 ASN cc_start: 0.7795 (m-40) cc_final: 0.7392 (p0) REVERT: B 2309 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7029 (mt-10) REVERT: B 2365 ASN cc_start: 0.8721 (t0) cc_final: 0.8314 (t0) REVERT: B 2368 ASN cc_start: 0.7765 (t0) cc_final: 0.7562 (m-40) REVERT: C 2099 ASP cc_start: 0.7620 (t0) cc_final: 0.7392 (t0) REVERT: C 2119 ASN cc_start: 0.7506 (t0) cc_final: 0.6925 (p0) REVERT: C 2186 ASN cc_start: 0.7831 (m-40) cc_final: 0.7502 (p0) REVERT: C 2309 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6813 (mt-10) REVERT: C 2322 ASN cc_start: 0.7818 (m-40) cc_final: 0.7522 (m110) REVERT: D 2099 ASP cc_start: 0.7639 (t0) cc_final: 0.7376 (t0) REVERT: D 2116 ASN cc_start: 0.8290 (t0) cc_final: 0.7922 (t0) REVERT: D 2119 ASN cc_start: 0.7455 (t0) cc_final: 0.6923 (p0) REVERT: D 2176 ASP cc_start: 0.7557 (t0) cc_final: 0.7319 (t70) REVERT: D 2186 ASN cc_start: 0.7812 (m-40) cc_final: 0.7336 (p0) REVERT: D 2309 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6724 (mt-10) REVERT: D 2365 ASN cc_start: 0.8599 (t0) cc_final: 0.8156 (t0) REVERT: E 2099 ASP cc_start: 0.7749 (t0) cc_final: 0.7472 (t0) REVERT: E 2119 ASN cc_start: 0.7448 (t0) cc_final: 0.6867 (p0) REVERT: E 2186 ASN cc_start: 0.7779 (m-40) cc_final: 0.7254 (p0) REVERT: E 2309 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6971 (mt-10) REVERT: E 2368 ASN cc_start: 0.7700 (t0) cc_final: 0.7483 (m-40) REVERT: F 2085 SER cc_start: 0.7843 (p) cc_final: 0.7567 (m) REVERT: F 2099 ASP cc_start: 0.7693 (t0) cc_final: 0.7438 (t0) REVERT: F 2119 ASN cc_start: 0.7395 (t0) cc_final: 0.6892 (p0) REVERT: F 2130 ASN cc_start: 0.8961 (t0) cc_final: 0.8674 (t0) REVERT: F 2186 ASN cc_start: 0.7665 (m-40) cc_final: 0.7416 (p0) REVERT: F 2309 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6882 (mt-10) REVERT: G 2099 ASP cc_start: 0.7717 (t0) cc_final: 0.7350 (p0) REVERT: G 2119 ASN cc_start: 0.7442 (t0) cc_final: 0.6897 (p0) REVERT: G 2176 ASP cc_start: 0.7047 (t70) cc_final: 0.6718 (t70) REVERT: G 2186 ASN cc_start: 0.7647 (m-40) cc_final: 0.7390 (p0) REVERT: G 2309 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6522 (tt0) REVERT: G 2368 ASN cc_start: 0.7738 (t0) cc_final: 0.7481 (m-40) outliers start: 68 outliers final: 61 residues processed: 239 average time/residue: 0.1986 time to fit residues: 84.7326 Evaluate side-chains 232 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 2118 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 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 2208 ILE Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2371 THR Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2078 THR 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 2078 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 2207 SER Chi-restraints excluded: chain D residue 2208 ILE 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 D residue 2391 VAL 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 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 2318 SER Chi-restraints excluded: chain E residue 2327 THR Chi-restraints excluded: chain E residue 2334 SER Chi-restraints excluded: chain E residue 2391 VAL Chi-restraints excluded: chain F residue 2063 SER Chi-restraints excluded: chain F residue 2078 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 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 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 2289 THR Chi-restraints excluded: chain G residue 2370 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 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 D2368 ASN F2322 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16947 Z= 0.403 Angle : 0.567 6.717 23464 Z= 0.295 Chirality : 0.047 0.162 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.694 21.186 2443 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.86 % Allowed : 11.94 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.18 (0.16), residues: 882 loop : 0.09 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2259 PHE 0.017 0.003 PHE F2106 TYR 0.011 0.002 TYR A2097 ARG 0.001 0.000 ARG G2260 *********************** 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 247 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 1.998 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7517 (t0) cc_final: 0.6946 (p0) REVERT: A 2186 ASN cc_start: 0.7741 (m-40) cc_final: 0.7389 (p0) REVERT: A 2309 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6731 (mt-10) REVERT: A 2375 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7120 (mp) REVERT: B 2099 ASP cc_start: 0.7634 (t0) cc_final: 0.7261 (p0) REVERT: B 2186 ASN cc_start: 0.7829 (m-40) cc_final: 0.7426 (p0) REVERT: B 2309 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6985 (mt-10) REVERT: B 2365 ASN cc_start: 0.8694 (t0) cc_final: 0.8231 (t0) REVERT: C 2099 ASP cc_start: 0.7605 (t0) cc_final: 0.7394 (p0) REVERT: C 2119 ASN cc_start: 0.7617 (t0) cc_final: 0.6988 (p0) REVERT: C 2186 ASN cc_start: 0.7845 (m-40) cc_final: 0.7487 (p0) REVERT: C 2309 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6651 (mt-10) REVERT: D 2099 ASP cc_start: 0.7654 (t0) cc_final: 0.7380 (p0) REVERT: D 2116 ASN cc_start: 0.8290 (t0) cc_final: 0.7947 (t0) REVERT: D 2119 ASN cc_start: 0.7472 (t0) cc_final: 0.6936 (p0) REVERT: D 2176 ASP cc_start: 0.7604 (t0) cc_final: 0.7334 (t70) REVERT: D 2186 ASN cc_start: 0.7852 (m-40) cc_final: 0.7321 (p0) REVERT: D 2309 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6702 (mt-10) REVERT: D 2365 ASN cc_start: 0.8665 (t0) cc_final: 0.8234 (t0) REVERT: E 2099 ASP cc_start: 0.7783 (t0) cc_final: 0.7520 (p0) REVERT: E 2119 ASN cc_start: 0.7531 (t0) cc_final: 0.6876 (p0) REVERT: E 2186 ASN cc_start: 0.7809 (m-40) cc_final: 0.7285 (p0) REVERT: E 2309 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6826 (mt-10) REVERT: E 2368 ASN cc_start: 0.7736 (t0) cc_final: 0.7519 (m-40) REVERT: F 2085 SER cc_start: 0.7844 (p) cc_final: 0.7552 (m) REVERT: F 2099 ASP cc_start: 0.7794 (t0) cc_final: 0.7471 (p0) REVERT: F 2119 ASN cc_start: 0.7499 (t0) cc_final: 0.6899 (p0) REVERT: F 2130 ASN cc_start: 0.9016 (t0) cc_final: 0.8771 (t0) REVERT: F 2186 ASN cc_start: 0.7758 (m-40) cc_final: 0.7427 (p0) REVERT: F 2309 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6658 (mt-10) REVERT: G 2099 ASP cc_start: 0.7810 (t0) cc_final: 0.7430 (p0) REVERT: G 2119 ASN cc_start: 0.7526 (t0) cc_final: 0.6939 (p0) REVERT: G 2176 ASP cc_start: 0.7172 (t70) cc_final: 0.6851 (t70) REVERT: G 2309 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6583 (tt0) REVERT: G 2365 ASN cc_start: 0.8672 (t0) cc_final: 0.8307 (t0) REVERT: G 2368 ASN cc_start: 0.7871 (t0) cc_final: 0.7570 (m-40) outliers start: 74 outliers final: 66 residues processed: 238 average time/residue: 0.1872 time to fit residues: 79.1262 Evaluate side-chains 228 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 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 2334 SER 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 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 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 2143 VAL Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 2207 SER 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 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 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 2391 VAL Chi-restraints excluded: chain F residue 2063 SER Chi-restraints excluded: chain F residue 2069 SER Chi-restraints excluded: chain F residue 2078 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 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 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 2289 THR Chi-restraints excluded: chain G residue 2334 SER 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 137 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 202 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2322 ASN D2368 ASN F2322 ASN G2186 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16947 Z= 0.182 Angle : 0.482 6.414 23464 Z= 0.247 Chirality : 0.043 0.175 2947 Planarity : 0.005 0.045 3073 Dihedral : 4.162 18.365 2443 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.82 % Allowed : 13.03 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.19 (0.16), residues: 896 loop : 0.36 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2177 PHE 0.013 0.002 PHE B2106 TYR 0.007 0.001 TYR B2124 ARG 0.000 0.000 ARG E2260 *********************** 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 237 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 1.870 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7372 (t0) cc_final: 0.6846 (p0) REVERT: A 2186 ASN cc_start: 0.7711 (m-40) cc_final: 0.7421 (p0) REVERT: A 2309 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 2375 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6995 (mp) REVERT: B 2099 ASP cc_start: 0.7560 (t0) cc_final: 0.7301 (t0) REVERT: B 2186 ASN cc_start: 0.7823 (m-40) cc_final: 0.7435 (p0) REVERT: B 2309 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6787 (pt0) REVERT: B 2365 ASN cc_start: 0.8669 (t0) cc_final: 0.8199 (t0) REVERT: B 2368 ASN cc_start: 0.7845 (m-40) cc_final: 0.7637 (m-40) REVERT: C 2099 ASP cc_start: 0.7693 (t0) cc_final: 0.7460 (t0) REVERT: C 2119 ASN cc_start: 0.7546 (t0) cc_final: 0.6967 (p0) REVERT: C 2186 ASN cc_start: 0.7876 (m-40) cc_final: 0.7559 (p0) REVERT: C 2309 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6707 (mt-10) REVERT: C 2322 ASN cc_start: 0.7752 (m-40) cc_final: 0.7430 (m110) REVERT: D 2099 ASP cc_start: 0.7654 (t0) cc_final: 0.7401 (p0) REVERT: D 2116 ASN cc_start: 0.8274 (t0) cc_final: 0.7941 (t0) REVERT: D 2119 ASN cc_start: 0.7447 (t0) cc_final: 0.6891 (p0) REVERT: D 2130 ASN cc_start: 0.8892 (t0) cc_final: 0.8504 (t0) REVERT: D 2176 ASP cc_start: 0.7591 (t0) cc_final: 0.7342 (t70) REVERT: D 2186 ASN cc_start: 0.7812 (m-40) cc_final: 0.7366 (p0) REVERT: D 2309 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6708 (mt-10) REVERT: D 2365 ASN cc_start: 0.8632 (t0) cc_final: 0.8185 (t0) REVERT: E 2099 ASP cc_start: 0.7654 (t0) cc_final: 0.7372 (t0) REVERT: E 2119 ASN cc_start: 0.7456 (t0) cc_final: 0.6830 (p0) REVERT: E 2186 ASN cc_start: 0.7798 (m-40) cc_final: 0.7309 (p0) REVERT: E 2309 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6920 (mt-10) REVERT: F 2085 SER cc_start: 0.7846 (p) cc_final: 0.7550 (m) REVERT: F 2119 ASN cc_start: 0.7447 (t0) cc_final: 0.6829 (p0) REVERT: F 2130 ASN cc_start: 0.8951 (t0) cc_final: 0.8712 (t0) REVERT: F 2309 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6950 (mt-10) REVERT: G 2099 ASP cc_start: 0.7713 (t0) cc_final: 0.7311 (p0) REVERT: G 2119 ASN cc_start: 0.7512 (t0) cc_final: 0.6976 (p0) REVERT: G 2136 LEU cc_start: 0.7084 (pp) cc_final: 0.6735 (pp) REVERT: G 2309 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6568 (tt0) REVERT: G 2365 ASN cc_start: 0.8663 (t0) cc_final: 0.8258 (t0) REVERT: G 2368 ASN cc_start: 0.7777 (t0) cc_final: 0.7486 (m-40) outliers start: 54 outliers final: 45 residues processed: 229 average time/residue: 0.1972 time to fit residues: 81.3985 Evaluate side-chains 216 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2085 SER 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 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 2208 ILE Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2312 SER 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 2126 LEU Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 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 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 2078 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 2391 VAL Chi-restraints excluded: chain G residue 2078 THR Chi-restraints excluded: chain G residue 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2289 THR Chi-restraints excluded: chain G residue 2329 THR 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 213 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 0.0770 chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN ** C2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2368 ASN F2186 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 16947 Z= 0.197 Angle : 0.485 6.446 23464 Z= 0.250 Chirality : 0.043 0.147 2947 Planarity : 0.004 0.043 3073 Dihedral : 4.036 17.665 2443 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.76 % Allowed : 13.50 % Favored : 83.73 % 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: 0.39 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.23 (0.16), residues: 896 loop : 0.41 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E2177 PHE 0.013 0.002 PHE B2106 TYR 0.006 0.001 TYR D2124 ARG 0.000 0.000 ARG B2260 *********************** 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 228 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.893 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7309 (t0) cc_final: 0.6725 (p0) REVERT: A 2186 ASN cc_start: 0.7732 (m-40) cc_final: 0.7441 (p0) REVERT: A 2309 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 2375 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7037 (mp) REVERT: B 2099 ASP cc_start: 0.7567 (t0) cc_final: 0.7316 (t0) REVERT: B 2186 ASN cc_start: 0.7752 (m-40) cc_final: 0.7400 (p0) REVERT: B 2309 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7017 (mt-10) REVERT: B 2365 ASN cc_start: 0.8677 (t0) cc_final: 0.8218 (t0) REVERT: C 2119 ASN cc_start: 0.7551 (t0) cc_final: 0.6953 (p0) REVERT: C 2186 ASN cc_start: 0.7839 (m-40) cc_final: 0.7538 (p0) REVERT: C 2309 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6712 (mt-10) REVERT: C 2322 ASN cc_start: 0.7723 (m-40) cc_final: 0.7445 (m110) REVERT: D 2116 ASN cc_start: 0.8262 (t0) cc_final: 0.7914 (t0) REVERT: D 2119 ASN cc_start: 0.7414 (t0) cc_final: 0.6875 (p0) REVERT: D 2130 ASN cc_start: 0.8871 (t0) cc_final: 0.8488 (t0) REVERT: D 2176 ASP cc_start: 0.7608 (t0) cc_final: 0.7359 (t70) REVERT: D 2186 ASN cc_start: 0.7840 (m-40) cc_final: 0.7388 (p0) REVERT: D 2309 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6756 (mt-10) REVERT: E 2099 ASP cc_start: 0.7655 (t0) cc_final: 0.7389 (t0) REVERT: E 2119 ASN cc_start: 0.7457 (t0) cc_final: 0.6843 (p0) REVERT: E 2186 ASN cc_start: 0.7737 (m-40) cc_final: 0.7294 (p0) REVERT: E 2309 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6806 (tt0) REVERT: F 2085 SER cc_start: 0.7873 (p) cc_final: 0.7553 (m) REVERT: F 2099 ASP cc_start: 0.7753 (t0) cc_final: 0.7500 (t0) REVERT: F 2119 ASN cc_start: 0.7348 (t0) cc_final: 0.6813 (p0) REVERT: F 2130 ASN cc_start: 0.8927 (t0) cc_final: 0.8686 (t0) REVERT: F 2309 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6910 (mt-10) REVERT: G 2099 ASP cc_start: 0.7731 (t0) cc_final: 0.7327 (p0) REVERT: G 2119 ASN cc_start: 0.7496 (t0) cc_final: 0.6949 (p0) REVERT: G 2309 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6611 (tt0) REVERT: G 2365 ASN cc_start: 0.8673 (t0) cc_final: 0.8247 (t0) REVERT: G 2368 ASN cc_start: 0.7726 (t0) cc_final: 0.7461 (m-40) outliers start: 53 outliers final: 48 residues processed: 220 average time/residue: 0.1950 time to fit residues: 76.8630 Evaluate side-chains 218 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 2375 LEU Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER Chi-restraints excluded: chain C residue 2063 SER Chi-restraints excluded: chain C residue 2121 SER Chi-restraints excluded: chain C residue 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 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 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 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 2111 ASN Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2208 ILE Chi-restraints excluded: chain F residue 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 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 230 optimal weight: 0.0020 chunk 211 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 112 optimal weight: 0.0570 chunk 145 optimal weight: 2.9990 overall best weight: 0.6908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN ** C2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2368 ASN F2186 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 16947 Z= 0.195 Angle : 0.482 6.414 23464 Z= 0.249 Chirality : 0.043 0.146 2947 Planarity : 0.004 0.042 3073 Dihedral : 3.954 18.455 2443 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.76 % Allowed : 13.66 % 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: 0.47 (0.17), residues: 2345 helix: None (None), residues: 0 sheet: 0.28 (0.16), residues: 896 loop : 0.47 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E2177 PHE 0.012 0.002 PHE B2106 TYR 0.007 0.001 TYR E2393 ARG 0.000 0.000 ARG C2260 ********************** 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 230 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.771 Fit side-chains REVERT: A 2119 ASN cc_start: 0.7351 (t0) cc_final: 0.6800 (p0) REVERT: A 2186 ASN cc_start: 0.7722 (m-40) cc_final: 0.7443 (p0) REVERT: A 2309 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6690 (mt-10) REVERT: A 2375 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7030 (mp) REVERT: A 2393 TYR cc_start: 0.8306 (m-10) cc_final: 0.8021 (m-10) REVERT: B 2099 ASP cc_start: 0.7573 (t0) cc_final: 0.7261 (p0) REVERT: B 2130 ASN cc_start: 0.8777 (t0) cc_final: 0.8448 (t0) REVERT: B 2151 SER cc_start: 0.7993 (t) cc_final: 0.7667 (m) REVERT: B 2186 ASN cc_start: 0.7753 (m-40) cc_final: 0.7411 (p0) REVERT: B 2309 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 2365 ASN cc_start: 0.8630 (t0) cc_final: 0.8189 (t0) REVERT: C 2119 ASN cc_start: 0.7545 (t0) cc_final: 0.6961 (p0) REVERT: C 2186 ASN cc_start: 0.7829 (m-40) cc_final: 0.7542 (p0) REVERT: C 2309 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6730 (mt-10) REVERT: C 2322 ASN cc_start: 0.7751 (m-40) cc_final: 0.7477 (m110) REVERT: D 2116 ASN cc_start: 0.8256 (t0) cc_final: 0.7928 (t0) REVERT: D 2119 ASN cc_start: 0.7395 (t0) cc_final: 0.6873 (p0) REVERT: D 2130 ASN cc_start: 0.8874 (t0) cc_final: 0.8495 (t0) REVERT: D 2176 ASP cc_start: 0.7500 (t0) cc_final: 0.7263 (t70) REVERT: D 2186 ASN cc_start: 0.7827 (m-40) cc_final: 0.7391 (p0) REVERT: D 2309 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6763 (mt-10) REVERT: E 2099 ASP cc_start: 0.7651 (t0) cc_final: 0.7376 (t0) REVERT: E 2119 ASN cc_start: 0.7447 (t0) cc_final: 0.6818 (p0) REVERT: E 2186 ASN cc_start: 0.7728 (m-40) cc_final: 0.7297 (p0) REVERT: E 2309 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6849 (tt0) REVERT: F 2085 SER cc_start: 0.7831 (p) cc_final: 0.7509 (m) REVERT: F 2099 ASP cc_start: 0.7708 (t0) cc_final: 0.7464 (t0) REVERT: F 2119 ASN cc_start: 0.7317 (t0) cc_final: 0.6768 (p0) REVERT: F 2130 ASN cc_start: 0.8896 (t0) cc_final: 0.8646 (t0) REVERT: F 2309 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6910 (mt-10) REVERT: G 2099 ASP cc_start: 0.7718 (t0) cc_final: 0.7328 (p0) REVERT: G 2119 ASN cc_start: 0.7484 (t0) cc_final: 0.6921 (p0) REVERT: G 2309 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6622 (tt0) REVERT: G 2365 ASN cc_start: 0.8659 (t0) cc_final: 0.8236 (t0) REVERT: G 2368 ASN cc_start: 0.7724 (t0) cc_final: 0.7457 (m-40) outliers start: 53 outliers final: 50 residues processed: 221 average time/residue: 0.1949 time to fit residues: 76.7648 Evaluate side-chains 221 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2085 SER 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 2073 ASN Chi-restraints excluded: chain B residue 2078 THR Chi-restraints excluded: chain B residue 2109 LEU Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2146 LEU Chi-restraints excluded: chain B residue 2185 SER Chi-restraints excluded: chain B residue 2208 ILE Chi-restraints excluded: chain B residue 2289 THR Chi-restraints excluded: chain B residue 2312 SER Chi-restraints excluded: chain B residue 2334 SER 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 2208 ILE Chi-restraints excluded: chain C residue 2277 VAL Chi-restraints excluded: chain C residue 2334 SER Chi-restraints excluded: chain C residue 2391 VAL Chi-restraints excluded: chain D residue 2078 THR Chi-restraints excluded: chain D residue 2121 SER Chi-restraints excluded: chain D residue 2185 SER Chi-restraints excluded: chain D residue 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 2208 ILE 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 2121 SER Chi-restraints excluded: chain F residue 2185 SER Chi-restraints excluded: chain F residue 2186 ASN Chi-restraints excluded: chain F residue 2208 ILE 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 2121 SER Chi-restraints excluded: chain G residue 2185 SER Chi-restraints excluded: chain G residue 2208 ILE Chi-restraints excluded: chain G residue 2289 THR Chi-restraints excluded: chain G residue 2334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2073 ASN ** C2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2368 ASN F2072 ASN ** G2263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.119978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.091407 restraints weight = 19319.334| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.68 r_work: 0.2708 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 16947 Z= 0.347 Angle : 0.546 6.602 23464 Z= 0.283 Chirality : 0.046 0.188 2947 Planarity : 0.005 0.047 3073 Dihedral : 4.336 19.929 2443 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.82 % Allowed : 13.66 % Favored : 83.52 % 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: 0.24 (0.16), residues: 2345 helix: None (None), residues: 0 sheet: 0.09 (0.16), residues: 896 loop : 0.34 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B2259 PHE 0.015 0.003 PHE F2106 TYR 0.009 0.001 TYR E2097 ARG 0.001 0.000 ARG G2260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.47 seconds wall clock time: 59 minutes 34.20 seconds (3574.20 seconds total)