Starting phenix.real_space_refine on Sat Oct 31 15:28:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kln_22917/10_2026/7kln_22917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kln_22917/10_2026/7kln_22917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kln_22917/10_2026/7kln_22917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kln_22917/10_2026/7kln_22917.map" model { file = "/net/cci-nas-00/data/ceres_data/7kln_22917/10_2026/7kln_22917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kln_22917/10_2026/7kln_22917.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.548 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 180 5.16 5 C 28776 2.51 5 N 7644 2.21 5 O 8964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 336 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 45564 Number of models: 1 Model: "" Number of chains: 2 Chain: "A1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "A2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Restraints were copied for chains: B1, C1, D1, E1, F1, G1, H1, I1, J1, K1, L1, B2, C2, D2, E2, F2, G2, H2, I2, J2, K2, L2 Time building chain proxies: 6.02, per 1000 atoms: 0.13 Number of scatterers: 45564 At special positions: 0 Unit cell: (159.57, 159.57, 153.09, 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 180 16.00 O 8964 8.00 N 7644 7.00 C 28776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSA2 32 " - pdb=" SG CYSB2 42 " distance=2.12 Simple disulfide: pdb=" SG CYSA2 42 " - pdb=" SG CYSL2 32 " distance=1.94 Simple disulfide: pdb=" SG CYSB2 32 " - pdb=" SG CYSC2 42 " distance=2.05 Simple disulfide: pdb=" SG CYSC2 32 " - pdb=" SG CYSD2 42 " distance=2.00 Simple disulfide: pdb=" SG CYSD2 32 " - pdb=" SG CYSE2 42 " distance=2.15 Simple disulfide: pdb=" SG CYSE2 32 " - pdb=" SG CYSF2 42 " distance=2.04 Simple disulfide: pdb=" SG CYSF2 32 " - pdb=" SG CYSG2 42 " distance=2.02 Simple disulfide: pdb=" SG CYSG2 32 " - pdb=" SG CYSH2 42 " distance=1.99 Simple disulfide: pdb=" SG CYSH2 32 " - pdb=" SG CYSI2 42 " distance=2.01 Simple disulfide: pdb=" SG CYSI2 32 " - pdb=" SG CYSJ2 42 " distance=2.14 Simple disulfide: pdb=" SG CYSJ2 32 " - pdb=" SG CYSK2 42 " distance=1.96 Simple disulfide: pdb=" SG CYSK2 32 " - pdb=" SG CYSL2 42 " distance=1.93 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: 4.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10632 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 49 sheets defined 52.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGA1 18 " --> pdb=" O LEUA1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNA1 19 " --> pdb=" O ILEA1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'A1' and resid 14 through 19' Processing helix chain 'A1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRA1 40 " --> pdb=" O META1 36 " (cutoff:3.500A) Processing helix chain 'A1' and resid 42 through 58 Processing helix chain 'A1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSA1 74 " --> pdb=" O GLUA1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGA1 75 " --> pdb=" O ILEA1 71 " (cutoff:3.500A) Processing helix chain 'A1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSA1 81 " --> pdb=" O SERA1 77 " (cutoff:3.500A) Processing helix chain 'A1' and resid 168 through 176 Proline residue: A1 173 - end of helix Processing helix chain 'A1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUA1 188 " --> pdb=" O GLUA1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNA1 189 " --> pdb=" O LEUA1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEA1 191 " --> pdb=" O TYRA1 187 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASNA1 192 " --> pdb=" O GLUA1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERA1 202 " --> pdb=" O ARGA1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEA1 204 " --> pdb=" O SERA1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUA1 205 " --> pdb=" O GLYA1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSA1 206 " --> pdb=" O SERA1 202 " (cutoff:3.500A) Processing helix chain 'A1' and resid 216 through 223 Processing helix chain 'A1' and resid 226 through 238 removed outlier: 3.527A pdb=" N ILEA1 230 " --> pdb=" O GLUA1 226 " (cutoff:3.500A) Processing helix chain 'A1' and resid 263 through 280 Processing helix chain 'A1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUA1 286 " --> pdb=" O GLYA1 282 " (cutoff:3.500A) Processing helix chain 'A1' and resid 301 through 304 Processing helix chain 'A1' and resid 305 through 314 Processing helix chain 'A1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEA1 328 " --> pdb=" O LEUA1 324 " (cutoff:3.500A) Processing helix chain 'A1' and resid 347 through 359 removed outlier: 4.035A pdb=" N LYSA1 352 " --> pdb=" O GLUA1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAA1 353 " --> pdb=" O TYRA1 349 " (cutoff:3.500A) Processing helix chain 'A1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSA1 372 " --> pdb=" O ALAA1 369 " (cutoff:3.500A) Processing helix chain 'B1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGB1 18 " --> pdb=" O LEUB1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNB1 19 " --> pdb=" O ILEB1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 14 through 19' Processing helix chain 'B1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRB1 40 " --> pdb=" O METB1 36 " (cutoff:3.500A) Processing helix chain 'B1' and resid 42 through 58 Processing helix chain 'B1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSB1 74 " --> pdb=" O GLUB1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGB1 75 " --> pdb=" O ILEB1 71 " (cutoff:3.500A) Processing helix chain 'B1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSB1 81 " --> pdb=" O SERB1 77 " (cutoff:3.500A) Processing helix chain 'B1' and resid 168 through 176 Proline residue: B1 173 - end of helix Processing helix chain 'B1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUB1 188 " --> pdb=" O GLUB1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNB1 189 " --> pdb=" O LEUB1 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEB1 191 " --> pdb=" O TYRB1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNB1 192 " --> pdb=" O GLUB1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERB1 202 " --> pdb=" O ARGB1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEB1 204 " --> pdb=" O SERB1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUB1 205 " --> pdb=" O GLYB1 201 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYSB1 206 " --> pdb=" O SERB1 202 " (cutoff:3.500A) Processing helix chain 'B1' and resid 216 through 223 Processing helix chain 'B1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEB1 230 " --> pdb=" O GLUB1 226 " (cutoff:3.500A) Processing helix chain 'B1' and resid 263 through 280 Processing helix chain 'B1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUB1 286 " --> pdb=" O GLYB1 282 " (cutoff:3.500A) Processing helix chain 'B1' and resid 301 through 304 Processing helix chain 'B1' and resid 305 through 314 Processing helix chain 'B1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEB1 328 " --> pdb=" O LEUB1 324 " (cutoff:3.500A) Processing helix chain 'B1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSB1 352 " --> pdb=" O GLUB1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAB1 353 " --> pdb=" O TYRB1 349 " (cutoff:3.500A) Processing helix chain 'B1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSB1 372 " --> pdb=" O ALAB1 369 " (cutoff:3.500A) Processing helix chain 'C1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGC1 18 " --> pdb=" O LEUC1 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASNC1 19 " --> pdb=" O ILEC1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 14 through 19' Processing helix chain 'C1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRC1 40 " --> pdb=" O METC1 36 " (cutoff:3.500A) Processing helix chain 'C1' and resid 42 through 58 Processing helix chain 'C1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSC1 74 " --> pdb=" O GLUC1 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGC1 75 " --> pdb=" O ILEC1 71 " (cutoff:3.500A) Processing helix chain 'C1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSC1 81 " --> pdb=" O SERC1 77 " (cutoff:3.500A) Processing helix chain 'C1' and resid 168 through 176 Proline residue: C1 173 - end of helix Processing helix chain 'C1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUC1 188 " --> pdb=" O GLUC1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNC1 189 " --> pdb=" O LEUC1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEC1 191 " --> pdb=" O TYRC1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNC1 192 " --> pdb=" O GLUC1 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERC1 202 " --> pdb=" O ARGC1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEC1 204 " --> pdb=" O SERC1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUC1 205 " --> pdb=" O GLYC1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSC1 206 " --> pdb=" O SERC1 202 " (cutoff:3.500A) Processing helix chain 'C1' and resid 216 through 223 Processing helix chain 'C1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEC1 230 " --> pdb=" O GLUC1 226 " (cutoff:3.500A) Processing helix chain 'C1' and resid 263 through 280 Processing helix chain 'C1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUC1 286 " --> pdb=" O GLYC1 282 " (cutoff:3.500A) Processing helix chain 'C1' and resid 301 through 304 Processing helix chain 'C1' and resid 305 through 314 Processing helix chain 'C1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEC1 328 " --> pdb=" O LEUC1 324 " (cutoff:3.500A) Processing helix chain 'C1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSC1 352 " --> pdb=" O GLUC1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAC1 353 " --> pdb=" O TYRC1 349 " (cutoff:3.500A) Processing helix chain 'C1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSC1 372 " --> pdb=" O ALAC1 369 " (cutoff:3.500A) Processing helix chain 'D1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGD1 18 " --> pdb=" O LEUD1 14 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASND1 19 " --> pdb=" O ILED1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D1' and resid 14 through 19' Processing helix chain 'D1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRD1 40 " --> pdb=" O METD1 36 " (cutoff:3.500A) Processing helix chain 'D1' and resid 42 through 58 Processing helix chain 'D1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSD1 74 " --> pdb=" O GLUD1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGD1 75 " --> pdb=" O ILED1 71 " (cutoff:3.500A) Processing helix chain 'D1' and resid 76 through 91 removed outlier: 3.723A pdb=" N LYSD1 81 " --> pdb=" O SERD1 77 " (cutoff:3.500A) Processing helix chain 'D1' and resid 168 through 176 Proline residue: D1 173 - end of helix Processing helix chain 'D1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUD1 188 " --> pdb=" O GLUD1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLND1 189 " --> pdb=" O LEUD1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILED1 191 " --> pdb=" O TYRD1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASND1 192 " --> pdb=" O GLUD1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERD1 202 " --> pdb=" O ARGD1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILED1 204 " --> pdb=" O SERD1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUD1 205 " --> pdb=" O GLYD1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSD1 206 " --> pdb=" O SERD1 202 " (cutoff:3.500A) Processing helix chain 'D1' and resid 216 through 223 Processing helix chain 'D1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILED1 230 " --> pdb=" O GLUD1 226 " (cutoff:3.500A) Processing helix chain 'D1' and resid 263 through 280 Processing helix chain 'D1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUD1 286 " --> pdb=" O GLYD1 282 " (cutoff:3.500A) Processing helix chain 'D1' and resid 301 through 304 Processing helix chain 'D1' and resid 305 through 314 Processing helix chain 'D1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHED1 328 " --> pdb=" O LEUD1 324 " (cutoff:3.500A) Processing helix chain 'D1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSD1 352 " --> pdb=" O GLUD1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAD1 353 " --> pdb=" O TYRD1 349 " (cutoff:3.500A) Processing helix chain 'D1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSD1 372 " --> pdb=" O ALAD1 369 " (cutoff:3.500A) Processing helix chain 'E1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGE1 18 " --> pdb=" O LEUE1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNE1 19 " --> pdb=" O ILEE1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'E1' and resid 14 through 19' Processing helix chain 'E1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRE1 40 " --> pdb=" O METE1 36 " (cutoff:3.500A) Processing helix chain 'E1' and resid 42 through 58 Processing helix chain 'E1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSE1 74 " --> pdb=" O GLUE1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGE1 75 " --> pdb=" O ILEE1 71 " (cutoff:3.500A) Processing helix chain 'E1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSE1 81 " --> pdb=" O SERE1 77 " (cutoff:3.500A) Processing helix chain 'E1' and resid 168 through 176 Proline residue: E1 173 - end of helix Processing helix chain 'E1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUE1 188 " --> pdb=" O GLUE1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNE1 189 " --> pdb=" O LEUE1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEE1 191 " --> pdb=" O TYRE1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNE1 192 " --> pdb=" O GLUE1 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERE1 202 " --> pdb=" O ARGE1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEE1 204 " --> pdb=" O SERE1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUE1 205 " --> pdb=" O GLYE1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSE1 206 " --> pdb=" O SERE1 202 " (cutoff:3.500A) Processing helix chain 'E1' and resid 216 through 223 Processing helix chain 'E1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEE1 230 " --> pdb=" O GLUE1 226 " (cutoff:3.500A) Processing helix chain 'E1' and resid 263 through 280 Processing helix chain 'E1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUE1 286 " --> pdb=" O GLYE1 282 " (cutoff:3.500A) Processing helix chain 'E1' and resid 301 through 304 Processing helix chain 'E1' and resid 305 through 314 Processing helix chain 'E1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEE1 328 " --> pdb=" O LEUE1 324 " (cutoff:3.500A) Processing helix chain 'E1' and resid 347 through 359 removed outlier: 4.033A pdb=" N LYSE1 352 " --> pdb=" O GLUE1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAE1 353 " --> pdb=" O TYRE1 349 " (cutoff:3.500A) Processing helix chain 'E1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSE1 372 " --> pdb=" O ALAE1 369 " (cutoff:3.500A) Processing helix chain 'F1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGF1 18 " --> pdb=" O LEUF1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNF1 19 " --> pdb=" O ILEF1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'F1' and resid 14 through 19' Processing helix chain 'F1' and resid 32 through 42 removed outlier: 3.524A pdb=" N TYRF1 40 " --> pdb=" O METF1 36 " (cutoff:3.500A) Processing helix chain 'F1' and resid 42 through 58 Processing helix chain 'F1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSF1 74 " --> pdb=" O GLUF1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGF1 75 " --> pdb=" O ILEF1 71 " (cutoff:3.500A) Processing helix chain 'F1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSF1 81 " --> pdb=" O SERF1 77 " (cutoff:3.500A) Processing helix chain 'F1' and resid 168 through 176 Proline residue: F1 173 - end of helix Processing helix chain 'F1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUF1 188 " --> pdb=" O GLUF1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNF1 189 " --> pdb=" O LEUF1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEF1 191 " --> pdb=" O TYRF1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNF1 192 " --> pdb=" O GLUF1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERF1 202 " --> pdb=" O ARGF1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEF1 204 " --> pdb=" O SERF1 200 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLUF1 205 " --> pdb=" O GLYF1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSF1 206 " --> pdb=" O SERF1 202 " (cutoff:3.500A) Processing helix chain 'F1' and resid 216 through 223 Processing helix chain 'F1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEF1 230 " --> pdb=" O GLUF1 226 " (cutoff:3.500A) Processing helix chain 'F1' and resid 263 through 280 Processing helix chain 'F1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUF1 286 " --> pdb=" O GLYF1 282 " (cutoff:3.500A) Processing helix chain 'F1' and resid 301 through 304 Processing helix chain 'F1' and resid 305 through 314 Processing helix chain 'F1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEF1 328 " --> pdb=" O LEUF1 324 " (cutoff:3.500A) Processing helix chain 'F1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSF1 352 " --> pdb=" O GLUF1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAF1 353 " --> pdb=" O TYRF1 349 " (cutoff:3.500A) Processing helix chain 'F1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSF1 372 " --> pdb=" O ALAF1 369 " (cutoff:3.500A) Processing helix chain 'G1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGG1 18 " --> pdb=" O LEUG1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNG1 19 " --> pdb=" O ILEG1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G1' and resid 14 through 19' Processing helix chain 'G1' and resid 32 through 42 removed outlier: 3.526A pdb=" N TYRG1 40 " --> pdb=" O METG1 36 " (cutoff:3.500A) Processing helix chain 'G1' and resid 42 through 58 Processing helix chain 'G1' and resid 70 through 76 removed outlier: 3.618A pdb=" N LYSG1 74 " --> pdb=" O GLUG1 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGG1 75 " --> pdb=" O ILEG1 71 " (cutoff:3.500A) Processing helix chain 'G1' and resid 76 through 91 removed outlier: 3.725A pdb=" N LYSG1 81 " --> pdb=" O SERG1 77 " (cutoff:3.500A) Processing helix chain 'G1' and resid 168 through 176 Proline residue: G1 173 - end of helix Processing helix chain 'G1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUG1 188 " --> pdb=" O GLUG1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNG1 189 " --> pdb=" O LEUG1 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEG1 191 " --> pdb=" O TYRG1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNG1 192 " --> pdb=" O GLUG1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERG1 202 " --> pdb=" O ARGG1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEG1 204 " --> pdb=" O SERG1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUG1 205 " --> pdb=" O GLYG1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSG1 206 " --> pdb=" O SERG1 202 " (cutoff:3.500A) Processing helix chain 'G1' and resid 216 through 223 Processing helix chain 'G1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEG1 230 " --> pdb=" O GLUG1 226 " (cutoff:3.500A) Processing helix chain 'G1' and resid 263 through 280 Processing helix chain 'G1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUG1 286 " --> pdb=" O GLYG1 282 " (cutoff:3.500A) Processing helix chain 'G1' and resid 301 through 304 Processing helix chain 'G1' and resid 305 through 314 Processing helix chain 'G1' and resid 317 through 328 removed outlier: 3.527A pdb=" N PHEG1 328 " --> pdb=" O LEUG1 324 " (cutoff:3.500A) Processing helix chain 'G1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSG1 352 " --> pdb=" O GLUG1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAG1 353 " --> pdb=" O TYRG1 349 " (cutoff:3.500A) Processing helix chain 'G1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSG1 372 " --> pdb=" O ALAG1 369 " (cutoff:3.500A) Processing helix chain 'H1' and resid 14 through 19 removed outlier: 3.624A pdb=" N ARGH1 18 " --> pdb=" O LEUH1 14 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASNH1 19 " --> pdb=" O ILEH1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'H1' and resid 14 through 19' Processing helix chain 'H1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRH1 40 " --> pdb=" O METH1 36 " (cutoff:3.500A) Processing helix chain 'H1' and resid 42 through 58 Processing helix chain 'H1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSH1 74 " --> pdb=" O GLUH1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGH1 75 " --> pdb=" O ILEH1 71 " (cutoff:3.500A) Processing helix chain 'H1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSH1 81 " --> pdb=" O SERH1 77 " (cutoff:3.500A) Processing helix chain 'H1' and resid 168 through 176 Proline residue: H1 173 - end of helix Processing helix chain 'H1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUH1 188 " --> pdb=" O GLUH1 184 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLNH1 189 " --> pdb=" O LEUH1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEH1 191 " --> pdb=" O TYRH1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNH1 192 " --> pdb=" O GLUH1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERH1 202 " --> pdb=" O ARGH1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEH1 204 " --> pdb=" O SERH1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUH1 205 " --> pdb=" O GLYH1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSH1 206 " --> pdb=" O SERH1 202 " (cutoff:3.500A) Processing helix chain 'H1' and resid 216 through 223 Processing helix chain 'H1' and resid 226 through 238 removed outlier: 3.527A pdb=" N ILEH1 230 " --> pdb=" O GLUH1 226 " (cutoff:3.500A) Processing helix chain 'H1' and resid 263 through 280 Processing helix chain 'H1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUH1 286 " --> pdb=" O GLYH1 282 " (cutoff:3.500A) Processing helix chain 'H1' and resid 301 through 304 Processing helix chain 'H1' and resid 305 through 314 Processing helix chain 'H1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEH1 328 " --> pdb=" O LEUH1 324 " (cutoff:3.500A) Processing helix chain 'H1' and resid 347 through 359 removed outlier: 4.035A pdb=" N LYSH1 352 " --> pdb=" O GLUH1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAH1 353 " --> pdb=" O TYRH1 349 " (cutoff:3.500A) Processing helix chain 'H1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSH1 372 " --> pdb=" O ALAH1 369 " (cutoff:3.500A) Processing helix chain 'I1' and resid 14 through 19 removed outlier: 3.624A pdb=" N ARGI1 18 " --> pdb=" O LEUI1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNI1 19 " --> pdb=" O ILEI1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'I1' and resid 14 through 19' Processing helix chain 'I1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRI1 40 " --> pdb=" O METI1 36 " (cutoff:3.500A) Processing helix chain 'I1' and resid 42 through 58 Processing helix chain 'I1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSI1 74 " --> pdb=" O GLUI1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGI1 75 " --> pdb=" O ILEI1 71 " (cutoff:3.500A) Processing helix chain 'I1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSI1 81 " --> pdb=" O SERI1 77 " (cutoff:3.500A) Processing helix chain 'I1' and resid 168 through 176 Proline residue: I1 173 - end of helix Processing helix chain 'I1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUI1 188 " --> pdb=" O GLUI1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNI1 189 " --> pdb=" O LEUI1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEI1 191 " --> pdb=" O TYRI1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNI1 192 " --> pdb=" O GLUI1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERI1 202 " --> pdb=" O ARGI1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEI1 204 " --> pdb=" O SERI1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUI1 205 " --> pdb=" O GLYI1 201 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYSI1 206 " --> pdb=" O SERI1 202 " (cutoff:3.500A) Processing helix chain 'I1' and resid 216 through 223 Processing helix chain 'I1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEI1 230 " --> pdb=" O GLUI1 226 " (cutoff:3.500A) Processing helix chain 'I1' and resid 263 through 280 Processing helix chain 'I1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUI1 286 " --> pdb=" O GLYI1 282 " (cutoff:3.500A) Processing helix chain 'I1' and resid 301 through 304 Processing helix chain 'I1' and resid 305 through 314 Processing helix chain 'I1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEI1 328 " --> pdb=" O LEUI1 324 " (cutoff:3.500A) Processing helix chain 'I1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSI1 352 " --> pdb=" O GLUI1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAI1 353 " --> pdb=" O TYRI1 349 " (cutoff:3.500A) Processing helix chain 'I1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSI1 372 " --> pdb=" O ALAI1 369 " (cutoff:3.500A) Processing helix chain 'J1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGJ1 18 " --> pdb=" O LEUJ1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNJ1 19 " --> pdb=" O ILEJ1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J1' and resid 14 through 19' Processing helix chain 'J1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRJ1 40 " --> pdb=" O METJ1 36 " (cutoff:3.500A) Processing helix chain 'J1' and resid 42 through 58 Processing helix chain 'J1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSJ1 74 " --> pdb=" O GLUJ1 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGJ1 75 " --> pdb=" O ILEJ1 71 " (cutoff:3.500A) Processing helix chain 'J1' and resid 76 through 91 removed outlier: 3.725A pdb=" N LYSJ1 81 " --> pdb=" O SERJ1 77 " (cutoff:3.500A) Processing helix chain 'J1' and resid 168 through 176 Proline residue: J1 173 - end of helix Processing helix chain 'J1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUJ1 188 " --> pdb=" O GLUJ1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNJ1 189 " --> pdb=" O LEUJ1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEJ1 191 " --> pdb=" O TYRJ1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNJ1 192 " --> pdb=" O GLUJ1 188 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SERJ1 202 " --> pdb=" O ARGJ1 198 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILEJ1 204 " --> pdb=" O SERJ1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUJ1 205 " --> pdb=" O GLYJ1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSJ1 206 " --> pdb=" O SERJ1 202 " (cutoff:3.500A) Processing helix chain 'J1' and resid 216 through 223 Processing helix chain 'J1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEJ1 230 " --> pdb=" O GLUJ1 226 " (cutoff:3.500A) Processing helix chain 'J1' and resid 263 through 280 Processing helix chain 'J1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUJ1 286 " --> pdb=" O GLYJ1 282 " (cutoff:3.500A) Processing helix chain 'J1' and resid 301 through 304 Processing helix chain 'J1' and resid 305 through 314 Processing helix chain 'J1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEJ1 328 " --> pdb=" O LEUJ1 324 " (cutoff:3.500A) Processing helix chain 'J1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSJ1 352 " --> pdb=" O GLUJ1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAJ1 353 " --> pdb=" O TYRJ1 349 " (cutoff:3.500A) Processing helix chain 'J1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSJ1 372 " --> pdb=" O ALAJ1 369 " (cutoff:3.500A) Processing helix chain 'K1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGK1 18 " --> pdb=" O LEUK1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNK1 19 " --> pdb=" O ILEK1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'K1' and resid 14 through 19' Processing helix chain 'K1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRK1 40 " --> pdb=" O METK1 36 " (cutoff:3.500A) Processing helix chain 'K1' and resid 42 through 58 Processing helix chain 'K1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSK1 74 " --> pdb=" O GLUK1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGK1 75 " --> pdb=" O ILEK1 71 " (cutoff:3.500A) Processing helix chain 'K1' and resid 76 through 91 removed outlier: 3.723A pdb=" N LYSK1 81 " --> pdb=" O SERK1 77 " (cutoff:3.500A) Processing helix chain 'K1' and resid 168 through 176 Proline residue: K1 173 - end of helix Processing helix chain 'K1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUK1 188 " --> pdb=" O GLUK1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNK1 189 " --> pdb=" O LEUK1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEK1 191 " --> pdb=" O TYRK1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNK1 192 " --> pdb=" O GLUK1 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERK1 202 " --> pdb=" O ARGK1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEK1 204 " --> pdb=" O SERK1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUK1 205 " --> pdb=" O GLYK1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSK1 206 " --> pdb=" O SERK1 202 " (cutoff:3.500A) Processing helix chain 'K1' and resid 216 through 223 Processing helix chain 'K1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEK1 230 " --> pdb=" O GLUK1 226 " (cutoff:3.500A) Processing helix chain 'K1' and resid 263 through 280 Processing helix chain 'K1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUK1 286 " --> pdb=" O GLYK1 282 " (cutoff:3.500A) Processing helix chain 'K1' and resid 301 through 304 Processing helix chain 'K1' and resid 305 through 314 Processing helix chain 'K1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEK1 328 " --> pdb=" O LEUK1 324 " (cutoff:3.500A) Processing helix chain 'K1' and resid 347 through 359 removed outlier: 4.035A pdb=" N LYSK1 352 " --> pdb=" O GLUK1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAK1 353 " --> pdb=" O TYRK1 349 " (cutoff:3.500A) Processing helix chain 'K1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSK1 372 " --> pdb=" O ALAK1 369 " (cutoff:3.500A) Processing helix chain 'L1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGL1 18 " --> pdb=" O LEUL1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNL1 19 " --> pdb=" O ILEL1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'L1' and resid 14 through 19' Processing helix chain 'L1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRL1 40 " --> pdb=" O METL1 36 " (cutoff:3.500A) Processing helix chain 'L1' and resid 42 through 58 Processing helix chain 'L1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSL1 74 " --> pdb=" O GLUL1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGL1 75 " --> pdb=" O ILEL1 71 " (cutoff:3.500A) Processing helix chain 'L1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSL1 81 " --> pdb=" O SERL1 77 " (cutoff:3.500A) Processing helix chain 'L1' and resid 168 through 176 Proline residue: L1 173 - end of helix Processing helix chain 'L1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUL1 188 " --> pdb=" O GLUL1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNL1 189 " --> pdb=" O LEUL1 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEL1 191 " --> pdb=" O TYRL1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNL1 192 " --> pdb=" O GLUL1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERL1 202 " --> pdb=" O ARGL1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEL1 204 " --> pdb=" O SERL1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUL1 205 " --> pdb=" O GLYL1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSL1 206 " --> pdb=" O SERL1 202 " (cutoff:3.500A) Processing helix chain 'L1' and resid 216 through 223 Processing helix chain 'L1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEL1 230 " --> pdb=" O GLUL1 226 " (cutoff:3.500A) Processing helix chain 'L1' and resid 263 through 280 Processing helix chain 'L1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUL1 286 " --> pdb=" O GLYL1 282 " (cutoff:3.500A) Processing helix chain 'L1' and resid 301 through 304 Processing helix chain 'L1' and resid 305 through 314 Processing helix chain 'L1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEL1 328 " --> pdb=" O LEUL1 324 " (cutoff:3.500A) Processing helix chain 'L1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSL1 352 " --> pdb=" O GLUL1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAL1 353 " --> pdb=" O TYRL1 349 " (cutoff:3.500A) Processing helix chain 'L1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSL1 372 " --> pdb=" O ALAL1 369 " (cutoff:3.500A) Processing helix chain 'A2' and resid 2 through 11 Processing helix chain 'A2' and resid 16 through 21 Processing helix chain 'A2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNA2 28 " --> pdb=" O PROA2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNA2 29 " --> pdb=" O VALA2 25 " (cutoff:3.500A) Processing helix chain 'A2' and resid 31 through 33 No H-bonds generated for 'chain 'A2' and resid 31 through 33' Processing helix chain 'A2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSA2 44 " --> pdb=" O ASNA2 40 " (cutoff:3.500A) Processing helix chain 'A2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERA2 62 " --> pdb=" O ASPA2 58 " (cutoff:3.500A) Processing helix chain 'A2' and resid 90 through 97 Processing helix chain 'A2' and resid 99 through 109 removed outlier: 3.829A pdb=" N META2 107 " --> pdb=" O GLNA2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRA2 109 " --> pdb=" O PHEA2 105 " (cutoff:3.500A) Processing helix chain 'B2' and resid 2 through 11 Processing helix chain 'B2' and resid 16 through 21 Processing helix chain 'B2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNB2 28 " --> pdb=" O PROB2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNB2 29 " --> pdb=" O VALB2 25 " (cutoff:3.500A) Processing helix chain 'B2' and resid 31 through 33 No H-bonds generated for 'chain 'B2' and resid 31 through 33' Processing helix chain 'B2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSB2 44 " --> pdb=" O ASNB2 40 " (cutoff:3.500A) Processing helix chain 'B2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERB2 62 " --> pdb=" O ASPB2 58 " (cutoff:3.500A) Processing helix chain 'B2' and resid 90 through 97 Processing helix chain 'B2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METB2 107 " --> pdb=" O GLNB2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRB2 109 " --> pdb=" O PHEB2 105 " (cutoff:3.500A) Processing helix chain 'C2' and resid 2 through 11 Processing helix chain 'C2' and resid 16 through 21 Processing helix chain 'C2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNC2 28 " --> pdb=" O PROC2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNC2 29 " --> pdb=" O VALC2 25 " (cutoff:3.500A) Processing helix chain 'C2' and resid 31 through 33 No H-bonds generated for 'chain 'C2' and resid 31 through 33' Processing helix chain 'C2' and resid 40 through 57 removed outlier: 3.619A pdb=" N LYSC2 44 " --> pdb=" O ASNC2 40 " (cutoff:3.500A) Processing helix chain 'C2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERC2 62 " --> pdb=" O ASPC2 58 " (cutoff:3.500A) Processing helix chain 'C2' and resid 90 through 97 Processing helix chain 'C2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METC2 107 " --> pdb=" O GLNC2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRC2 109 " --> pdb=" O PHEC2 105 " (cutoff:3.500A) Processing helix chain 'D2' and resid 2 through 11 Processing helix chain 'D2' and resid 16 through 21 Processing helix chain 'D2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASND2 28 " --> pdb=" O PROD2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASND2 29 " --> pdb=" O VALD2 25 " (cutoff:3.500A) Processing helix chain 'D2' and resid 31 through 33 No H-bonds generated for 'chain 'D2' and resid 31 through 33' Processing helix chain 'D2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSD2 44 " --> pdb=" O ASND2 40 " (cutoff:3.500A) Processing helix chain 'D2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERD2 62 " --> pdb=" O ASPD2 58 " (cutoff:3.500A) Processing helix chain 'D2' and resid 90 through 97 Processing helix chain 'D2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METD2 107 " --> pdb=" O GLND2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRD2 109 " --> pdb=" O PHED2 105 " (cutoff:3.500A) Processing helix chain 'E2' and resid 2 through 11 Processing helix chain 'E2' and resid 16 through 21 Processing helix chain 'E2' and resid 22 through 30 removed outlier: 4.511A pdb=" N ASNE2 28 " --> pdb=" O PROE2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNE2 29 " --> pdb=" O VALE2 25 " (cutoff:3.500A) Processing helix chain 'E2' and resid 31 through 33 No H-bonds generated for 'chain 'E2' and resid 31 through 33' Processing helix chain 'E2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSE2 44 " --> pdb=" O ASNE2 40 " (cutoff:3.500A) Processing helix chain 'E2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERE2 62 " --> pdb=" O ASPE2 58 " (cutoff:3.500A) Processing helix chain 'E2' and resid 90 through 97 Processing helix chain 'E2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METE2 107 " --> pdb=" O GLNE2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRE2 109 " --> pdb=" O PHEE2 105 " (cutoff:3.500A) Processing helix chain 'F2' and resid 2 through 11 Processing helix chain 'F2' and resid 16 through 21 Processing helix chain 'F2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNF2 28 " --> pdb=" O PROF2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNF2 29 " --> pdb=" O VALF2 25 " (cutoff:3.500A) Processing helix chain 'F2' and resid 31 through 33 No H-bonds generated for 'chain 'F2' and resid 31 through 33' Processing helix chain 'F2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSF2 44 " --> pdb=" O ASNF2 40 " (cutoff:3.500A) Processing helix chain 'F2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERF2 62 " --> pdb=" O ASPF2 58 " (cutoff:3.500A) Processing helix chain 'F2' and resid 90 through 97 Processing helix chain 'F2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METF2 107 " --> pdb=" O GLNF2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRF2 109 " --> pdb=" O PHEF2 105 " (cutoff:3.500A) Processing helix chain 'G2' and resid 2 through 11 Processing helix chain 'G2' and resid 16 through 21 Processing helix chain 'G2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNG2 28 " --> pdb=" O PROG2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNG2 29 " --> pdb=" O VALG2 25 " (cutoff:3.500A) Processing helix chain 'G2' and resid 31 through 33 No H-bonds generated for 'chain 'G2' and resid 31 through 33' Processing helix chain 'G2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSG2 44 " --> pdb=" O ASNG2 40 " (cutoff:3.500A) Processing helix chain 'G2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERG2 62 " --> pdb=" O ASPG2 58 " (cutoff:3.500A) Processing helix chain 'G2' and resid 90 through 97 Processing helix chain 'G2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METG2 107 " --> pdb=" O GLNG2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRG2 109 " --> pdb=" O PHEG2 105 " (cutoff:3.500A) Processing helix chain 'H2' and resid 2 through 11 Processing helix chain 'H2' and resid 16 through 21 Processing helix chain 'H2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNH2 28 " --> pdb=" O PROH2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNH2 29 " --> pdb=" O VALH2 25 " (cutoff:3.500A) Processing helix chain 'H2' and resid 31 through 33 No H-bonds generated for 'chain 'H2' and resid 31 through 33' Processing helix chain 'H2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSH2 44 " --> pdb=" O ASNH2 40 " (cutoff:3.500A) Processing helix chain 'H2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERH2 62 " --> pdb=" O ASPH2 58 " (cutoff:3.500A) Processing helix chain 'H2' and resid 90 through 97 Processing helix chain 'H2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METH2 107 " --> pdb=" O GLNH2 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THRH2 109 " --> pdb=" O PHEH2 105 " (cutoff:3.500A) Processing helix chain 'I2' and resid 2 through 11 Processing helix chain 'I2' and resid 16 through 21 Processing helix chain 'I2' and resid 22 through 30 removed outlier: 4.511A pdb=" N ASNI2 28 " --> pdb=" O PROI2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNI2 29 " --> pdb=" O VALI2 25 " (cutoff:3.500A) Processing helix chain 'I2' and resid 31 through 33 No H-bonds generated for 'chain 'I2' and resid 31 through 33' Processing helix chain 'I2' and resid 40 through 57 removed outlier: 3.619A pdb=" N LYSI2 44 " --> pdb=" O ASNI2 40 " (cutoff:3.500A) Processing helix chain 'I2' and resid 58 through 63 removed outlier: 3.553A pdb=" N SERI2 62 " --> pdb=" O ASPI2 58 " (cutoff:3.500A) Processing helix chain 'I2' and resid 90 through 97 Processing helix chain 'I2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METI2 107 " --> pdb=" O GLNI2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRI2 109 " --> pdb=" O PHEI2 105 " (cutoff:3.500A) Processing helix chain 'J2' and resid 2 through 11 Processing helix chain 'J2' and resid 16 through 21 Processing helix chain 'J2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNJ2 28 " --> pdb=" O PROJ2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNJ2 29 " --> pdb=" O VALJ2 25 " (cutoff:3.500A) Processing helix chain 'J2' and resid 31 through 33 No H-bonds generated for 'chain 'J2' and resid 31 through 33' Processing helix chain 'J2' and resid 40 through 57 removed outlier: 3.619A pdb=" N LYSJ2 44 " --> pdb=" O ASNJ2 40 " (cutoff:3.500A) Processing helix chain 'J2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERJ2 62 " --> pdb=" O ASPJ2 58 " (cutoff:3.500A) Processing helix chain 'J2' and resid 90 through 97 Processing helix chain 'J2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METJ2 107 " --> pdb=" O GLNJ2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRJ2 109 " --> pdb=" O PHEJ2 105 " (cutoff:3.500A) Processing helix chain 'K2' and resid 2 through 11 Processing helix chain 'K2' and resid 16 through 21 Processing helix chain 'K2' and resid 22 through 30 removed outlier: 4.511A pdb=" N ASNK2 28 " --> pdb=" O PROK2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNK2 29 " --> pdb=" O VALK2 25 " (cutoff:3.500A) Processing helix chain 'K2' and resid 31 through 33 No H-bonds generated for 'chain 'K2' and resid 31 through 33' Processing helix chain 'K2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSK2 44 " --> pdb=" O ASNK2 40 " (cutoff:3.500A) Processing helix chain 'K2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERK2 62 " --> pdb=" O ASPK2 58 " (cutoff:3.500A) Processing helix chain 'K2' and resid 90 through 97 Processing helix chain 'K2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METK2 107 " --> pdb=" O GLNK2 103 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THRK2 109 " --> pdb=" O PHEK2 105 " (cutoff:3.500A) Processing helix chain 'L2' and resid 2 through 11 Processing helix chain 'L2' and resid 16 through 21 Processing helix chain 'L2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNL2 28 " --> pdb=" O PROL2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNL2 29 " --> pdb=" O VALL2 25 " (cutoff:3.500A) Processing helix chain 'L2' and resid 31 through 33 No H-bonds generated for 'chain 'L2' and resid 31 through 33' Processing helix chain 'L2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSL2 44 " --> pdb=" O ASNL2 40 " (cutoff:3.500A) Processing helix chain 'L2' and resid 58 through 63 removed outlier: 3.553A pdb=" N SERL2 62 " --> pdb=" O ASPL2 58 " (cutoff:3.500A) Processing helix chain 'L2' and resid 90 through 97 Processing helix chain 'L2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METL2 107 " --> pdb=" O GLNL2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRL2 109 " --> pdb=" O PHEL2 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A1' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A1' and resid 117 through 122 removed outlier: 3.675A pdb=" N PHEA1 98 " --> pdb=" O LYSA1 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRA1 147 " --> pdb=" O ILEA1 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A1' and resid 253 through 258 removed outlier: 8.222A pdb=" N LEUL1 246 " --> pdb=" O SERA1 208 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHEA1 210 " --> pdb=" O LEUL1 246 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THRL1 248 " --> pdb=" O PHEA1 210 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYRA1 212 " --> pdb=" O THRL1 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A1' and resid 246 through 249 Processing sheet with id=AA6, first strand: chain 'B1' and resid 61 through 63 Processing sheet with id=AA7, first strand: chain 'B1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEB1 98 " --> pdb=" O LYSB1 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B1' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'B1' and resid 246 through 248 Processing sheet with id=AB1, first strand: chain 'C1' and resid 61 through 63 Processing sheet with id=AB2, first strand: chain 'C1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEC1 98 " --> pdb=" O LYSC1 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRC1 147 " --> pdb=" O ILEC1 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C1' and resid 246 through 249 Processing sheet with id=AB5, first strand: chain 'D1' and resid 61 through 63 Processing sheet with id=AB6, first strand: chain 'D1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHED1 98 " --> pdb=" O LYSD1 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D1' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'D1' and resid 246 through 249 removed outlier: 6.787A pdb=" N LEUD1 246 " --> pdb=" O TYRE1 212 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILEE1 214 " --> pdb=" O LEUD1 246 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THRD1 248 " --> pdb=" O ILEE1 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E1' and resid 61 through 63 Processing sheet with id=AC1, first strand: chain 'E1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEE1 98 " --> pdb=" O LYSE1 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E1' and resid 146 through 147 Processing sheet with id=AC3, first strand: chain 'E1' and resid 246 through 249 Processing sheet with id=AC4, first strand: chain 'F1' and resid 61 through 63 Processing sheet with id=AC5, first strand: chain 'F1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEF1 98 " --> pdb=" O LYSF1 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRF1 147 " --> pdb=" O ILEF1 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F1' and resid 246 through 249 Processing sheet with id=AC8, first strand: chain 'G1' and resid 61 through 63 Processing sheet with id=AC9, first strand: chain 'G1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEG1 98 " --> pdb=" O LYSG1 118 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRG1 147 " --> pdb=" O ILEG1 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G1' and resid 246 through 249 Processing sheet with id=AD3, first strand: chain 'H1' and resid 61 through 63 Processing sheet with id=AD4, first strand: chain 'H1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEH1 98 " --> pdb=" O LYSH1 118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRH1 147 " --> pdb=" O ILEH1 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H1' and resid 246 through 249 Processing sheet with id=AD7, first strand: chain 'I1' and resid 61 through 63 Processing sheet with id=AD8, first strand: chain 'I1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEI1 98 " --> pdb=" O LYSI1 118 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I1' and resid 146 through 147 Processing sheet with id=AE1, first strand: chain 'I1' and resid 246 through 249 Processing sheet with id=AE2, first strand: chain 'J1' and resid 61 through 63 Processing sheet with id=AE3, first strand: chain 'J1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEJ1 98 " --> pdb=" O LYSJ1 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J1' and resid 146 through 147 removed outlier: 3.501A pdb=" N TYRJ1 147 " --> pdb=" O ILEJ1 154 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J1' and resid 246 through 249 Processing sheet with id=AE6, first strand: chain 'K1' and resid 61 through 63 Processing sheet with id=AE7, first strand: chain 'K1' and resid 117 through 122 removed outlier: 3.673A pdb=" N PHEK1 98 " --> pdb=" O LYSK1 118 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K1' and resid 146 through 147 Processing sheet with id=AE9, first strand: chain 'K1' and resid 246 through 249 Processing sheet with id=AF1, first strand: chain 'L1' and resid 61 through 63 Processing sheet with id=AF2, first strand: chain 'L1' and resid 117 through 122 removed outlier: 3.673A pdb=" N PHEL1 98 " --> pdb=" O LYSL1 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L1' and resid 146 through 147 Processing sheet with id=AF4, first strand: chain 'A2' and resid 71 through 76 removed outlier: 6.228A pdb=" N ALAA2 72 " --> pdb=" O PHEA2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAL2 72 " --> pdb=" O PHEL2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAK2 72 " --> pdb=" O PHEK2 83 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALAJ2 72 " --> pdb=" O PHEJ2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAI2 72 " --> pdb=" O PHEI2 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALAH2 72 " --> pdb=" O PHEH2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAG2 72 " --> pdb=" O PHEG2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAF2 72 " --> pdb=" O PHEF2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAE2 72 " --> pdb=" O PHEE2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAD2 72 " --> pdb=" O PHED2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAC2 72 " --> pdb=" O PHEC2 83 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALAB2 72 " --> pdb=" O PHEB2 83 " (cutoff:3.500A) 1953 hydrogen bonds defined for protein. 5541 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: 10.07 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14968 1.34 - 1.46: 8303 1.46 - 1.57: 22761 1.57 - 1.69: 0 1.69 - 1.81: 324 Bond restraints: 46356 Sorted by residual: bond pdb=" CB GLND1 197 " pdb=" CG GLND1 197 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.71e+00 bond pdb=" CB GLNA1 197 " pdb=" CG GLNA1 197 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.67e+00 bond pdb=" CB GLNH1 197 " pdb=" CG GLNH1 197 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.64e+00 bond pdb=" CB GLNB1 197 " pdb=" CG GLNB1 197 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.62e+00 bond pdb=" CB GLNK1 197 " pdb=" CG GLNK1 197 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.62e+00 ... (remaining 46351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 59261 1.67 - 3.33: 2574 3.33 - 5.00: 519 5.00 - 6.67: 94 6.67 - 8.33: 72 Bond angle restraints: 62520 Sorted by residual: angle pdb=" CG META2 107 " pdb=" SD META2 107 " pdb=" CE META2 107 " ideal model delta sigma weight residual 100.90 92.57 8.33 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METF2 107 " pdb=" SD METF2 107 " pdb=" CE METF2 107 " ideal model delta sigma weight residual 100.90 92.57 8.33 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METH2 107 " pdb=" SD METH2 107 " pdb=" CE METH2 107 " ideal model delta sigma weight residual 100.90 92.58 8.32 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METI2 107 " pdb=" SD METI2 107 " pdb=" CE METI2 107 " ideal model delta sigma weight residual 100.90 92.58 8.32 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METD2 107 " pdb=" SD METD2 107 " pdb=" CE METD2 107 " ideal model delta sigma weight residual 100.90 92.58 8.32 2.20e+00 2.07e-01 1.43e+01 ... (remaining 62515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 24229 16.37 - 32.74: 2805 32.74 - 49.10: 758 49.10 - 65.47: 120 65.47 - 81.84: 48 Dihedral angle restraints: 27960 sinusoidal: 11280 harmonic: 16680 Sorted by residual: dihedral pdb=" CA LEUF2 106 " pdb=" C LEUF2 106 " pdb=" N METF2 107 " pdb=" CA METF2 107 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA LEUB2 106 " pdb=" C LEUB2 106 " pdb=" N METB2 107 " pdb=" CA METB2 107 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LEUC2 106 " pdb=" C LEUC2 106 " pdb=" N METC2 107 " pdb=" CA METC2 107 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 27957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3578 0.029 - 0.059: 1988 0.059 - 0.088: 913 0.088 - 0.118: 357 0.118 - 0.147: 40 Chirality restraints: 6876 Sorted by residual: chirality pdb=" CA CYSB2 32 " pdb=" N CYSB2 32 " pdb=" C CYSB2 32 " pdb=" CB CYSB2 32 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA CYSJ2 32 " pdb=" N CYSJ2 32 " pdb=" C CYSJ2 32 " pdb=" CB CYSJ2 32 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA CYSI2 32 " pdb=" N CYSI2 32 " pdb=" C CYSI2 32 " pdb=" CB CYSI2 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 6873 not shown) Planarity restraints: 8064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALE2 23 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PROE2 24 " 0.098 5.00e-02 4.00e+02 pdb=" CA PROE2 24 " -0.029 5.00e-02 4.00e+02 pdb=" CD PROE2 24 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALK2 23 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PROK2 24 " -0.098 5.00e-02 4.00e+02 pdb=" CA PROK2 24 " 0.029 5.00e-02 4.00e+02 pdb=" CD PROK2 24 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALF2 23 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PROF2 24 " 0.097 5.00e-02 4.00e+02 pdb=" CA PROF2 24 " -0.029 5.00e-02 4.00e+02 pdb=" CD PROF2 24 " -0.032 5.00e-02 4.00e+02 ... (remaining 8061 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 463 2.46 - 3.07: 35429 3.07 - 3.68: 71360 3.68 - 4.29: 106267 4.29 - 4.90: 166190 Nonbonded interactions: 379709 Sorted by model distance: nonbonded pdb=" NE2 GLNH1 197 " pdb=" OE1 GLNI1 189 " model vdw 1.854 3.120 nonbonded pdb=" OH TYRK1 55 " pdb=" OD2 ASPL1 307 " model vdw 1.906 3.040 nonbonded pdb=" NE2 GLNK1 197 " pdb=" OE1 GLNL1 189 " model vdw 1.910 3.120 nonbonded pdb=" O ARGK1 25 " pdb=" N ASPL1 9 " model vdw 1.966 3.120 nonbonded pdb=" NE2 GLND1 197 " pdb=" OE1 GLNE1 189 " model vdw 1.973 3.120 ... (remaining 379704 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A1' selection = chain 'B1' selection = chain 'C1' selection = chain 'D1' selection = chain 'E1' selection = chain 'F1' selection = chain 'G1' selection = chain 'H1' selection = chain 'I1' selection = chain 'J1' selection = chain 'K1' selection = chain 'L1' } ncs_group { reference = chain 'A2' selection = chain 'B2' selection = chain 'C2' selection = chain 'D2' selection = chain 'E2' selection = chain 'F2' selection = chain 'G2' selection = chain 'H2' selection = chain 'I2' selection = chain 'J2' selection = chain 'K2' selection = chain 'L2' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.580 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: 0.060 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 38.270 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.110 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.007 0.122 46368 Z= 0.322 Angle : 0.864 12.779 62544 Z= 0.475 Chirality : 0.045 0.147 6876 Planarity : 0.004 0.057 8064 Dihedral : 15.041 81.840 17292 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 0.48 % Allowed : 0.42 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.11), residues: 5676 helix: -0.46 (0.11), residues: 2292 sheet: 1.38 (0.29), residues: 288 loop : -1.79 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGE1 140 TYR 0.032 0.003 TYRL1 177 PHE 0.014 0.002 PHEG2 117 TRP 0.012 0.002 TRPF2 95 HIS 0.004 0.001 HISJ1 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.32 (46356) covalent geometry : angle 0.85961 / 0.47 (62520) SS BOND : bond 0.07220 / 5.04 ( 12) SS BOND : angle 4.59511 / 2.83 ( 24) hydrogen bonds : bond 0.25784 / 17.15 ( 1953) hydrogen bonds : angle 9.52373 / 6.66 ( 5541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1543 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 21 MET cc_start: 0.8240 (mmm) cc_final: 0.7927 (mmp) REVERT: B1 73 LYS cc_start: 0.7534 (tptt) cc_final: 0.7286 (ttmm) REVERT: B1 82 ASN cc_start: 0.8757 (m110) cc_final: 0.8479 (m110) REVERT: B1 227 GLU cc_start: 0.7893 (tp30) cc_final: 0.7468 (tp30) REVERT: B1 236 CYS cc_start: 0.8438 (t) cc_final: 0.8218 (t) REVERT: C1 33 ASP cc_start: 0.7727 (t70) cc_final: 0.7333 (t70) REVERT: C1 82 ASN cc_start: 0.8507 (m110) cc_final: 0.8279 (m110) REVERT: C1 156 TRP cc_start: 0.7028 (t60) cc_final: 0.6795 (t-100) REVERT: C1 236 CYS cc_start: 0.8416 (t) cc_final: 0.8196 (t) REVERT: C1 326 GLU cc_start: 0.8233 (pp20) cc_final: 0.8000 (pp20) REVERT: D1 82 ASN cc_start: 0.8285 (m110) cc_final: 0.8024 (m110) REVERT: D1 176 TYR cc_start: 0.5423 (m-80) cc_final: 0.5206 (m-80) REVERT: D1 227 GLU cc_start: 0.7864 (tp30) cc_final: 0.7457 (tp30) REVERT: D1 236 CYS cc_start: 0.8387 (t) cc_final: 0.8111 (t) REVERT: E1 84 THR cc_start: 0.9116 (t) cc_final: 0.8657 (p) REVERT: E1 166 MET cc_start: 0.7523 (mtm) cc_final: 0.7176 (mtt) REVERT: E1 200 SER cc_start: 0.9151 (p) cc_final: 0.8922 (p) REVERT: E1 268 ASP cc_start: 0.8033 (t0) cc_final: 0.7747 (t0) REVERT: E1 326 GLU cc_start: 0.8269 (pp20) cc_final: 0.7961 (pp20) REVERT: F1 84 THR cc_start: 0.9142 (t) cc_final: 0.8612 (p) REVERT: F1 175 TYR cc_start: 0.8243 (m-80) cc_final: 0.7956 (m-80) REVERT: F1 200 SER cc_start: 0.9212 (p) cc_final: 0.8948 (p) REVERT: F1 373 ASP cc_start: 0.6812 (t0) cc_final: 0.6577 (t0) REVERT: G1 200 SER cc_start: 0.9240 (p) cc_final: 0.9037 (p) REVERT: G1 301 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7486 (mp0) REVERT: G1 373 ASP cc_start: 0.7008 (t0) cc_final: 0.6774 (t0) REVERT: H1 98 PHE cc_start: 0.8582 (p90) cc_final: 0.8349 (p90) REVERT: H1 103 ASP cc_start: 0.7648 (m-30) cc_final: 0.7367 (m-30) REVERT: H1 214 ILE cc_start: 0.8496 (mt) cc_final: 0.8237 (mt) REVERT: H1 269 ASN cc_start: 0.8606 (t0) cc_final: 0.8398 (t0) REVERT: H1 273 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7612 (tpp80) REVERT: H1 301 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7300 (mp0) REVERT: H1 316 TYR cc_start: 0.8902 (m-80) cc_final: 0.8698 (m-10) REVERT: H1 373 ASP cc_start: 0.7189 (t0) cc_final: 0.6877 (t0) REVERT: I1 33 ASP cc_start: 0.7474 (t70) cc_final: 0.7125 (t70) REVERT: I1 103 ASP cc_start: 0.7730 (m-30) cc_final: 0.7520 (m-30) REVERT: I1 175 TYR cc_start: 0.8180 (m-80) cc_final: 0.7906 (m-80) REVERT: I1 200 SER cc_start: 0.9164 (p) cc_final: 0.8917 (p) REVERT: I1 214 ILE cc_start: 0.8333 (mt) cc_final: 0.8109 (mt) REVERT: I1 249 ASP cc_start: 0.6876 (m-30) cc_final: 0.6668 (m-30) REVERT: I1 326 GLU cc_start: 0.8136 (pp20) cc_final: 0.7822 (pp20) REVERT: J1 103 ASP cc_start: 0.7489 (m-30) cc_final: 0.7280 (m-30) REVERT: J1 166 MET cc_start: 0.7515 (mtm) cc_final: 0.7156 (mtt) REVERT: J1 175 TYR cc_start: 0.8126 (m-80) cc_final: 0.7670 (m-80) REVERT: J1 176 TYR cc_start: 0.5446 (m-80) cc_final: 0.5216 (m-80) REVERT: J1 180 MET cc_start: 0.8372 (ttm) cc_final: 0.8094 (ttt) REVERT: J1 273 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7818 (tpp80) REVERT: J1 301 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7170 (mp0) REVERT: J1 334 GLU cc_start: 0.6692 (mp0) cc_final: 0.6453 (mp0) REVERT: K1 236 CYS cc_start: 0.8496 (t) cc_final: 0.8222 (t) REVERT: K1 273 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7560 (tpp80) REVERT: L1 190 PHE cc_start: 0.8459 (t80) cc_final: 0.8214 (t80) REVERT: L1 318 GLU cc_start: 0.8295 (tt0) cc_final: 0.8055 (mt-10) REVERT: A2 43 ASP cc_start: 0.7501 (t0) cc_final: 0.7151 (t0) REVERT: A2 90 SER cc_start: 0.8949 (t) cc_final: 0.8719 (t) REVERT: B2 34 TYR cc_start: 0.8480 (t80) cc_final: 0.8269 (t80) REVERT: B2 43 ASP cc_start: 0.7415 (t0) cc_final: 0.7053 (t0) REVERT: B2 90 SER cc_start: 0.8981 (t) cc_final: 0.8744 (t) REVERT: B2 113 MET cc_start: 0.8197 (ttp) cc_final: 0.7906 (ttp) REVERT: C2 43 ASP cc_start: 0.7964 (t0) cc_final: 0.7708 (t0) REVERT: C2 90 SER cc_start: 0.8948 (t) cc_final: 0.8657 (t) REVERT: D2 90 SER cc_start: 0.8909 (t) cc_final: 0.8696 (t) REVERT: E2 11 PHE cc_start: 0.8608 (m-80) cc_final: 0.8406 (m-10) REVERT: E2 43 ASP cc_start: 0.7574 (t0) cc_final: 0.7229 (t0) REVERT: E2 90 SER cc_start: 0.8961 (t) cc_final: 0.8734 (t) REVERT: E2 113 MET cc_start: 0.8236 (ttp) cc_final: 0.8007 (ttp) REVERT: F2 11 PHE cc_start: 0.8695 (m-80) cc_final: 0.8368 (m-10) REVERT: F2 90 SER cc_start: 0.8960 (t) cc_final: 0.8692 (t) REVERT: G2 43 ASP cc_start: 0.7819 (t0) cc_final: 0.7441 (t0) REVERT: G2 90 SER cc_start: 0.8985 (t) cc_final: 0.8758 (t) REVERT: H2 11 PHE cc_start: 0.8643 (m-80) cc_final: 0.8344 (m-10) REVERT: H2 90 SER cc_start: 0.8924 (t) cc_final: 0.8690 (t) REVERT: I2 43 ASP cc_start: 0.7609 (t0) cc_final: 0.7317 (t0) REVERT: I2 90 SER cc_start: 0.8798 (t) cc_final: 0.8469 (t) REVERT: J2 90 SER cc_start: 0.8947 (t) cc_final: 0.8721 (t) REVERT: K2 90 SER cc_start: 0.9047 (t) cc_final: 0.8810 (t) REVERT: L2 15 ASP cc_start: 0.7822 (m-30) cc_final: 0.7575 (m-30) REVERT: L2 43 ASP cc_start: 0.7745 (t0) cc_final: 0.7544 (t0) REVERT: L2 90 SER cc_start: 0.8914 (t) cc_final: 0.8682 (t) outliers start: 24 outliers final: 1 residues processed: 1551 average time/residue: 0.2480 time to fit residues: 659.2147 Evaluate side-chains 1349 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1348 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I1 residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 0.6980 chunk 497 optimal weight: 0.2980 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 0.7980 chunk 366 optimal weight: 0.4980 chunk 223 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 82 ASN A1 313 GLN B1 313 GLN C1 24 ASN C1 313 GLN D1 313 GLN ** E1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 82 ASN E1 222 GLN E1 313 GLN F1 82 ASN F1 222 GLN G1 222 GLN G1 313 GLN H1 24 ASN H1 222 GLN H1 313 GLN ** I1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 82 ASN I1 313 GLN J1 24 ASN J1 82 ASN J1 313 GLN K1 24 ASN K1 82 ASN K1 197 GLN K1 313 GLN L1 82 ASN L1 189 GLN L1 313 GLN ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.160319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.122521 restraints weight = 64148.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.126591 restraints weight = 28920.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.129099 restraints weight = 16595.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.130626 restraints weight = 11360.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.131533 restraints weight = 8940.177| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46368 Z= 0.166 Angle : 0.736 9.673 62544 Z= 0.388 Chirality : 0.044 0.167 6876 Planarity : 0.005 0.056 8064 Dihedral : 5.971 24.789 6338 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.76 % Allowed : 14.03 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5676 helix: -0.36 (0.10), residues: 2520 sheet: 1.16 (0.30), residues: 288 loop : -1.62 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGE1 140 TYR 0.024 0.003 TYRC1 370 PHE 0.018 0.002 PHEG1 122 TRP 0.009 0.001 TRPH2 95 HIS 0.003 0.001 HISH2 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (46356) covalent geometry : angle 0.73496 / 0.39 (62520) SS BOND : bond 0.00227 / 0.14 ( 12) SS BOND : angle 1.93119 / 1.19 ( 24) hydrogen bonds : bond 0.04607 / 3.03 ( 1953) hydrogen bonds : angle 6.33301 / 4.41 ( 5541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1493 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 326 GLU cc_start: 0.7980 (pp20) cc_final: 0.7651 (pp20) REVERT: A1 373 ASP cc_start: 0.6500 (t0) cc_final: 0.6209 (t0) REVERT: B1 33 ASP cc_start: 0.7120 (t70) cc_final: 0.6813 (t70) REVERT: B1 277 MET cc_start: 0.8611 (tpt) cc_final: 0.8380 (tpt) REVERT: B1 351 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8126 (mtmt) REVERT: C1 73 LYS cc_start: 0.7672 (tptt) cc_final: 0.7411 (ttmm) REVERT: C1 277 MET cc_start: 0.8591 (tpt) cc_final: 0.8319 (tpt) REVERT: C1 301 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7247 (mp0) REVERT: D1 82 ASN cc_start: 0.8147 (m110) cc_final: 0.7895 (m110) REVERT: D1 197 GLN cc_start: 0.8621 (tt0) cc_final: 0.8367 (tt0) REVERT: D1 277 MET cc_start: 0.8615 (tpt) cc_final: 0.8336 (tpt) REVERT: E1 45 MET cc_start: 0.8628 (mtm) cc_final: 0.8258 (ttm) REVERT: E1 162 PHE cc_start: 0.8169 (m-80) cc_final: 0.7886 (m-80) REVERT: E1 166 MET cc_start: 0.7323 (mtm) cc_final: 0.6977 (mtt) REVERT: E1 273 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7155 (tpp80) REVERT: E1 372 LYS cc_start: 0.8032 (tppt) cc_final: 0.7150 (ptmm) REVERT: E1 373 ASP cc_start: 0.6727 (t0) cc_final: 0.6389 (t0) REVERT: F1 82 ASN cc_start: 0.7394 (m-40) cc_final: 0.7168 (m110) REVERT: F1 316 TYR cc_start: 0.8940 (m-10) cc_final: 0.8040 (m-10) REVERT: F1 373 ASP cc_start: 0.6803 (t0) cc_final: 0.6571 (t0) REVERT: G1 277 MET cc_start: 0.8534 (tpt) cc_final: 0.7994 (tpt) REVERT: G1 301 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7302 (mp0) REVERT: G1 334 GLU cc_start: 0.6315 (mp0) cc_final: 0.5957 (mp0) REVERT: H1 73 LYS cc_start: 0.7693 (tptt) cc_final: 0.7195 (ttmm) REVERT: H1 103 ASP cc_start: 0.7657 (m-30) cc_final: 0.7450 (m-30) REVERT: H1 273 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7363 (tpp80) REVERT: H1 301 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7264 (mp0) REVERT: H1 326 GLU cc_start: 0.7977 (pp20) cc_final: 0.7728 (pp20) REVERT: H1 373 ASP cc_start: 0.7234 (t0) cc_final: 0.6984 (t0) REVERT: I1 273 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7341 (mtt90) REVERT: J1 87 MET cc_start: 0.8465 (ttm) cc_final: 0.8101 (tpp) REVERT: J1 103 ASP cc_start: 0.7437 (m-30) cc_final: 0.7219 (m-30) REVERT: J1 175 TYR cc_start: 0.7618 (m-80) cc_final: 0.7225 (m-80) REVERT: J1 232 TYR cc_start: 0.7368 (m-80) cc_final: 0.7062 (m-80) REVERT: J1 277 MET cc_start: 0.8490 (tpt) cc_final: 0.8210 (tpt) REVERT: J1 301 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7163 (mp0) REVERT: J1 326 GLU cc_start: 0.8190 (pp20) cc_final: 0.7913 (pp20) REVERT: J1 327 ILE cc_start: 0.8408 (tt) cc_final: 0.7984 (tt) REVERT: K1 73 LYS cc_start: 0.7740 (tptt) cc_final: 0.7292 (ttmm) REVERT: K1 273 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.6886 (ttm-80) REVERT: K1 277 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8182 (tpt) REVERT: K1 326 GLU cc_start: 0.8170 (pp20) cc_final: 0.7960 (pp20) REVERT: L1 73 LYS cc_start: 0.7482 (tttp) cc_final: 0.7251 (ttmm) REVERT: L1 87 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (tpp) REVERT: L1 122 PHE cc_start: 0.8628 (m-80) cc_final: 0.8415 (m-80) REVERT: L1 326 GLU cc_start: 0.7925 (pp20) cc_final: 0.7537 (pp20) REVERT: A2 15 ASP cc_start: 0.7915 (m-30) cc_final: 0.7548 (m-30) REVERT: A2 43 ASP cc_start: 0.7658 (t0) cc_final: 0.6842 (t0) REVERT: A2 90 SER cc_start: 0.8564 (t) cc_final: 0.8200 (t) REVERT: B2 15 ASP cc_start: 0.7785 (m-30) cc_final: 0.7424 (m-30) REVERT: B2 90 SER cc_start: 0.8584 (t) cc_final: 0.8238 (t) REVERT: C2 43 ASP cc_start: 0.7737 (t0) cc_final: 0.6874 (t70) REVERT: C2 90 SER cc_start: 0.8486 (t) cc_final: 0.8167 (t) REVERT: D2 15 ASP cc_start: 0.7826 (m-30) cc_final: 0.7444 (m-30) REVERT: D2 58 ASP cc_start: 0.8322 (t70) cc_final: 0.8104 (t70) REVERT: D2 90 SER cc_start: 0.8563 (t) cc_final: 0.8203 (t) REVERT: E2 15 ASP cc_start: 0.7801 (m-30) cc_final: 0.7438 (m-30) REVERT: E2 58 ASP cc_start: 0.8391 (t70) cc_final: 0.8136 (t70) REVERT: E2 90 SER cc_start: 0.8557 (t) cc_final: 0.8215 (t) REVERT: E2 113 MET cc_start: 0.8144 (ttp) cc_final: 0.7772 (ttp) REVERT: F2 1 MET cc_start: 0.6552 (mmt) cc_final: 0.5150 (mmt) REVERT: F2 43 ASP cc_start: 0.7593 (t0) cc_final: 0.6837 (t70) REVERT: F2 90 SER cc_start: 0.8562 (t) cc_final: 0.8246 (t) REVERT: G2 15 ASP cc_start: 0.7813 (m-30) cc_final: 0.7510 (m-30) REVERT: G2 43 ASP cc_start: 0.7865 (t0) cc_final: 0.7203 (t0) REVERT: G2 90 SER cc_start: 0.8773 (t) cc_final: 0.8469 (t) REVERT: H2 15 ASP cc_start: 0.7784 (m-30) cc_final: 0.7567 (m-30) REVERT: H2 90 SER cc_start: 0.8538 (t) cc_final: 0.8217 (t) REVERT: J2 90 SER cc_start: 0.8716 (t) cc_final: 0.8405 (t) REVERT: K2 15 ASP cc_start: 0.7676 (m-30) cc_final: 0.7391 (m-30) REVERT: K2 43 ASP cc_start: 0.7598 (t0) cc_final: 0.7019 (t70) REVERT: K2 90 SER cc_start: 0.8637 (t) cc_final: 0.8332 (t) REVERT: L2 15 ASP cc_start: 0.7841 (m-30) cc_final: 0.7418 (m-30) REVERT: L2 43 ASP cc_start: 0.7792 (t0) cc_final: 0.7063 (t0) REVERT: L2 90 SER cc_start: 0.8733 (t) cc_final: 0.8398 (t) outliers start: 88 outliers final: 46 residues processed: 1524 average time/residue: 0.2515 time to fit residues: 649.3877 Evaluate side-chains 1367 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1319 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain E1 residue 74 LYS Chi-restraints excluded: chain E1 residue 246 LEU Chi-restraints excluded: chain E1 residue 371 LEU Chi-restraints excluded: chain F1 residue 371 LEU Chi-restraints excluded: chain G1 residue 74 LYS Chi-restraints excluded: chain G1 residue 135 ASP Chi-restraints excluded: chain G1 residue 371 LEU Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 131 ASN Chi-restraints excluded: chain H1 residue 309 ILE Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 74 LYS Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 74 LYS Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 135 ASP Chi-restraints excluded: chain K1 residue 277 MET Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 87 MET Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain G2 residue 13 ASN Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain I2 residue 113 MET Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 82 SER Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [12, 3, 458, 560, 231, 380, 219, 249, 193, 72, 551] chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 458 optimal weight: 0.3980 chunk 560 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 380 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 551 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 82 ASN C1 24 ASN C1 82 ASN ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 82 ASN I1 24 ASN I1 82 ASN I1 311 ASN J1 24 ASN ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 82 ASN ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 40 ASN ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 40 ASN ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 40 ASN ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.160552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.122211 restraints weight = 63862.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.126264 restraints weight = 29166.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.128765 restraints weight = 16897.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.130296 restraints weight = 11662.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.131205 restraints weight = 9212.530| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 46368 Z= 0.157 Angle : 0.701 8.835 62544 Z= 0.363 Chirality : 0.043 0.149 6876 Planarity : 0.005 0.077 8064 Dihedral : 5.631 20.839 6336 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.26 % Allowed : 19.96 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.11), residues: 5676 helix: -0.22 (0.10), residues: 2448 sheet: 0.43 (0.30), residues: 312 loop : -1.54 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGA1 140 TYR 0.026 0.002 TYRK1 177 PHE 0.021 0.002 PHEL1 190 TRP 0.010 0.001 TRPC2 95 HIS 0.003 0.001 HISG1 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (46356) covalent geometry : angle 0.69992 / 0.36 (62520) SS BOND : bond 0.00140 / 0.08 ( 12) SS BOND : angle 2.18209 / 1.32 ( 24) hydrogen bonds : bond 0.03896 / 2.56 ( 1953) hydrogen bonds : angle 5.91499 / 4.12 ( 5541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1607 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1444 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8427 (m-40) cc_final: 0.8187 (m110) REVERT: A1 87 MET cc_start: 0.8295 (tpp) cc_final: 0.8027 (tpp) REVERT: A1 166 MET cc_start: 0.7583 (mtm) cc_final: 0.7105 (mtt) REVERT: A1 326 GLU cc_start: 0.7961 (pp20) cc_final: 0.7749 (pp20) REVERT: A1 373 ASP cc_start: 0.6613 (t0) cc_final: 0.6330 (t0) REVERT: B1 33 ASP cc_start: 0.6980 (t70) cc_final: 0.6657 (t0) REVERT: B1 189 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8588 (mm-40) REVERT: B1 277 MET cc_start: 0.8570 (tpt) cc_final: 0.8186 (tpt) REVERT: B1 350 ASP cc_start: 0.8825 (t0) cc_final: 0.8538 (t0) REVERT: C1 82 ASN cc_start: 0.8344 (m-40) cc_final: 0.8044 (m110) REVERT: C1 143 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6972 (tppt) REVERT: C1 180 MET cc_start: 0.7573 (tpp) cc_final: 0.7102 (tpp) REVERT: C1 277 MET cc_start: 0.8517 (tpt) cc_final: 0.8093 (tpt) REVERT: C1 301 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7248 (mp0) REVERT: C1 326 GLU cc_start: 0.8198 (pp20) cc_final: 0.7923 (pp20) REVERT: C1 350 ASP cc_start: 0.8986 (t0) cc_final: 0.8775 (t0) REVERT: D1 122 PHE cc_start: 0.8583 (m-80) cc_final: 0.8244 (m-80) REVERT: D1 197 GLN cc_start: 0.8638 (tt0) cc_final: 0.8277 (tt0) REVERT: D1 277 MET cc_start: 0.8576 (tpt) cc_final: 0.8093 (tpt) REVERT: D1 301 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7266 (mp0) REVERT: E1 45 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8114 (ttm) REVERT: E1 76 LEU cc_start: 0.7957 (pt) cc_final: 0.7710 (pp) REVERT: E1 78 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7503 (ttpt) REVERT: E1 87 MET cc_start: 0.8700 (ttm) cc_final: 0.8356 (tpp) REVERT: E1 143 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7282 (mmmt) REVERT: E1 175 TYR cc_start: 0.7992 (m-80) cc_final: 0.7722 (m-80) REVERT: E1 277 MET cc_start: 0.8435 (tpt) cc_final: 0.8091 (tpt) REVERT: E1 316 TYR cc_start: 0.8630 (m-10) cc_final: 0.8315 (m-10) REVERT: E1 372 LYS cc_start: 0.7990 (tppt) cc_final: 0.7088 (ptmm) REVERT: E1 373 ASP cc_start: 0.6792 (t0) cc_final: 0.6418 (t0) REVERT: F1 40 TYR cc_start: 0.9357 (t80) cc_final: 0.9007 (t80) REVERT: F1 165 TYR cc_start: 0.8199 (t80) cc_final: 0.7922 (t80) REVERT: F1 259 GLN cc_start: 0.8867 (pt0) cc_final: 0.8575 (pt0) REVERT: F1 316 TYR cc_start: 0.8951 (m-80) cc_final: 0.7982 (m-10) REVERT: F1 373 ASP cc_start: 0.6862 (t0) cc_final: 0.6647 (t0) REVERT: G1 21 MET cc_start: 0.8607 (mmt) cc_final: 0.8206 (mmt) REVERT: G1 82 ASN cc_start: 0.7511 (m-40) cc_final: 0.7229 (m110) REVERT: G1 277 MET cc_start: 0.8422 (tpt) cc_final: 0.7853 (tpt) REVERT: H1 73 LYS cc_start: 0.7640 (tptt) cc_final: 0.7192 (ttmm) REVERT: H1 128 LYS cc_start: 0.6582 (mmtp) cc_final: 0.6226 (mmmt) REVERT: H1 273 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.6687 (ttm-80) REVERT: H1 301 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7256 (mp0) REVERT: H1 326 GLU cc_start: 0.8060 (pp20) cc_final: 0.7810 (pp20) REVERT: H1 330 LEU cc_start: 0.8572 (mm) cc_final: 0.8280 (mm) REVERT: H1 373 ASP cc_start: 0.7208 (t0) cc_final: 0.6962 (t0) REVERT: I1 87 MET cc_start: 0.8537 (ttm) cc_final: 0.8221 (tpp) REVERT: I1 272 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8179 (mm) REVERT: I1 350 ASP cc_start: 0.8863 (t0) cc_final: 0.8625 (t0) REVERT: J1 82 ASN cc_start: 0.8184 (m-40) cc_final: 0.7929 (m110) REVERT: J1 166 MET cc_start: 0.7297 (mtm) cc_final: 0.6748 (mtt) REVERT: J1 232 TYR cc_start: 0.7355 (m-80) cc_final: 0.7044 (m-80) REVERT: J1 273 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7802 (mtt90) REVERT: J1 277 MET cc_start: 0.8505 (tpt) cc_final: 0.8229 (tpt) REVERT: J1 301 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7065 (mp0) REVERT: J1 316 TYR cc_start: 0.8897 (m-10) cc_final: 0.8662 (m-10) REVERT: J1 350 ASP cc_start: 0.8943 (t0) cc_final: 0.8708 (t0) REVERT: K1 82 ASN cc_start: 0.8067 (m-40) cc_final: 0.7842 (m110) REVERT: K1 175 TYR cc_start: 0.7505 (m-80) cc_final: 0.7286 (m-80) REVERT: K1 180 MET cc_start: 0.8148 (tpp) cc_final: 0.7843 (tpp) REVERT: L1 73 LYS cc_start: 0.7560 (tttp) cc_final: 0.7351 (ttmm) REVERT: L1 82 ASN cc_start: 0.8379 (m-40) cc_final: 0.8088 (m110) REVERT: L1 87 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7871 (tpp) REVERT: L1 122 PHE cc_start: 0.8619 (m-80) cc_final: 0.8400 (m-80) REVERT: L1 326 GLU cc_start: 0.7946 (pp20) cc_final: 0.7651 (pp20) REVERT: A2 15 ASP cc_start: 0.7925 (m-30) cc_final: 0.7430 (m-30) REVERT: A2 41 ASP cc_start: 0.5735 (OUTLIER) cc_final: 0.5381 (t70) REVERT: A2 43 ASP cc_start: 0.7621 (t0) cc_final: 0.6816 (t0) REVERT: A2 90 SER cc_start: 0.8608 (t) cc_final: 0.8266 (t) REVERT: B2 15 ASP cc_start: 0.7809 (m-30) cc_final: 0.7258 (m-30) REVERT: B2 41 ASP cc_start: 0.5615 (OUTLIER) cc_final: 0.5384 (t70) REVERT: B2 90 SER cc_start: 0.8561 (t) cc_final: 0.8209 (t) REVERT: C2 15 ASP cc_start: 0.8041 (m-30) cc_final: 0.7500 (m-30) REVERT: C2 43 ASP cc_start: 0.7756 (t0) cc_final: 0.6857 (t70) REVERT: C2 90 SER cc_start: 0.8531 (t) cc_final: 0.8166 (t) REVERT: C2 107 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: D2 15 ASP cc_start: 0.7914 (m-30) cc_final: 0.7412 (m-30) REVERT: D2 41 ASP cc_start: 0.5560 (OUTLIER) cc_final: 0.5240 (t70) REVERT: D2 58 ASP cc_start: 0.8375 (t70) cc_final: 0.8109 (t70) REVERT: D2 90 SER cc_start: 0.8620 (t) cc_final: 0.8241 (t) REVERT: E2 15 ASP cc_start: 0.7835 (m-30) cc_final: 0.7374 (m-30) REVERT: E2 90 SER cc_start: 0.8522 (t) cc_final: 0.8170 (t) REVERT: E2 117 PHE cc_start: 0.8086 (t80) cc_final: 0.7821 (t80) REVERT: F2 1 MET cc_start: 0.6512 (mmt) cc_final: 0.5182 (mmt) REVERT: F2 15 ASP cc_start: 0.7763 (m-30) cc_final: 0.7495 (m-30) REVERT: F2 43 ASP cc_start: 0.7677 (t0) cc_final: 0.7332 (t70) REVERT: F2 90 SER cc_start: 0.8543 (t) cc_final: 0.8202 (t) REVERT: F2 107 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: G2 15 ASP cc_start: 0.7743 (m-30) cc_final: 0.7446 (m-30) REVERT: G2 43 ASP cc_start: 0.7794 (t0) cc_final: 0.7109 (t0) REVERT: G2 90 SER cc_start: 0.8787 (t) cc_final: 0.8480 (t) REVERT: H2 15 ASP cc_start: 0.7802 (m-30) cc_final: 0.7562 (m-30) REVERT: H2 90 SER cc_start: 0.8504 (t) cc_final: 0.8133 (t) REVERT: I2 90 SER cc_start: 0.8580 (t) cc_final: 0.8200 (t) REVERT: J2 90 SER cc_start: 0.8637 (t) cc_final: 0.8306 (t) REVERT: K2 15 ASP cc_start: 0.7810 (m-30) cc_final: 0.7572 (m-30) REVERT: K2 41 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5446 (t70) REVERT: K2 90 SER cc_start: 0.8578 (t) cc_final: 0.8225 (t) REVERT: L2 15 ASP cc_start: 0.7909 (m-30) cc_final: 0.7390 (m-30) REVERT: L2 28 ASN cc_start: 0.8463 (t0) cc_final: 0.8119 (t0) REVERT: L2 90 SER cc_start: 0.8657 (t) cc_final: 0.8341 (t) outliers start: 163 outliers final: 89 residues processed: 1516 average time/residue: 0.2441 time to fit residues: 630.4394 Evaluate side-chains 1405 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1306 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 140 ARG Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain C1 residue 24 ASN Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain E1 residue 32 SER Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 78 LYS Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain H1 residue 32 SER Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 131 ASN Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 87 MET Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 82 SER Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain B2 residue 113 MET Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 13 ASN Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 98 SER Chi-restraints excluded: chain H2 residue 5 ASP Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 113 MET Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 60 SER Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 88 THR Chi-restraints excluded: chain L2 residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [552, 229, 97, 96, 191, 539, 51, 245, 192, 208, 128] chunk 552 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 539 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 197 GLN C1 24 ASN ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 24 ASN I1 24 ASN I1 82 ASN I1 311 ASN J1 24 ASN K1 24 ASN K1 58 ASN K1 197 GLN L1 24 ASN L1 58 ASN L1 197 GLN ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.154985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.115924 restraints weight = 65113.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119811 restraints weight = 30299.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.122241 restraints weight = 17790.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.123728 restraints weight = 12367.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.124611 restraints weight = 9824.100| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 46368 Z= 0.255 Angle : 0.768 10.566 62544 Z= 0.394 Chirality : 0.046 0.158 6876 Planarity : 0.005 0.063 8064 Dihedral : 5.740 23.413 6336 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.32 % Allowed : 20.90 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.11), residues: 5676 helix: -0.17 (0.10), residues: 2424 sheet: 0.33 (0.30), residues: 312 loop : -1.66 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGA1 140 TYR 0.031 0.003 TYRH1 316 PHE 0.024 0.002 PHEG1 190 TRP 0.011 0.001 TRPF2 95 HIS 0.005 0.001 HISB1 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (46356) covalent geometry : angle 0.76630 / 0.39 (62520) SS BOND : bond 0.00348 / 0.20 ( 12) SS BOND : angle 2.70788 / 1.62 ( 24) hydrogen bonds : bond 0.03987 / 2.63 ( 1953) hydrogen bonds : angle 5.87054 / 4.08 ( 5541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 1394 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8526 (m-40) cc_final: 0.8177 (m110) REVERT: A1 87 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8148 (tpp) REVERT: A1 156 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.7233 (t60) REVERT: A1 326 GLU cc_start: 0.7980 (pp20) cc_final: 0.7697 (pp20) REVERT: B1 122 PHE cc_start: 0.8861 (m-80) cc_final: 0.8629 (m-80) REVERT: B1 277 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8022 (tpt) REVERT: C1 45 MET cc_start: 0.8474 (mmm) cc_final: 0.8088 (ttm) REVERT: C1 82 ASN cc_start: 0.8449 (m-40) cc_final: 0.7999 (m110) REVERT: C1 87 MET cc_start: 0.8522 (tpp) cc_final: 0.8209 (tpp) REVERT: C1 273 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7605 (mmm-85) REVERT: C1 277 MET cc_start: 0.8527 (tpt) cc_final: 0.7975 (tpt) REVERT: C1 301 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7301 (mp0) REVERT: C1 326 GLU cc_start: 0.8095 (pp20) cc_final: 0.7888 (pp20) REVERT: D1 122 PHE cc_start: 0.8655 (m-80) cc_final: 0.8405 (m-80) REVERT: D1 197 GLN cc_start: 0.8608 (tt0) cc_final: 0.8094 (tt0) REVERT: D1 277 MET cc_start: 0.8536 (tpt) cc_final: 0.7967 (tpt) REVERT: E1 45 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8243 (ttm) REVERT: E1 143 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7562 (mmmt) REVERT: E1 175 TYR cc_start: 0.8211 (m-80) cc_final: 0.7711 (m-80) REVERT: E1 180 MET cc_start: 0.8235 (tpp) cc_final: 0.7623 (tpp) REVERT: E1 217 TYR cc_start: 0.8114 (t80) cc_final: 0.7808 (t80) REVERT: E1 273 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7125 (tpp80) REVERT: E1 277 MET cc_start: 0.8501 (tpt) cc_final: 0.8114 (tpt) REVERT: E1 316 TYR cc_start: 0.8752 (m-10) cc_final: 0.8338 (m-10) REVERT: E1 327 ILE cc_start: 0.8427 (tt) cc_final: 0.8064 (tt) REVERT: F1 40 TYR cc_start: 0.9364 (t80) cc_final: 0.8980 (t80) REVERT: F1 82 ASN cc_start: 0.7670 (m-40) cc_final: 0.7308 (m110) REVERT: F1 175 TYR cc_start: 0.8140 (m-80) cc_final: 0.7612 (m-80) REVERT: F1 316 TYR cc_start: 0.8971 (m-80) cc_final: 0.8007 (m-10) REVERT: F1 326 GLU cc_start: 0.8467 (pp20) cc_final: 0.7809 (pp20) REVERT: G1 11 LEU cc_start: 0.7574 (tp) cc_final: 0.7364 (tt) REVERT: G1 21 MET cc_start: 0.8635 (mmt) cc_final: 0.8279 (mmt) REVERT: G1 40 TYR cc_start: 0.9381 (t80) cc_final: 0.9026 (t80) REVERT: G1 82 ASN cc_start: 0.7798 (m-40) cc_final: 0.7384 (m110) REVERT: G1 175 TYR cc_start: 0.8412 (m-80) cc_final: 0.7818 (m-80) REVERT: G1 182 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: G1 277 MET cc_start: 0.8412 (tpt) cc_final: 0.7786 (tpt) REVERT: H1 21 MET cc_start: 0.8613 (mmt) cc_final: 0.8306 (mmt) REVERT: H1 73 LYS cc_start: 0.7677 (tptt) cc_final: 0.7235 (ttmm) REVERT: H1 136 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7660 (mt) REVERT: H1 176 TYR cc_start: 0.5386 (m-80) cc_final: 0.4804 (m-80) REVERT: H1 182 GLU cc_start: 0.8807 (mm-30) cc_final: 0.7566 (mp0) REVERT: H1 187 TYR cc_start: 0.8615 (t80) cc_final: 0.8248 (t80) REVERT: H1 249 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: H1 273 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.6772 (ttm-80) REVERT: H1 301 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7358 (mp0) REVERT: H1 326 GLU cc_start: 0.8097 (pp20) cc_final: 0.7843 (pp20) REVERT: H1 330 LEU cc_start: 0.8517 (mm) cc_final: 0.8281 (mm) REVERT: I1 162 PHE cc_start: 0.8218 (m-10) cc_final: 0.7884 (m-10) REVERT: I1 272 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8264 (mm) REVERT: I1 273 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7321 (mtt90) REVERT: I1 350 ASP cc_start: 0.8882 (t0) cc_final: 0.8638 (t0) REVERT: J1 82 ASN cc_start: 0.8393 (m-40) cc_final: 0.8092 (m110) REVERT: J1 277 MET cc_start: 0.8490 (tpt) cc_final: 0.8250 (tpt) REVERT: J1 327 ILE cc_start: 0.8435 (tt) cc_final: 0.8173 (tt) REVERT: J1 350 ASP cc_start: 0.8891 (t0) cc_final: 0.8646 (t0) REVERT: K1 187 TYR cc_start: 0.8539 (t80) cc_final: 0.8324 (t80) REVERT: K1 305 PHE cc_start: 0.8869 (p90) cc_final: 0.8582 (p90) REVERT: K1 326 GLU cc_start: 0.8440 (pp20) cc_final: 0.7837 (pp20) REVERT: L1 11 LEU cc_start: 0.7696 (tp) cc_final: 0.7441 (tt) REVERT: L1 73 LYS cc_start: 0.7739 (tttp) cc_final: 0.7539 (ttmm) REVERT: L1 82 ASN cc_start: 0.8517 (m-40) cc_final: 0.8173 (m110) REVERT: L1 122 PHE cc_start: 0.8592 (m-80) cc_final: 0.8298 (m-80) REVERT: L1 165 TYR cc_start: 0.7893 (t80) cc_final: 0.7608 (t80) REVERT: L1 180 MET cc_start: 0.8373 (tpp) cc_final: 0.7672 (tpp) REVERT: L1 326 GLU cc_start: 0.7955 (pp20) cc_final: 0.7634 (pp20) REVERT: A2 15 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: A2 90 SER cc_start: 0.8948 (t) cc_final: 0.8650 (t) REVERT: A2 107 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7981 (mtp) REVERT: B2 15 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: B2 90 SER cc_start: 0.8901 (t) cc_final: 0.8566 (t) REVERT: C2 15 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: C2 34 TYR cc_start: 0.8532 (t80) cc_final: 0.8263 (t80) REVERT: C2 90 SER cc_start: 0.8912 (t) cc_final: 0.8603 (t) REVERT: C2 107 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7884 (mtp) REVERT: D2 1 MET cc_start: 0.6164 (mmt) cc_final: 0.5555 (mmm) REVERT: D2 15 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: D2 41 ASP cc_start: 0.5735 (OUTLIER) cc_final: 0.5359 (t70) REVERT: D2 58 ASP cc_start: 0.8359 (t70) cc_final: 0.8138 (t70) REVERT: D2 90 SER cc_start: 0.8936 (t) cc_final: 0.8620 (t) REVERT: E2 15 ASP cc_start: 0.8028 (m-30) cc_final: 0.7438 (m-30) REVERT: E2 41 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5581 (t70) REVERT: E2 90 SER cc_start: 0.8894 (t) cc_final: 0.8559 (t) REVERT: E2 117 PHE cc_start: 0.8166 (t80) cc_final: 0.7961 (t80) REVERT: F2 1 MET cc_start: 0.6374 (mmt) cc_final: 0.5616 (mmm) REVERT: F2 15 ASP cc_start: 0.7964 (m-30) cc_final: 0.7481 (m-30) REVERT: F2 34 TYR cc_start: 0.8512 (t80) cc_final: 0.8122 (t80) REVERT: F2 41 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5633 (t70) REVERT: F2 90 SER cc_start: 0.8884 (t) cc_final: 0.8550 (t) REVERT: F2 107 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: F2 117 PHE cc_start: 0.8166 (t80) cc_final: 0.7865 (t80) REVERT: G2 1 MET cc_start: 0.6481 (mmt) cc_final: 0.5269 (mmt) REVERT: G2 15 ASP cc_start: 0.7973 (m-30) cc_final: 0.7448 (m-30) REVERT: G2 41 ASP cc_start: 0.6132 (OUTLIER) cc_final: 0.5768 (t70) REVERT: G2 43 ASP cc_start: 0.7831 (t0) cc_final: 0.7407 (t70) REVERT: G2 90 SER cc_start: 0.8953 (t) cc_final: 0.8647 (t) REVERT: G2 117 PHE cc_start: 0.8320 (t80) cc_final: 0.8056 (t80) REVERT: H2 15 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: H2 41 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5722 (t70) REVERT: H2 90 SER cc_start: 0.8841 (t) cc_final: 0.8500 (t) REVERT: I2 15 ASP cc_start: 0.7804 (m-30) cc_final: 0.7555 (m-30) REVERT: I2 41 ASP cc_start: 0.5752 (OUTLIER) cc_final: 0.5415 (t70) REVERT: I2 90 SER cc_start: 0.8906 (t) cc_final: 0.8582 (t) REVERT: I2 107 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: J2 15 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: J2 90 SER cc_start: 0.8924 (t) cc_final: 0.8599 (t) REVERT: K2 15 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: K2 41 ASP cc_start: 0.6005 (OUTLIER) cc_final: 0.5630 (t70) REVERT: K2 90 SER cc_start: 0.8861 (t) cc_final: 0.8533 (t) REVERT: L2 15 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: L2 41 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.5524 (t70) REVERT: L2 90 SER cc_start: 0.8922 (t) cc_final: 0.8598 (t) REVERT: L2 107 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8130 (mtp) outliers start: 266 outliers final: 160 residues processed: 1501 average time/residue: 0.2399 time to fit residues: 617.5691 Evaluate side-chains 1478 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1289 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 174 ASP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain A1 residue 321 LEU Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 163 THR Chi-restraints excluded: chain B1 residue 256 THR Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 94 VAL Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 163 THR Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 256 THR Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 74 LYS Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 256 THR Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 78 LYS Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 256 THR Chi-restraints excluded: chain F1 residue 281 LEU Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 24 ASN Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 182 GLU Chi-restraints excluded: chain G1 residue 256 THR Chi-restraints excluded: chain G1 residue 371 LEU Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 98 PHE Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 136 LEU Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 163 THR Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 249 ASP Chi-restraints excluded: chain H1 residue 256 THR Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 256 THR Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain I1 residue 321 LEU Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 256 THR Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 126 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 163 THR Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 256 THR Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 131 ASN Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 256 THR Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 79 VAL Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 82 SER Chi-restraints excluded: chain A2 residue 88 THR Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 58 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 79 VAL Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 88 THR Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain B2 residue 113 MET Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 82 SER Chi-restraints excluded: chain D2 residue 88 THR Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 64 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 88 THR Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 58 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 82 SER Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 82 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 88 THR Chi-restraints excluded: chain G2 residue 98 SER Chi-restraints excluded: chain H2 residue 5 ASP Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 58 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 88 THR Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain H2 residue 113 MET Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 79 VAL Chi-restraints excluded: chain I2 residue 88 THR Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 88 THR Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 88 THR Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 88 THR Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [524, 87, 68, 442, 70, 271, 298, 512, 347, 370, 443] chunk 524 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 442 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 271 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 512 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 443 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 24 ASN E1 24 ASN ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 24 ASN G1 24 ASN I1 82 ASN J1 24 ASN K1 82 ASN K1 197 GLN ** L1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 111 ASN ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2 111 ASN ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 112 ASN ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 40 ASN ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118924 restraints weight = 64389.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.122915 restraints weight = 29774.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.125391 restraints weight = 17406.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126913 restraints weight = 12070.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.127856 restraints weight = 9569.677| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 46368 Z= 0.176 Angle : 0.723 15.020 62544 Z= 0.367 Chirality : 0.044 0.191 6876 Planarity : 0.005 0.082 8064 Dihedral : 5.624 24.366 6336 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.14 % Allowed : 22.60 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5676 helix: -0.21 (0.10), residues: 2496 sheet: 0.28 (0.30), residues: 312 loop : -1.69 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGG1 140 TYR 0.036 0.002 TYRJ1 177 PHE 0.020 0.002 PHEG1 190 TRP 0.010 0.001 TRPF2 95 HIS 0.003 0.001 HISB1 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (46356) covalent geometry : angle 0.72153 / 0.37 (62520) SS BOND : bond 0.00110 / 0.07 ( 12) SS BOND : angle 2.12379 / 1.30 ( 24) hydrogen bonds : bond 0.03628 / 2.39 ( 1953) hydrogen bonds : angle 5.68523 / 3.95 ( 5541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1643 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 1386 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8508 (m-40) cc_final: 0.8154 (m110) REVERT: A1 87 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8126 (tpp) REVERT: A1 156 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.7248 (t60) REVERT: A1 319 ASP cc_start: 0.8595 (m-30) cc_final: 0.8302 (m-30) REVERT: A1 326 GLU cc_start: 0.7956 (pp20) cc_final: 0.7750 (pp20) REVERT: B1 39 MET cc_start: 0.9094 (mtt) cc_final: 0.8811 (mtp) REVERT: B1 48 ILE cc_start: 0.9497 (mm) cc_final: 0.9288 (tt) REVERT: B1 87 MET cc_start: 0.8543 (tpp) cc_final: 0.8318 (tpp) REVERT: B1 277 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7897 (tpt) REVERT: B1 316 TYR cc_start: 0.8831 (m-10) cc_final: 0.8550 (m-10) REVERT: B1 350 ASP cc_start: 0.8779 (t0) cc_final: 0.8566 (t0) REVERT: C1 45 MET cc_start: 0.8479 (mmm) cc_final: 0.7762 (ttm) REVERT: C1 82 ASN cc_start: 0.8465 (m-40) cc_final: 0.7988 (m110) REVERT: C1 182 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8589 (mm-30) REVERT: C1 273 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.6671 (ttm-80) REVERT: C1 277 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7947 (tpt) REVERT: C1 301 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7293 (mp0) REVERT: D1 21 MET cc_start: 0.8584 (mmt) cc_final: 0.8124 (mmt) REVERT: D1 197 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: D1 269 ASN cc_start: 0.8042 (t0) cc_final: 0.7791 (t0) REVERT: D1 277 MET cc_start: 0.8443 (tpt) cc_final: 0.8053 (tpt) REVERT: E1 45 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8113 (ttm) REVERT: E1 76 LEU cc_start: 0.8142 (pt) cc_final: 0.7917 (pp) REVERT: E1 143 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7341 (mmmt) REVERT: E1 175 TYR cc_start: 0.8052 (m-80) cc_final: 0.7718 (m-80) REVERT: E1 273 ARG cc_start: 0.7707 (mmm-85) cc_final: 0.7152 (tpp80) REVERT: E1 277 MET cc_start: 0.8426 (tpt) cc_final: 0.7981 (tpt) REVERT: E1 316 TYR cc_start: 0.8762 (m-10) cc_final: 0.8365 (m-10) REVERT: F1 36 MET cc_start: 0.7479 (ttm) cc_final: 0.7180 (ttm) REVERT: F1 40 TYR cc_start: 0.9366 (t80) cc_final: 0.9155 (t80) REVERT: F1 82 ASN cc_start: 0.7689 (m-40) cc_final: 0.7312 (m110) REVERT: F1 175 TYR cc_start: 0.8126 (m-80) cc_final: 0.7554 (m-80) REVERT: F1 180 MET cc_start: 0.8086 (tpp) cc_final: 0.7498 (tpp) REVERT: F1 197 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: F1 316 TYR cc_start: 0.8964 (m-80) cc_final: 0.8080 (m-10) REVERT: F1 326 GLU cc_start: 0.8448 (pp20) cc_final: 0.7845 (pp20) REVERT: F1 327 ILE cc_start: 0.8518 (tt) cc_final: 0.8293 (tt) REVERT: G1 21 MET cc_start: 0.8514 (mmp) cc_final: 0.8235 (mmt) REVERT: G1 82 ASN cc_start: 0.7901 (m-40) cc_final: 0.7418 (m110) REVERT: G1 175 TYR cc_start: 0.8305 (m-80) cc_final: 0.7699 (m-80) REVERT: G1 182 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8181 (mm-30) REVERT: G1 197 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: G1 277 MET cc_start: 0.8367 (tpt) cc_final: 0.7770 (tpt) REVERT: H1 21 MET cc_start: 0.8554 (mmt) cc_final: 0.8261 (mmt) REVERT: H1 73 LYS cc_start: 0.7704 (tptt) cc_final: 0.7253 (ttmm) REVERT: H1 171 GLU cc_start: 0.8158 (pt0) cc_final: 0.7432 (pt0) REVERT: H1 182 GLU cc_start: 0.8718 (mm-30) cc_final: 0.7481 (mp0) REVERT: H1 273 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.6789 (ttm-80) REVERT: H1 301 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7309 (mp0) REVERT: H1 330 LEU cc_start: 0.8512 (mm) cc_final: 0.8245 (mm) REVERT: I1 82 ASN cc_start: 0.8077 (m-40) cc_final: 0.7875 (m110) REVERT: I1 162 PHE cc_start: 0.8158 (m-10) cc_final: 0.7939 (m-10) REVERT: I1 175 TYR cc_start: 0.8165 (m-80) cc_final: 0.7645 (m-80) REVERT: I1 272 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8258 (mm) REVERT: I1 326 GLU cc_start: 0.8141 (pp20) cc_final: 0.7905 (pp20) REVERT: I1 350 ASP cc_start: 0.8854 (t0) cc_final: 0.8610 (t0) REVERT: J1 45 MET cc_start: 0.8154 (ttm) cc_final: 0.7803 (ttm) REVERT: J1 82 ASN cc_start: 0.8280 (m-40) cc_final: 0.8004 (m110) REVERT: J1 180 MET cc_start: 0.8415 (tpp) cc_final: 0.8037 (tpp) REVERT: J1 197 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: J1 301 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7193 (mp0) REVERT: J1 318 GLU cc_start: 0.8310 (tt0) cc_final: 0.8048 (tt0) REVERT: J1 327 ILE cc_start: 0.8424 (tt) cc_final: 0.8212 (tt) REVERT: J1 350 ASP cc_start: 0.8935 (t0) cc_final: 0.8716 (t0) REVERT: K1 182 GLU cc_start: 0.8642 (mm-30) cc_final: 0.7473 (mp0) REVERT: K1 326 GLU cc_start: 0.8369 (pp20) cc_final: 0.7777 (pp20) REVERT: L1 73 LYS cc_start: 0.7746 (tttp) cc_final: 0.7545 (ttmm) REVERT: L1 78 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7052 (tppt) REVERT: L1 82 ASN cc_start: 0.8487 (m-40) cc_final: 0.8120 (m110) REVERT: L1 122 PHE cc_start: 0.8530 (m-80) cc_final: 0.8223 (m-80) REVERT: L1 180 MET cc_start: 0.8113 (tpp) cc_final: 0.7468 (tpp) REVERT: L1 274 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7295 (tpp80) REVERT: L1 326 GLU cc_start: 0.7965 (pp20) cc_final: 0.7695 (pp20) REVERT: A2 1 MET cc_start: 0.6131 (mmt) cc_final: 0.5408 (mmm) REVERT: A2 15 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: A2 41 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5473 (t70) REVERT: A2 90 SER cc_start: 0.8819 (t) cc_final: 0.8506 (t) REVERT: A2 107 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: B2 15 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: B2 38 TYR cc_start: 0.8472 (t80) cc_final: 0.8257 (t80) REVERT: B2 41 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5399 (t70) REVERT: B2 90 SER cc_start: 0.8791 (t) cc_final: 0.8473 (t) REVERT: C2 15 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: C2 41 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5582 (t70) REVERT: C2 43 ASP cc_start: 0.7830 (t0) cc_final: 0.7548 (t70) REVERT: C2 90 SER cc_start: 0.8801 (t) cc_final: 0.8477 (t) REVERT: C2 107 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7800 (mtp) REVERT: C2 117 PHE cc_start: 0.8451 (t80) cc_final: 0.8251 (t80) REVERT: D2 1 MET cc_start: 0.6152 (mmt) cc_final: 0.5483 (mmm) REVERT: D2 15 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: D2 41 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5331 (t70) REVERT: D2 43 ASP cc_start: 0.7475 (t0) cc_final: 0.6811 (t70) REVERT: D2 90 SER cc_start: 0.8870 (t) cc_final: 0.8566 (t) REVERT: E2 15 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: E2 41 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.5488 (t70) REVERT: E2 43 ASP cc_start: 0.7519 (t0) cc_final: 0.6982 (t70) REVERT: E2 90 SER cc_start: 0.8754 (t) cc_final: 0.8416 (t) REVERT: E2 107 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8112 (mtp) REVERT: E2 117 PHE cc_start: 0.7893 (t80) cc_final: 0.7607 (t80) REVERT: F2 1 MET cc_start: 0.6379 (mmt) cc_final: 0.5596 (mmm) REVERT: F2 15 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: F2 41 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5592 (t70) REVERT: F2 43 ASP cc_start: 0.7844 (t0) cc_final: 0.7361 (t70) REVERT: F2 90 SER cc_start: 0.8746 (t) cc_final: 0.8413 (t) REVERT: F2 107 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7795 (mtp) REVERT: F2 117 PHE cc_start: 0.7996 (t80) cc_final: 0.7796 (t80) REVERT: G2 1 MET cc_start: 0.6299 (mmt) cc_final: 0.5187 (mmt) REVERT: G2 15 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: G2 41 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.5667 (t70) REVERT: G2 43 ASP cc_start: 0.7661 (t0) cc_final: 0.7280 (t70) REVERT: G2 90 SER cc_start: 0.8929 (t) cc_final: 0.8634 (t) REVERT: H2 1 MET cc_start: 0.5634 (mmt) cc_final: 0.4859 (mmt) REVERT: H2 15 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: H2 38 TYR cc_start: 0.8377 (t80) cc_final: 0.8149 (t80) REVERT: H2 41 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5689 (t70) REVERT: H2 90 SER cc_start: 0.8729 (t) cc_final: 0.8362 (t) REVERT: I2 15 ASP cc_start: 0.7790 (m-30) cc_final: 0.7468 (m-30) REVERT: I2 41 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5373 (t70) REVERT: I2 90 SER cc_start: 0.8847 (t) cc_final: 0.8509 (t) REVERT: I2 107 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7885 (mtp) REVERT: J2 15 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: J2 41 ASP cc_start: 0.5895 (OUTLIER) cc_final: 0.5526 (t70) REVERT: J2 90 SER cc_start: 0.8829 (t) cc_final: 0.8491 (t) REVERT: K2 15 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: K2 41 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5694 (t70) REVERT: K2 90 SER cc_start: 0.8741 (t) cc_final: 0.8389 (t) REVERT: L2 15 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: L2 28 ASN cc_start: 0.8408 (t0) cc_final: 0.8053 (t0) REVERT: L2 41 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.5374 (t70) REVERT: L2 43 ASP cc_start: 0.7504 (t0) cc_final: 0.6857 (t70) REVERT: L2 90 SER cc_start: 0.8879 (t) cc_final: 0.8569 (t) REVERT: L2 107 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7972 (mtp) outliers start: 257 outliers final: 146 residues processed: 1519 average time/residue: 0.2431 time to fit residues: 633.6843 Evaluate side-chains 1492 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1305 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 174 ASP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 163 THR Chi-restraints excluded: chain B1 residue 221 ILE Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 94 VAL Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 277 MET Chi-restraints excluded: chain D1 residue 24 ASN Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 163 THR Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 197 GLN Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain D1 residue 332 PHE Chi-restraints excluded: chain E1 residue 24 ASN Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 117 LEU Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain F1 residue 24 ASN Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 156 TRP Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 174 ASP Chi-restraints excluded: chain G1 residue 182 GLU Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 256 THR Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain G1 residue 371 LEU Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 128 LYS Chi-restraints excluded: chain H1 residue 140 ARG Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 256 THR Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 78 LYS Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 94 VAL Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 131 ASN Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 58 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain B2 residue 113 MET Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 64 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 15 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 15 ASP Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 88 THR Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 88 THR Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain H2 residue 113 MET Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 88 THR Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 84 VAL Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [151, 310, 477, 170, 337, 348, 419, 28, 126, 377, 411] chunk 151 optimal weight: 0.8980 chunk 310 optimal weight: 0.7980 chunk 477 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 348 optimal weight: 0.8980 chunk 419 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 377 optimal weight: 0.7980 chunk 411 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 24 ASN H1 82 ASN ** K1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 82 ASN ** L1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2 111 ASN ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.160663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.121611 restraints weight = 64294.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125709 restraints weight = 29759.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128228 restraints weight = 17347.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.129796 restraints weight = 11990.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130739 restraints weight = 9458.719| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 46368 Z= 0.150 Angle : 0.710 15.368 62544 Z= 0.359 Chirality : 0.043 0.186 6876 Planarity : 0.004 0.062 8064 Dihedral : 5.500 23.610 6336 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.02 % Allowed : 23.38 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.11), residues: 5676 helix: -0.12 (0.10), residues: 2496 sheet: 0.21 (0.29), residues: 312 loop : -1.66 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGH1 140 TYR 0.037 0.002 TYRJ1 177 PHE 0.023 0.001 PHEE1 190 TRP 0.008 0.001 TRPJ2 92 HIS 0.002 0.001 HISB1 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (46356) covalent geometry : angle 0.70958 / 0.36 (62520) SS BOND : bond 0.00187 / 0.12 ( 12) SS BOND : angle 1.72474 / 1.05 ( 24) hydrogen bonds : bond 0.03494 / 2.30 ( 1953) hydrogen bonds : angle 5.58053 / 3.88 ( 5541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 1383 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8497 (m-40) cc_final: 0.8143 (m110) REVERT: A1 87 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: A1 162 PHE cc_start: 0.7823 (m-10) cc_final: 0.7366 (m-10) REVERT: A1 166 MET cc_start: 0.7591 (mtm) cc_final: 0.7096 (mtt) REVERT: B1 39 MET cc_start: 0.9060 (mtt) cc_final: 0.8756 (mtp) REVERT: B1 48 ILE cc_start: 0.9474 (mm) cc_final: 0.9251 (tt) REVERT: B1 87 MET cc_start: 0.8504 (tpp) cc_final: 0.8227 (tpp) REVERT: B1 277 MET cc_start: 0.8523 (tpt) cc_final: 0.7879 (tpt) REVERT: C1 82 ASN cc_start: 0.8389 (m-40) cc_final: 0.7909 (m110) REVERT: C1 182 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C1 277 MET cc_start: 0.8480 (tpt) cc_final: 0.7828 (tpt) REVERT: C1 326 GLU cc_start: 0.8207 (pp20) cc_final: 0.7900 (pp20) REVERT: D1 21 MET cc_start: 0.8552 (mmt) cc_final: 0.8132 (mmt) REVERT: D1 197 GLN cc_start: 0.8670 (tt0) cc_final: 0.8338 (tt0) REVERT: D1 269 ASN cc_start: 0.8003 (t0) cc_final: 0.7712 (t0) REVERT: D1 277 MET cc_start: 0.8454 (tpt) cc_final: 0.8050 (tpt) REVERT: E1 45 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: E1 103 ASP cc_start: 0.7736 (m-30) cc_final: 0.7495 (m-30) REVERT: E1 277 MET cc_start: 0.8422 (tpt) cc_final: 0.7936 (tpt) REVERT: E1 316 TYR cc_start: 0.8777 (m-10) cc_final: 0.8428 (m-10) REVERT: F1 36 MET cc_start: 0.7441 (ttm) cc_final: 0.7172 (ttm) REVERT: F1 55 TYR cc_start: 0.8221 (m-80) cc_final: 0.7958 (m-10) REVERT: F1 76 LEU cc_start: 0.8107 (pt) cc_final: 0.7850 (pp) REVERT: F1 82 ASN cc_start: 0.7724 (m-40) cc_final: 0.7244 (m110) REVERT: F1 175 TYR cc_start: 0.7971 (m-80) cc_final: 0.7416 (m-80) REVERT: F1 180 MET cc_start: 0.7997 (tpp) cc_final: 0.7420 (tpp) REVERT: F1 197 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: F1 301 GLU cc_start: 0.7837 (mp0) cc_final: 0.7601 (mp0) REVERT: F1 316 TYR cc_start: 0.8951 (m-80) cc_final: 0.8164 (m-10) REVERT: G1 21 MET cc_start: 0.8404 (mmp) cc_final: 0.8196 (mmt) REVERT: G1 25 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.6500 (ptm160) REVERT: G1 82 ASN cc_start: 0.7841 (m-40) cc_final: 0.7255 (m110) REVERT: G1 175 TYR cc_start: 0.8171 (m-80) cc_final: 0.7657 (m-80) REVERT: G1 197 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: G1 277 MET cc_start: 0.8308 (tpt) cc_final: 0.7934 (tpt) REVERT: H1 21 MET cc_start: 0.8554 (mmt) cc_final: 0.8245 (mmt) REVERT: H1 40 TYR cc_start: 0.9355 (t80) cc_final: 0.9120 (t80) REVERT: H1 171 GLU cc_start: 0.8154 (pt0) cc_final: 0.7418 (pt0) REVERT: H1 182 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7357 (mp0) REVERT: H1 197 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: H1 273 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.6770 (ttm-80) REVERT: H1 305 PHE cc_start: 0.8599 (p90) cc_final: 0.8346 (p90) REVERT: H1 316 TYR cc_start: 0.9019 (m-10) cc_final: 0.8377 (m-10) REVERT: H1 326 GLU cc_start: 0.8065 (pp20) cc_final: 0.7859 (pp20) REVERT: H1 330 LEU cc_start: 0.8547 (mm) cc_final: 0.8241 (mm) REVERT: I1 82 ASN cc_start: 0.8179 (m-40) cc_final: 0.7827 (m110) REVERT: I1 175 TYR cc_start: 0.8048 (m-80) cc_final: 0.7589 (m-80) REVERT: I1 269 ASN cc_start: 0.8068 (t0) cc_final: 0.7838 (t0) REVERT: I1 272 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8273 (mm) REVERT: I1 326 GLU cc_start: 0.8160 (pp20) cc_final: 0.7616 (pp20) REVERT: I1 350 ASP cc_start: 0.8792 (t0) cc_final: 0.8538 (t0) REVERT: J1 82 ASN cc_start: 0.8290 (m-40) cc_final: 0.7977 (m110) REVERT: J1 182 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8001 (mp0) REVERT: J1 197 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: J1 301 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7079 (mp0) REVERT: J1 316 TYR cc_start: 0.8694 (m-10) cc_final: 0.8301 (m-80) REVERT: J1 318 GLU cc_start: 0.8224 (tt0) cc_final: 0.8014 (tt0) REVERT: K1 182 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8344 (mp0) REVERT: K1 301 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7421 (mp0) REVERT: K1 326 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: L1 33 ASP cc_start: 0.7232 (t0) cc_final: 0.7031 (t70) REVERT: L1 58 ASN cc_start: 0.8697 (m-40) cc_final: 0.8444 (m110) REVERT: L1 73 LYS cc_start: 0.7651 (tttp) cc_final: 0.7396 (ttmm) REVERT: L1 82 ASN cc_start: 0.8512 (m-40) cc_final: 0.8106 (m110) REVERT: L1 180 MET cc_start: 0.7989 (tpp) cc_final: 0.7368 (tpp) REVERT: L1 197 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: L1 326 GLU cc_start: 0.7862 (pp20) cc_final: 0.7628 (pp20) REVERT: L1 334 GLU cc_start: 0.6600 (mp0) cc_final: 0.6317 (mp0) REVERT: A2 1 MET cc_start: 0.6053 (mmt) cc_final: 0.5328 (mmm) REVERT: A2 15 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: A2 41 ASP cc_start: 0.5745 (OUTLIER) cc_final: 0.5298 (t70) REVERT: A2 43 ASP cc_start: 0.7442 (t0) cc_final: 0.7061 (t0) REVERT: A2 90 SER cc_start: 0.8742 (t) cc_final: 0.8421 (t) REVERT: A2 107 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7721 (mtp) REVERT: A2 117 PHE cc_start: 0.8226 (t80) cc_final: 0.7991 (t80) REVERT: B2 15 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: B2 41 ASP cc_start: 0.5704 (OUTLIER) cc_final: 0.5387 (t70) REVERT: B2 61 TYR cc_start: 0.8772 (t80) cc_final: 0.8571 (t80) REVERT: B2 90 SER cc_start: 0.8693 (t) cc_final: 0.8365 (t) REVERT: C2 1 MET cc_start: 0.4947 (mmt) cc_final: 0.4448 (mmm) REVERT: C2 15 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: C2 34 TYR cc_start: 0.8492 (t80) cc_final: 0.8228 (t80) REVERT: C2 41 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.5563 (t70) REVERT: C2 90 SER cc_start: 0.8695 (t) cc_final: 0.8364 (t) REVERT: C2 107 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7730 (mtp) REVERT: C2 117 PHE cc_start: 0.8336 (t80) cc_final: 0.8112 (t80) REVERT: D2 1 MET cc_start: 0.6081 (mmt) cc_final: 0.5369 (mmm) REVERT: D2 15 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: D2 41 ASP cc_start: 0.5612 (OUTLIER) cc_final: 0.5243 (t70) REVERT: D2 43 ASP cc_start: 0.7376 (t0) cc_final: 0.6904 (t70) REVERT: D2 90 SER cc_start: 0.8769 (t) cc_final: 0.8446 (t) REVERT: E2 15 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7268 (m-30) REVERT: E2 41 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.5585 (t70) REVERT: E2 43 ASP cc_start: 0.7567 (t0) cc_final: 0.7133 (t70) REVERT: E2 90 SER cc_start: 0.8702 (t) cc_final: 0.8360 (t) REVERT: E2 107 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: F2 1 MET cc_start: 0.6266 (mmt) cc_final: 0.5504 (mmm) REVERT: F2 15 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: F2 28 ASN cc_start: 0.8164 (t0) cc_final: 0.7750 (t0) REVERT: F2 41 ASP cc_start: 0.5964 (OUTLIER) cc_final: 0.5555 (t70) REVERT: F2 43 ASP cc_start: 0.7787 (t0) cc_final: 0.6864 (t70) REVERT: F2 90 SER cc_start: 0.8634 (t) cc_final: 0.8302 (t) REVERT: F2 107 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7740 (mtp) REVERT: G2 1 MET cc_start: 0.6180 (mmt) cc_final: 0.5368 (mmm) REVERT: G2 15 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: G2 41 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5628 (t70) REVERT: G2 43 ASP cc_start: 0.7722 (t0) cc_final: 0.7363 (t70) REVERT: G2 90 SER cc_start: 0.8835 (t) cc_final: 0.8517 (t) REVERT: H2 1 MET cc_start: 0.5598 (mmt) cc_final: 0.4807 (mmt) REVERT: H2 15 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: H2 41 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5643 (t70) REVERT: H2 90 SER cc_start: 0.8705 (t) cc_final: 0.8330 (t) REVERT: I2 15 ASP cc_start: 0.7854 (m-30) cc_final: 0.7437 (m-30) REVERT: I2 28 ASN cc_start: 0.8190 (t0) cc_final: 0.7793 (t0) REVERT: I2 41 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.5336 (t70) REVERT: I2 90 SER cc_start: 0.8736 (t) cc_final: 0.8420 (t) REVERT: J2 15 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: J2 41 ASP cc_start: 0.5868 (OUTLIER) cc_final: 0.5491 (t70) REVERT: J2 90 SER cc_start: 0.8754 (t) cc_final: 0.8404 (t) REVERT: K2 15 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: K2 41 ASP cc_start: 0.5898 (OUTLIER) cc_final: 0.5551 (t70) REVERT: K2 90 SER cc_start: 0.8624 (t) cc_final: 0.8279 (t) REVERT: K2 113 MET cc_start: 0.8227 (ttp) cc_final: 0.7933 (ttp) REVERT: L2 15 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: L2 28 ASN cc_start: 0.8371 (t0) cc_final: 0.7943 (t0) REVERT: L2 41 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.5283 (t70) REVERT: L2 43 ASP cc_start: 0.7448 (t0) cc_final: 0.7017 (t70) REVERT: L2 90 SER cc_start: 0.8757 (t) cc_final: 0.8445 (t) REVERT: L2 107 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7882 (mtp) outliers start: 251 outliers final: 165 residues processed: 1513 average time/residue: 0.2423 time to fit residues: 625.3881 Evaluate side-chains 1496 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1294 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 131 ASN Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 174 ASP Chi-restraints excluded: chain A1 residue 197 GLN Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 163 THR Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 256 THR Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 94 VAL Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 163 THR Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain D1 residue 332 PHE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 87 MET Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 117 LEU Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 156 TRP Chi-restraints excluded: chain F1 residue 163 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain F1 residue 371 LEU Chi-restraints excluded: chain G1 residue 24 ASN Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 156 TRP Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain G1 residue 371 LEU Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 128 LYS Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 78 LYS Chi-restraints excluded: chain I1 residue 87 MET Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 78 LYS Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 94 VAL Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 163 THR Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain K1 residue 326 GLU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 197 GLN Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 79 VAL Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 84 VAL Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 84 VAL Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 88 THR Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 15 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 15 ASP Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 88 THR Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 88 THR Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 84 VAL Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 88 THR Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [104, 281, 93, 524, 416, 39, 270, 359, 114, 344, 185] chunk 104 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 524 optimal weight: 0.5980 chunk 416 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 359 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 344 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.7101 > 50:) chunk 185 optimal weight: 6.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 82 ASN ** K1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 82 ASN K1 197 GLN ** L1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 112 ASN ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K2 28 ASN ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.117586 restraints weight = 64628.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121518 restraints weight = 30250.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123972 restraints weight = 17803.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.125478 restraints weight = 12405.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.126420 restraints weight = 9855.957| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 46368 Z= 0.217 Angle : 0.756 15.812 62544 Z= 0.383 Chirality : 0.046 0.259 6876 Planarity : 0.004 0.055 8064 Dihedral : 5.603 24.809 6336 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.80 % Allowed : 24.20 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.11), residues: 5676 helix: -0.02 (0.10), residues: 2424 sheet: 0.15 (0.29), residues: 312 loop : -1.65 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGB2 100 TYR 0.041 0.002 TYRJ1 177 PHE 0.019 0.002 PHEA1 190 TRP 0.010 0.001 TRPJ1 361 HIS 0.004 0.001 HISB1 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (46356) covalent geometry : angle 0.75512 / 0.38 (62520) SS BOND : bond 0.00121 / 0.08 ( 12) SS BOND : angle 2.34001 / 1.41 ( 24) hydrogen bonds : bond 0.03742 / 2.46 ( 1953) hydrogen bonds : angle 5.67532 / 3.94 ( 5541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1657 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 290 poor density : 1367 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8583 (m-40) cc_final: 0.8221 (m110) REVERT: A1 87 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8123 (tpp) REVERT: A1 162 PHE cc_start: 0.8009 (m-10) cc_final: 0.7630 (m-10) REVERT: A1 180 MET cc_start: 0.8351 (ttm) cc_final: 0.7962 (tpp) REVERT: A1 350 ASP cc_start: 0.8704 (t0) cc_final: 0.8458 (t0) REVERT: B1 87 MET cc_start: 0.8504 (tpp) cc_final: 0.8156 (tpp) REVERT: B1 277 MET cc_start: 0.8545 (tpt) cc_final: 0.7827 (tpt) REVERT: C1 45 MET cc_start: 0.8449 (mmm) cc_final: 0.8010 (ttm) REVERT: C1 76 LEU cc_start: 0.8690 (pt) cc_final: 0.8067 (pp) REVERT: C1 82 ASN cc_start: 0.8479 (m-40) cc_final: 0.7952 (m110) REVERT: C1 182 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8630 (mm-30) REVERT: C1 277 MET cc_start: 0.8592 (tpt) cc_final: 0.8035 (tpt) REVERT: C1 326 GLU cc_start: 0.8125 (pp20) cc_final: 0.7923 (pp20) REVERT: D1 21 MET cc_start: 0.8612 (mmt) cc_final: 0.8103 (mmt) REVERT: D1 197 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: D1 277 MET cc_start: 0.8494 (tpt) cc_final: 0.8024 (tpt) REVERT: E1 45 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8189 (ttm) REVERT: E1 103 ASP cc_start: 0.7724 (m-30) cc_final: 0.7492 (m-30) REVERT: E1 180 MET cc_start: 0.8232 (tpp) cc_final: 0.7575 (tpt) REVERT: E1 277 MET cc_start: 0.8468 (tpt) cc_final: 0.7998 (tpt) REVERT: E1 316 TYR cc_start: 0.8801 (m-10) cc_final: 0.8381 (m-10) REVERT: F1 36 MET cc_start: 0.7501 (ttm) cc_final: 0.7253 (ttm) REVERT: F1 82 ASN cc_start: 0.7999 (m-40) cc_final: 0.7507 (m110) REVERT: F1 175 TYR cc_start: 0.8115 (m-80) cc_final: 0.7657 (m-80) REVERT: F1 197 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: F1 301 GLU cc_start: 0.7907 (mp0) cc_final: 0.7670 (mp0) REVERT: F1 316 TYR cc_start: 0.8980 (m-80) cc_final: 0.8138 (m-10) REVERT: F1 326 GLU cc_start: 0.8363 (pp20) cc_final: 0.7744 (pp20) REVERT: G1 21 MET cc_start: 0.8466 (mmp) cc_final: 0.8232 (mmt) REVERT: G1 82 ASN cc_start: 0.8129 (m-40) cc_final: 0.7537 (m110) REVERT: G1 175 TYR cc_start: 0.8433 (m-80) cc_final: 0.7748 (m-80) REVERT: G1 182 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: G1 197 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: G1 277 MET cc_start: 0.8375 (tpt) cc_final: 0.7937 (tpt) REVERT: H1 21 MET cc_start: 0.8600 (mmt) cc_final: 0.8310 (mmt) REVERT: H1 171 GLU cc_start: 0.8189 (pt0) cc_final: 0.7423 (pt0) REVERT: H1 197 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: H1 326 GLU cc_start: 0.8079 (pp20) cc_final: 0.7850 (pp20) REVERT: H1 330 LEU cc_start: 0.8532 (mm) cc_final: 0.8234 (mm) REVERT: I1 21 MET cc_start: 0.8500 (mmt) cc_final: 0.8040 (mmt) REVERT: I1 82 ASN cc_start: 0.8373 (m-40) cc_final: 0.7973 (m110) REVERT: I1 175 TYR cc_start: 0.8265 (m-80) cc_final: 0.7793 (m-80) REVERT: I1 182 GLU cc_start: 0.8845 (mm-30) cc_final: 0.7794 (mp0) REVERT: I1 197 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: I1 326 GLU cc_start: 0.8242 (pp20) cc_final: 0.7685 (pp20) REVERT: I1 350 ASP cc_start: 0.8856 (t0) cc_final: 0.8577 (t0) REVERT: J1 82 ASN cc_start: 0.8362 (m-40) cc_final: 0.8020 (m110) REVERT: J1 180 MET cc_start: 0.8421 (tpp) cc_final: 0.8162 (tpp) REVERT: J1 283 MET cc_start: 0.7731 (tpp) cc_final: 0.7522 (tpp) REVERT: J1 316 TYR cc_start: 0.8757 (m-10) cc_final: 0.8315 (m-80) REVERT: J1 318 GLU cc_start: 0.8273 (tt0) cc_final: 0.8049 (tt0) REVERT: J1 350 ASP cc_start: 0.8882 (t0) cc_final: 0.8656 (t0) REVERT: K1 187 TYR cc_start: 0.8521 (t80) cc_final: 0.8288 (t80) REVERT: K1 326 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7794 (pp20) REVERT: L1 58 ASN cc_start: 0.8746 (m-40) cc_final: 0.8459 (m110) REVERT: L1 73 LYS cc_start: 0.7715 (tttp) cc_final: 0.7504 (ttmm) REVERT: L1 82 ASN cc_start: 0.8542 (m-40) cc_final: 0.8159 (m110) REVERT: L1 92 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7618 (tpp80) REVERT: L1 122 PHE cc_start: 0.8650 (m-80) cc_final: 0.8353 (m-80) REVERT: L1 180 MET cc_start: 0.8236 (tpp) cc_final: 0.7737 (tpp) REVERT: L1 197 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: L1 326 GLU cc_start: 0.7942 (pp20) cc_final: 0.7706 (pp20) REVERT: L1 334 GLU cc_start: 0.6589 (mp0) cc_final: 0.6274 (mp0) REVERT: A2 1 MET cc_start: 0.5961 (mmt) cc_final: 0.5381 (mmm) REVERT: A2 15 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A2 43 ASP cc_start: 0.7631 (t0) cc_final: 0.7367 (t0) REVERT: A2 90 SER cc_start: 0.8958 (t) cc_final: 0.8673 (t) REVERT: A2 107 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7840 (mtp) REVERT: B2 15 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: B2 38 TYR cc_start: 0.8520 (t80) cc_final: 0.8192 (t80) REVERT: B2 41 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5513 (t70) REVERT: B2 90 SER cc_start: 0.8891 (t) cc_final: 0.8588 (t) REVERT: B2 117 PHE cc_start: 0.8245 (t80) cc_final: 0.7959 (t80) REVERT: C2 15 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: C2 28 ASN cc_start: 0.8154 (t0) cc_final: 0.7783 (t0) REVERT: C2 41 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5702 (t70) REVERT: C2 43 ASP cc_start: 0.7865 (t0) cc_final: 0.7596 (t70) REVERT: C2 90 SER cc_start: 0.8827 (t) cc_final: 0.8515 (t) REVERT: C2 107 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: D2 1 MET cc_start: 0.6016 (mmt) cc_final: 0.5395 (mmm) REVERT: D2 15 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: D2 41 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5389 (t70) REVERT: D2 43 ASP cc_start: 0.7567 (t0) cc_final: 0.7258 (t70) REVERT: D2 90 SER cc_start: 0.8943 (t) cc_final: 0.8645 (t) REVERT: E2 15 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: E2 41 ASP cc_start: 0.6024 (OUTLIER) cc_final: 0.5660 (t70) REVERT: E2 43 ASP cc_start: 0.7614 (t0) cc_final: 0.7378 (t70) REVERT: E2 90 SER cc_start: 0.8858 (t) cc_final: 0.8529 (t) REVERT: E2 107 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: E2 117 PHE cc_start: 0.7890 (t80) cc_final: 0.7578 (t80) REVERT: F2 1 MET cc_start: 0.6024 (mmt) cc_final: 0.5318 (mmm) REVERT: F2 15 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: F2 41 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5623 (t70) REVERT: F2 43 ASP cc_start: 0.7678 (t0) cc_final: 0.7375 (t0) REVERT: F2 90 SER cc_start: 0.8799 (t) cc_final: 0.8482 (t) REVERT: F2 107 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7784 (mtp) REVERT: G2 1 MET cc_start: 0.6061 (mmt) cc_final: 0.5360 (mmm) REVERT: G2 15 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: G2 41 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5789 (t70) REVERT: G2 43 ASP cc_start: 0.7819 (t0) cc_final: 0.7538 (t0) REVERT: G2 90 SER cc_start: 0.9014 (t) cc_final: 0.8718 (t) REVERT: H2 15 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: H2 41 ASP cc_start: 0.6007 (OUTLIER) cc_final: 0.5653 (t70) REVERT: H2 90 SER cc_start: 0.8810 (t) cc_final: 0.8463 (t) REVERT: I2 15 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: I2 28 ASN cc_start: 0.8188 (t0) cc_final: 0.7777 (t0) REVERT: I2 41 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5522 (t70) REVERT: I2 90 SER cc_start: 0.8917 (t) cc_final: 0.8596 (t) REVERT: J2 15 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: J2 41 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5588 (t70) REVERT: J2 90 SER cc_start: 0.8880 (t) cc_final: 0.8580 (t) REVERT: K2 15 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: K2 28 ASN cc_start: 0.8250 (t0) cc_final: 0.7883 (t0) REVERT: K2 41 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5557 (t70) REVERT: K2 90 SER cc_start: 0.8779 (t) cc_final: 0.8457 (t) REVERT: L2 15 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: L2 28 ASN cc_start: 0.8390 (t0) cc_final: 0.8136 (t0) REVERT: L2 41 ASP cc_start: 0.5916 (OUTLIER) cc_final: 0.5483 (t70) REVERT: L2 43 ASP cc_start: 0.7652 (t0) cc_final: 0.7285 (t0) REVERT: L2 90 SER cc_start: 0.8945 (t) cc_final: 0.8640 (t) REVERT: L2 107 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7948 (mtp) outliers start: 290 outliers final: 201 residues processed: 1510 average time/residue: 0.2437 time to fit residues: 630.3326 Evaluate side-chains 1547 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1308 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 174 ASP Chi-restraints excluded: chain A1 residue 197 GLN Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 277 MET Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain A1 residue 321 LEU Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 163 THR Chi-restraints excluded: chain B1 residue 197 GLN Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 256 THR Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 94 VAL Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 140 ARG Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 163 THR Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 197 GLN Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain D1 residue 332 PHE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 117 LEU Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 256 THR Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 87 MET Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 156 TRP Chi-restraints excluded: chain F1 residue 163 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain F1 residue 371 LEU Chi-restraints excluded: chain G1 residue 45 MET Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 156 TRP Chi-restraints excluded: chain G1 residue 182 GLU Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 256 THR Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 98 PHE Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 128 LYS Chi-restraints excluded: chain H1 residue 140 ARG Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 157 THR Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 256 THR Chi-restraints excluded: chain H1 residue 277 MET Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 78 LYS Chi-restraints excluded: chain I1 residue 87 MET Chi-restraints excluded: chain I1 residue 94 VAL Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 197 GLN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 78 LYS Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 148 THR Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 163 THR Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain K1 residue 326 GLU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 197 GLN Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 79 VAL Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 84 VAL Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 58 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 88 THR Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 84 VAL Chi-restraints excluded: chain D2 residue 91 ASP Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 88 THR Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 15 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 58 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 15 ASP Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 88 THR Chi-restraints excluded: chain G2 residue 98 SER Chi-restraints excluded: chain H2 residue 5 ASP Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 58 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 88 THR Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain H2 residue 113 MET Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 15 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 42 CYS Chi-restraints excluded: chain I2 residue 84 VAL Chi-restraints excluded: chain I2 residue 88 THR Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 88 THR Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 84 VAL Chi-restraints excluded: chain L2 residue 88 THR Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [165, 518, 446, 293, 394, 257, 231, 147, 543, 141, 32] chunk 165 optimal weight: 0.9990 chunk 518 optimal weight: 0.2980 chunk 446 optimal weight: 0.6980 chunk 293 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 231 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 543 optimal weight: 0.4980 chunk 141 optimal weight: 7.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 24 ASN H1 82 ASN K1 24 ASN K1 82 ASN ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2 111 ASN ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.163350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.124132 restraints weight = 63909.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.128278 restraints weight = 29683.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130856 restraints weight = 17327.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.132433 restraints weight = 11969.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.133386 restraints weight = 9443.076| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46368 Z= 0.140 Angle : 0.731 14.970 62544 Z= 0.365 Chirality : 0.044 0.159 6876 Planarity : 0.004 0.091 8064 Dihedral : 5.451 24.951 6336 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.00 % Allowed : 25.30 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.11), residues: 5676 helix: -0.08 (0.10), residues: 2496 sheet: 0.10 (0.29), residues: 312 loop : -1.60 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGB2 100 TYR 0.038 0.002 TYRB1 177 PHE 0.024 0.001 PHEF2 117 TRP 0.010 0.001 TRPK2 92 HIS 0.003 0.001 HISG1 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (46356) covalent geometry : angle 0.73073 / 0.37 (62520) SS BOND : bond 0.00370 / 0.20 ( 12) SS BOND : angle 1.50447 / 0.92 ( 24) hydrogen bonds : bond 0.03448 / 2.26 ( 1953) hydrogen bonds : angle 5.54244 / 3.85 ( 5541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 1409 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8554 (m-40) cc_final: 0.8193 (m110) REVERT: A1 87 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8003 (tpp) REVERT: A1 162 PHE cc_start: 0.7819 (m-10) cc_final: 0.7487 (m-10) REVERT: A1 166 MET cc_start: 0.7613 (mtm) cc_final: 0.7125 (mtt) REVERT: A1 197 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: A1 274 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7529 (tpp80) REVERT: B1 21 MET cc_start: 0.8344 (tpp) cc_final: 0.7714 (mmt) REVERT: B1 39 MET cc_start: 0.9111 (mtt) cc_final: 0.8847 (mtp) REVERT: B1 48 ILE cc_start: 0.9472 (mm) cc_final: 0.9259 (tt) REVERT: B1 87 MET cc_start: 0.8432 (tpp) cc_final: 0.8097 (tpp) REVERT: B1 269 ASN cc_start: 0.7930 (t0) cc_final: 0.7703 (t0) REVERT: B1 277 MET cc_start: 0.8476 (tpt) cc_final: 0.7730 (tpt) REVERT: C1 82 ASN cc_start: 0.8368 (m-40) cc_final: 0.7813 (m110) REVERT: C1 180 MET cc_start: 0.7715 (tpp) cc_final: 0.7132 (tpp) REVERT: C1 182 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8630 (mm-30) REVERT: C1 273 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: C1 277 MET cc_start: 0.8593 (tpt) cc_final: 0.7973 (tpt) REVERT: D1 21 MET cc_start: 0.8547 (mmt) cc_final: 0.7966 (mmt) REVERT: D1 87 MET cc_start: 0.8475 (tpp) cc_final: 0.8235 (tpp) REVERT: D1 197 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: D1 269 ASN cc_start: 0.8012 (t0) cc_final: 0.7679 (t0) REVERT: D1 277 MET cc_start: 0.8393 (tpt) cc_final: 0.7939 (tpt) REVERT: E1 45 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7635 (ttm) REVERT: E1 103 ASP cc_start: 0.7707 (m-30) cc_final: 0.7503 (m-30) REVERT: E1 277 MET cc_start: 0.8457 (tpt) cc_final: 0.7940 (tpt) REVERT: E1 316 TYR cc_start: 0.8739 (m-10) cc_final: 0.8403 (m-10) REVERT: F1 36 MET cc_start: 0.7440 (ttm) cc_final: 0.7225 (ttm) REVERT: F1 76 LEU cc_start: 0.7968 (pt) cc_final: 0.7742 (pp) REVERT: F1 82 ASN cc_start: 0.7917 (m-40) cc_final: 0.7410 (m110) REVERT: F1 175 TYR cc_start: 0.7769 (m-80) cc_final: 0.7225 (m-80) REVERT: F1 180 MET cc_start: 0.7942 (tpp) cc_final: 0.7395 (tpp) REVERT: F1 197 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: F1 269 ASN cc_start: 0.7834 (t0) cc_final: 0.7454 (t0) REVERT: F1 301 GLU cc_start: 0.7824 (mp0) cc_final: 0.7590 (mp0) REVERT: F1 316 TYR cc_start: 0.8876 (m-80) cc_final: 0.8289 (m-10) REVERT: F1 326 GLU cc_start: 0.8334 (pp20) cc_final: 0.7939 (pp20) REVERT: G1 25 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.6507 (ptm160) REVERT: G1 82 ASN cc_start: 0.7991 (m-40) cc_final: 0.7347 (m110) REVERT: G1 175 TYR cc_start: 0.8104 (m-80) cc_final: 0.7569 (m-80) REVERT: G1 197 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: G1 277 MET cc_start: 0.8368 (tpt) cc_final: 0.7965 (tpt) REVERT: G1 326 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7838 (pp20) REVERT: H1 82 ASN cc_start: 0.7531 (m-40) cc_final: 0.7322 (m110) REVERT: H1 171 GLU cc_start: 0.8157 (pt0) cc_final: 0.7424 (pt0) REVERT: H1 197 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: H1 316 TYR cc_start: 0.9020 (m-10) cc_final: 0.8582 (m-10) REVERT: H1 326 GLU cc_start: 0.7986 (pp20) cc_final: 0.7781 (pp20) REVERT: I1 21 MET cc_start: 0.8394 (mmt) cc_final: 0.8043 (mmt) REVERT: I1 82 ASN cc_start: 0.8264 (m-40) cc_final: 0.7827 (m110) REVERT: I1 175 TYR cc_start: 0.7977 (m-80) cc_final: 0.7618 (m-80) REVERT: I1 182 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8458 (mp0) REVERT: I1 197 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: I1 269 ASN cc_start: 0.8151 (t0) cc_final: 0.7876 (t0) REVERT: I1 326 GLU cc_start: 0.8222 (pp20) cc_final: 0.7861 (pp20) REVERT: J1 82 ASN cc_start: 0.8286 (m-40) cc_final: 0.7928 (m110) REVERT: J1 128 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6416 (mmtp) REVERT: J1 180 MET cc_start: 0.8069 (tpp) cc_final: 0.7851 (tpp) REVERT: J1 182 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7913 (mp0) REVERT: J1 197 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: J1 274 ARG cc_start: 0.8435 (tpp80) cc_final: 0.7883 (tpp80) REVERT: J1 316 TYR cc_start: 0.8660 (m-10) cc_final: 0.8327 (m-80) REVERT: K1 76 LEU cc_start: 0.8606 (pt) cc_final: 0.7973 (pp) REVERT: K1 180 MET cc_start: 0.7863 (tpp) cc_final: 0.7240 (tpp) REVERT: K1 187 TYR cc_start: 0.8513 (t80) cc_final: 0.8220 (t80) REVERT: K1 301 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7429 (mp0) REVERT: K1 326 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7808 (pp20) REVERT: L1 73 LYS cc_start: 0.7684 (tttp) cc_final: 0.7431 (ttmm) REVERT: L1 82 ASN cc_start: 0.8475 (m-40) cc_final: 0.8036 (m110) REVERT: L1 92 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7526 (tpp80) REVERT: L1 122 PHE cc_start: 0.8547 (m-80) cc_final: 0.8248 (m-80) REVERT: L1 180 MET cc_start: 0.7838 (tpp) cc_final: 0.7604 (tpp) REVERT: L1 197 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: L1 269 ASN cc_start: 0.8067 (t0) cc_final: 0.7867 (t0) REVERT: L1 334 GLU cc_start: 0.6578 (mp0) cc_final: 0.6241 (mp0) REVERT: A2 1 MET cc_start: 0.5838 (mmt) cc_final: 0.5157 (mmm) REVERT: A2 15 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: A2 41 ASP cc_start: 0.5730 (OUTLIER) cc_final: 0.5184 (t70) REVERT: A2 90 SER cc_start: 0.8739 (t) cc_final: 0.8436 (t) REVERT: A2 107 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7761 (mtp) REVERT: B2 15 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: B2 41 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5442 (t70) REVERT: B2 61 TYR cc_start: 0.8767 (t80) cc_final: 0.8541 (t80) REVERT: B2 90 SER cc_start: 0.8633 (t) cc_final: 0.8300 (t) REVERT: B2 117 PHE cc_start: 0.8075 (t80) cc_final: 0.7798 (t80) REVERT: C2 15 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: C2 28 ASN cc_start: 0.8111 (t0) cc_final: 0.7709 (t0) REVERT: C2 41 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5508 (t70) REVERT: C2 90 SER cc_start: 0.8596 (t) cc_final: 0.8250 (t) REVERT: C2 107 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: D2 1 MET cc_start: 0.5874 (mmt) cc_final: 0.5208 (mmm) REVERT: D2 15 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: D2 41 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.5338 (t70) REVERT: D2 90 SER cc_start: 0.8696 (t) cc_final: 0.8335 (t) REVERT: E2 15 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: E2 41 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5501 (t70) REVERT: E2 43 ASP cc_start: 0.7627 (t0) cc_final: 0.7369 (t70) REVERT: E2 90 SER cc_start: 0.8612 (t) cc_final: 0.8251 (t) REVERT: E2 107 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: F2 1 MET cc_start: 0.6134 (mmt) cc_final: 0.5397 (mmm) REVERT: F2 15 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: F2 41 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5439 (t70) REVERT: F2 43 ASP cc_start: 0.7453 (t0) cc_final: 0.7241 (t0) REVERT: F2 90 SER cc_start: 0.8541 (t) cc_final: 0.8187 (t) REVERT: F2 107 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: G2 1 MET cc_start: 0.5995 (mmt) cc_final: 0.5276 (mmm) REVERT: G2 15 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: G2 41 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.5598 (t70) REVERT: G2 90 SER cc_start: 0.8831 (t) cc_final: 0.8516 (t) REVERT: H2 1 MET cc_start: 0.5553 (mmt) cc_final: 0.4822 (mmt) REVERT: H2 15 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: H2 41 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5557 (t70) REVERT: H2 90 SER cc_start: 0.8611 (t) cc_final: 0.8275 (t) REVERT: I2 15 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: I2 28 ASN cc_start: 0.8168 (t0) cc_final: 0.7774 (t0) REVERT: I2 41 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5311 (t70) REVERT: I2 90 SER cc_start: 0.8690 (t) cc_final: 0.8348 (t) REVERT: J2 15 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: J2 41 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5465 (t70) REVERT: J2 43 ASP cc_start: 0.7971 (t70) cc_final: 0.7739 (t70) REVERT: J2 90 SER cc_start: 0.8683 (t) cc_final: 0.8349 (t) REVERT: K2 15 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: K2 41 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.5472 (t70) REVERT: K2 90 SER cc_start: 0.8538 (t) cc_final: 0.8201 (t) REVERT: K2 113 MET cc_start: 0.8245 (ttp) cc_final: 0.7959 (ttp) REVERT: L2 15 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: L2 28 ASN cc_start: 0.8309 (t0) cc_final: 0.7865 (t0) REVERT: L2 41 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5365 (t70) REVERT: L2 90 SER cc_start: 0.8658 (t) cc_final: 0.8329 (t) REVERT: L2 107 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7826 (mtp) outliers start: 250 outliers final: 170 residues processed: 1553 average time/residue: 0.2507 time to fit residues: 660.0717 Evaluate side-chains 1539 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1329 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 131 ASN Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 197 GLN Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 277 MET Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 148 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 94 VAL Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 287 ILE Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 126 ILE Chi-restraints excluded: chain D1 residue 140 ARG Chi-restraints excluded: chain D1 residue 148 THR Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 197 GLN Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain D1 residue 332 PHE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 117 LEU Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 87 MET Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 156 TRP Chi-restraints excluded: chain F1 residue 163 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain F1 residue 371 LEU Chi-restraints excluded: chain G1 residue 24 ASN Chi-restraints excluded: chain G1 residue 45 MET Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 156 TRP Chi-restraints excluded: chain G1 residue 182 GLU Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 128 LYS Chi-restraints excluded: chain H1 residue 140 ARG Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 78 LYS Chi-restraints excluded: chain I1 residue 94 VAL Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 148 THR Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 197 GLN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 242 ILE Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 78 LYS Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 140 ARG Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 148 THR Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain K1 residue 326 GLU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 159 VAL Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 197 GLN Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 30 TYR Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 84 VAL Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 30 TYR Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 30 TYR Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 91 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 15 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 15 ASP Chi-restraints excluded: chain G2 residue 30 TYR Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 98 SER Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 30 TYR Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 15 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 84 VAL Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 30 TYR Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain K2 residue 107 MET Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 30 TYR Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 84 VAL Chi-restraints excluded: chain L2 residue 107 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [360, 414, 169, 195, 260, 438, 322, 144, 313, 79, 50] chunk 360 optimal weight: 0.1980 chunk 414 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 438 optimal weight: 6.9990 chunk 322 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 313 GLN K1 24 ASN K1 82 ASN K1 197 GLN ** L1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 40 ASN ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2 112 ASN ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K2 28 ASN ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.163006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123714 restraints weight = 63845.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127844 restraints weight = 29847.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130393 restraints weight = 17496.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131969 restraints weight = 12133.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132932 restraints weight = 9588.977| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46368 Z= 0.159 Angle : 0.754 14.793 62544 Z= 0.376 Chirality : 0.045 0.184 6876 Planarity : 0.004 0.073 8064 Dihedral : 5.433 26.497 6336 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.72 % Allowed : 26.32 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.11), residues: 5676 helix: -0.02 (0.10), residues: 2460 sheet: 0.09 (0.29), residues: 312 loop : -1.50 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGA2 69 TYR 0.035 0.002 TYRB1 177 PHE 0.024 0.002 PHEH1 190 TRP 0.008 0.001 TRPG2 92 HIS 0.003 0.001 HISA1 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (46356) covalent geometry : angle 0.75320 / 0.38 (62520) SS BOND : bond 0.00088 / 0.05 ( 12) SS BOND : angle 1.67664 / 1.01 ( 24) hydrogen bonds : bond 0.03539 / 2.32 ( 1953) hydrogen bonds : angle 5.56426 / 3.86 ( 5541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1621 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 1385 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8571 (m-40) cc_final: 0.8181 (m110) REVERT: A1 87 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8108 (tpp) REVERT: A1 166 MET cc_start: 0.7659 (mtm) cc_final: 0.7146 (mtt) REVERT: A1 197 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: A1 274 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7422 (tpp80) REVERT: B1 21 MET cc_start: 0.8416 (tpp) cc_final: 0.7826 (mmt) REVERT: B1 48 ILE cc_start: 0.9474 (mm) cc_final: 0.9248 (tt) REVERT: B1 87 MET cc_start: 0.8447 (tpp) cc_final: 0.8118 (tpp) REVERT: B1 180 MET cc_start: 0.7897 (tpp) cc_final: 0.7431 (tpp) REVERT: B1 269 ASN cc_start: 0.7996 (t0) cc_final: 0.7778 (t0) REVERT: B1 277 MET cc_start: 0.8489 (tpt) cc_final: 0.7671 (tpt) REVERT: C1 45 MET cc_start: 0.8306 (mmm) cc_final: 0.7732 (ttm) REVERT: C1 76 LEU cc_start: 0.8633 (pt) cc_final: 0.8019 (pp) REVERT: C1 82 ASN cc_start: 0.8313 (m-40) cc_final: 0.7768 (m110) REVERT: C1 96 VAL cc_start: 0.8784 (t) cc_final: 0.8441 (m) REVERT: C1 180 MET cc_start: 0.7813 (tpp) cc_final: 0.7156 (tpp) REVERT: C1 182 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8539 (mm-30) REVERT: C1 273 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7575 (mmm-85) REVERT: C1 277 MET cc_start: 0.8549 (tpt) cc_final: 0.7966 (tpt) REVERT: C1 305 PHE cc_start: 0.8661 (p90) cc_final: 0.8420 (p90) REVERT: C1 326 GLU cc_start: 0.8207 (pp20) cc_final: 0.7955 (pp20) REVERT: D1 21 MET cc_start: 0.8509 (mmt) cc_final: 0.7989 (mmt) REVERT: D1 197 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: D1 269 ASN cc_start: 0.8015 (t0) cc_final: 0.7688 (t0) REVERT: D1 277 MET cc_start: 0.8467 (tpt) cc_final: 0.7991 (tpt) REVERT: D1 373 ASP cc_start: 0.6877 (t0) cc_final: 0.6655 (t0) REVERT: E1 45 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: E1 79 HIS cc_start: 0.7682 (m-70) cc_final: 0.7071 (t-90) REVERT: E1 103 ASP cc_start: 0.7689 (m-30) cc_final: 0.7487 (m-30) REVERT: E1 116 LEU cc_start: 0.8550 (mt) cc_final: 0.8334 (pp) REVERT: E1 175 TYR cc_start: 0.7839 (m-80) cc_final: 0.7452 (m-80) REVERT: E1 277 MET cc_start: 0.8510 (tpt) cc_final: 0.8022 (tpt) REVERT: E1 316 TYR cc_start: 0.8816 (m-10) cc_final: 0.8390 (m-10) REVERT: F1 25 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.6641 (ptt90) REVERT: F1 36 MET cc_start: 0.7379 (ttm) cc_final: 0.7100 (ttm) REVERT: F1 45 MET cc_start: 0.8590 (mmm) cc_final: 0.7899 (ttm) REVERT: F1 76 LEU cc_start: 0.7961 (pt) cc_final: 0.7648 (pp) REVERT: F1 82 ASN cc_start: 0.7916 (m-40) cc_final: 0.7389 (m110) REVERT: F1 175 TYR cc_start: 0.7666 (m-80) cc_final: 0.7318 (m-80) REVERT: F1 197 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: F1 301 GLU cc_start: 0.7869 (mp0) cc_final: 0.7635 (mp0) REVERT: F1 316 TYR cc_start: 0.8863 (m-80) cc_final: 0.8149 (m-10) REVERT: F1 326 GLU cc_start: 0.8363 (pp20) cc_final: 0.7993 (pp20) REVERT: F1 350 ASP cc_start: 0.8678 (t0) cc_final: 0.8454 (t0) REVERT: G1 82 ASN cc_start: 0.7976 (m-40) cc_final: 0.7317 (m110) REVERT: G1 171 GLU cc_start: 0.8404 (pt0) cc_final: 0.7356 (pt0) REVERT: G1 175 TYR cc_start: 0.8084 (m-80) cc_final: 0.7115 (m-80) REVERT: G1 182 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: G1 197 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: G1 277 MET cc_start: 0.8367 (tpt) cc_final: 0.7939 (tpt) REVERT: G1 326 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7877 (pp20) REVERT: H1 21 MET cc_start: 0.8517 (mmt) cc_final: 0.8064 (mmt) REVERT: H1 82 ASN cc_start: 0.7549 (m-40) cc_final: 0.7234 (m110) REVERT: H1 171 GLU cc_start: 0.8202 (pt0) cc_final: 0.7459 (pt0) REVERT: H1 176 TYR cc_start: 0.5004 (m-80) cc_final: 0.4801 (m-80) REVERT: H1 182 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8104 (mp0) REVERT: H1 197 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: H1 272 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8254 (mm) REVERT: H1 316 TYR cc_start: 0.8979 (m-10) cc_final: 0.8392 (m-10) REVERT: H1 326 GLU cc_start: 0.8008 (pp20) cc_final: 0.7770 (pp20) REVERT: I1 21 MET cc_start: 0.8430 (mmt) cc_final: 0.8136 (mmt) REVERT: I1 82 ASN cc_start: 0.8278 (m-40) cc_final: 0.7832 (m110) REVERT: I1 175 TYR cc_start: 0.8070 (m-80) cc_final: 0.7658 (m-80) REVERT: I1 197 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: I1 269 ASN cc_start: 0.8062 (t0) cc_final: 0.7620 (t0) REVERT: I1 273 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7260 (mmm-85) REVERT: I1 326 GLU cc_start: 0.8262 (pp20) cc_final: 0.7764 (pp20) REVERT: I1 373 ASP cc_start: 0.6800 (t0) cc_final: 0.6592 (t0) REVERT: J1 82 ASN cc_start: 0.8269 (m-40) cc_final: 0.7889 (m110) REVERT: J1 128 LYS cc_start: 0.6900 (ttmt) cc_final: 0.6315 (mmtp) REVERT: J1 180 MET cc_start: 0.8113 (tpp) cc_final: 0.7902 (tpp) REVERT: J1 182 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8014 (mp0) REVERT: J1 269 ASN cc_start: 0.8004 (t0) cc_final: 0.7788 (t0) REVERT: J1 274 ARG cc_start: 0.8340 (tpp80) cc_final: 0.7838 (tpp80) REVERT: J1 316 TYR cc_start: 0.8691 (m-10) cc_final: 0.8292 (m-80) REVERT: K1 76 LEU cc_start: 0.8587 (pt) cc_final: 0.7952 (pp) REVERT: K1 187 TYR cc_start: 0.8468 (t80) cc_final: 0.8208 (t80) REVERT: K1 301 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7456 (mp0) REVERT: K1 326 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7803 (pp20) REVERT: L1 73 LYS cc_start: 0.7680 (tttp) cc_final: 0.7429 (ttmm) REVERT: L1 82 ASN cc_start: 0.8474 (m-40) cc_final: 0.8002 (m110) REVERT: L1 92 ARG cc_start: 0.7746 (tpp80) cc_final: 0.7499 (tpp80) REVERT: L1 122 PHE cc_start: 0.8544 (m-80) cc_final: 0.8228 (m-80) REVERT: L1 180 MET cc_start: 0.7928 (tpp) cc_final: 0.7291 (tpp) REVERT: L1 197 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: L1 269 ASN cc_start: 0.8080 (t0) cc_final: 0.7858 (t0) REVERT: A2 1 MET cc_start: 0.5739 (mmt) cc_final: 0.5103 (mmm) REVERT: A2 15 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: A2 90 SER cc_start: 0.8770 (t) cc_final: 0.8459 (t) REVERT: A2 107 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7825 (mtp) REVERT: B2 15 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: B2 41 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5340 (t70) REVERT: B2 61 TYR cc_start: 0.8755 (t80) cc_final: 0.8518 (t80) REVERT: B2 90 SER cc_start: 0.8654 (t) cc_final: 0.8321 (t) REVERT: B2 117 PHE cc_start: 0.8093 (t80) cc_final: 0.7783 (t80) REVERT: C2 15 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: C2 28 ASN cc_start: 0.8081 (t0) cc_final: 0.7654 (t0) REVERT: C2 41 ASP cc_start: 0.5916 (OUTLIER) cc_final: 0.5569 (t70) REVERT: C2 90 SER cc_start: 0.8353 (t) cc_final: 0.8020 (t) REVERT: C2 107 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7702 (mtp) REVERT: D2 1 MET cc_start: 0.5644 (mmt) cc_final: 0.5016 (mmm) REVERT: D2 15 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: D2 41 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5321 (t70) REVERT: D2 90 SER cc_start: 0.8759 (t) cc_final: 0.8409 (t) REVERT: E2 15 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: E2 41 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5582 (t70) REVERT: E2 90 SER cc_start: 0.8648 (t) cc_final: 0.8302 (t) REVERT: E2 107 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7940 (mtp) REVERT: F2 1 MET cc_start: 0.6118 (mmt) cc_final: 0.5390 (mmm) REVERT: F2 15 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: F2 41 ASP cc_start: 0.5821 (OUTLIER) cc_final: 0.5438 (t70) REVERT: F2 90 SER cc_start: 0.8370 (t) cc_final: 0.8047 (t) REVERT: F2 107 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7705 (mtp) REVERT: G2 1 MET cc_start: 0.5930 (mmt) cc_final: 0.5257 (mmm) REVERT: G2 15 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: G2 41 ASP cc_start: 0.6057 (OUTLIER) cc_final: 0.5625 (t70) REVERT: G2 90 SER cc_start: 0.8807 (t) cc_final: 0.8521 (t) REVERT: H2 1 MET cc_start: 0.5562 (mmt) cc_final: 0.4862 (mmt) REVERT: H2 15 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: H2 41 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5558 (t70) REVERT: H2 90 SER cc_start: 0.8625 (t) cc_final: 0.8284 (t) REVERT: I2 1 MET cc_start: 0.6237 (mmt) cc_final: 0.5406 (mmm) REVERT: I2 15 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: I2 28 ASN cc_start: 0.8252 (t0) cc_final: 0.7888 (t0) REVERT: I2 41 ASP cc_start: 0.5624 (OUTLIER) cc_final: 0.5278 (t70) REVERT: I2 90 SER cc_start: 0.8503 (t) cc_final: 0.8196 (t) REVERT: J2 15 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: J2 41 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.5494 (t70) REVERT: J2 90 SER cc_start: 0.8710 (t) cc_final: 0.8384 (t) REVERT: K2 15 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: K2 28 ASN cc_start: 0.8006 (t0) cc_final: 0.7639 (t0) REVERT: K2 41 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5505 (t70) REVERT: K2 90 SER cc_start: 0.8601 (t) cc_final: 0.8268 (t) REVERT: K2 113 MET cc_start: 0.8340 (ttp) cc_final: 0.8032 (ttp) REVERT: L2 15 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: L2 28 ASN cc_start: 0.8321 (t0) cc_final: 0.8067 (t0) REVERT: L2 41 ASP cc_start: 0.5817 (OUTLIER) cc_final: 0.5384 (t70) REVERT: L2 90 SER cc_start: 0.8722 (t) cc_final: 0.8396 (t) outliers start: 236 outliers final: 169 residues processed: 1521 average time/residue: 0.2457 time to fit residues: 638.4087 Evaluate side-chains 1537 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1328 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 197 GLN Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 277 MET Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 148 THR Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 287 ILE Chi-restraints excluded: chain D1 residue 40 TYR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 126 ILE Chi-restraints excluded: chain D1 residue 140 ARG Chi-restraints excluded: chain D1 residue 148 THR Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 197 GLN Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain D1 residue 332 PHE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 117 LEU Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 87 MET Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 156 TRP Chi-restraints excluded: chain F1 residue 157 THR Chi-restraints excluded: chain F1 residue 163 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 45 MET Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 156 TRP Chi-restraints excluded: chain G1 residue 182 GLU Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 128 LYS Chi-restraints excluded: chain H1 residue 140 ARG Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 272 LEU Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain H1 residue 371 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 76 LEU Chi-restraints excluded: chain I1 residue 78 LYS Chi-restraints excluded: chain I1 residue 87 MET Chi-restraints excluded: chain I1 residue 94 VAL Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 148 THR Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 197 GLN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 242 ILE Chi-restraints excluded: chain I1 residue 273 ARG Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 78 LYS Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 140 ARG Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 148 THR Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain K1 residue 326 GLU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 159 VAL Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 197 GLN Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain L1 residue 318 GLU Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 91 ASP Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 30 TYR Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 91 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 30 TYR Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 15 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 15 ASP Chi-restraints excluded: chain G2 residue 30 TYR Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain I2 residue 15 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 30 TYR Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain K2 residue 107 MET Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [408, 45, 119, 552, 291, 65, 282, 175, 463, 322, 281] chunk 408 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 552 optimal weight: 0.2980 chunk 291 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 282 optimal weight: 7.9990 chunk 175 optimal weight: 0.0070 chunk 463 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 24 ASN ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 82 ASN ** L1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 28 ASN ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 112 ASN ** 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 = 0.3736 r_free = 0.3736 target = 0.163398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.124096 restraints weight = 64252.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.128240 restraints weight = 29971.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.130789 restraints weight = 17593.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132343 restraints weight = 12209.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.133375 restraints weight = 9649.626| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46368 Z= 0.164 Angle : 0.764 16.541 62544 Z= 0.381 Chirality : 0.045 0.359 6876 Planarity : 0.004 0.060 8064 Dihedral : 5.433 26.603 6336 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.40 % Allowed : 26.86 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.11), residues: 5676 helix: -0.11 (0.10), residues: 2520 sheet: 0.12 (0.30), residues: 312 loop : -1.70 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGG2 69 TYR 0.033 0.002 TYRJ1 177 PHE 0.024 0.002 PHEH1 190 TRP 0.008 0.001 TRPK1 361 HIS 0.002 0.001 HISB1 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (46356) covalent geometry : angle 0.76397 / 0.38 (62520) SS BOND : bond 0.00269 / 0.14 ( 12) SS BOND : angle 1.63049 / 0.99 ( 24) hydrogen bonds : bond 0.03547 / 2.33 ( 1953) hydrogen bonds : angle 5.56227 / 3.85 ( 5541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1363 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8527 (m-40) cc_final: 0.8183 (m110) REVERT: A1 87 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7912 (tpp) REVERT: A1 269 ASN cc_start: 0.7919 (t0) cc_final: 0.7587 (t0) REVERT: A1 274 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7521 (tpp80) REVERT: B1 21 MET cc_start: 0.8388 (tpp) cc_final: 0.7828 (mmt) REVERT: B1 48 ILE cc_start: 0.9504 (mm) cc_final: 0.9241 (tt) REVERT: B1 87 MET cc_start: 0.8460 (tpp) cc_final: 0.8111 (tpp) REVERT: B1 96 VAL cc_start: 0.8880 (t) cc_final: 0.8574 (m) REVERT: B1 175 TYR cc_start: 0.7407 (m-80) cc_final: 0.7168 (m-80) REVERT: B1 269 ASN cc_start: 0.7998 (t0) cc_final: 0.7766 (t0) REVERT: B1 277 MET cc_start: 0.8515 (tpt) cc_final: 0.7722 (tpt) REVERT: C1 76 LEU cc_start: 0.8642 (pt) cc_final: 0.8021 (pp) REVERT: C1 82 ASN cc_start: 0.8268 (m-40) cc_final: 0.7710 (m110) REVERT: C1 180 MET cc_start: 0.7905 (tpp) cc_final: 0.7303 (tpp) REVERT: C1 182 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C1 273 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7589 (mmm-85) REVERT: C1 277 MET cc_start: 0.8566 (tpt) cc_final: 0.7987 (tpt) REVERT: C1 318 GLU cc_start: 0.7894 (tt0) cc_final: 0.7600 (mt-10) REVERT: D1 197 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: D1 269 ASN cc_start: 0.8032 (t0) cc_final: 0.7703 (t0) REVERT: D1 277 MET cc_start: 0.8461 (tpt) cc_final: 0.7986 (tpt) REVERT: D1 373 ASP cc_start: 0.6870 (t0) cc_final: 0.6669 (t0) REVERT: E1 45 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7554 (ttm) REVERT: E1 79 HIS cc_start: 0.7657 (m-70) cc_final: 0.7042 (t-90) REVERT: E1 103 ASP cc_start: 0.7709 (m-30) cc_final: 0.7507 (m-30) REVERT: E1 166 MET cc_start: 0.7478 (mtm) cc_final: 0.7009 (mtt) REVERT: E1 171 GLU cc_start: 0.8471 (pt0) cc_final: 0.7743 (pt0) REVERT: E1 174 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8238 (t0) REVERT: E1 175 TYR cc_start: 0.7858 (m-80) cc_final: 0.7303 (m-80) REVERT: E1 277 MET cc_start: 0.8511 (tpt) cc_final: 0.7989 (tpt) REVERT: E1 301 GLU cc_start: 0.7861 (mp0) cc_final: 0.7587 (mp0) REVERT: E1 316 TYR cc_start: 0.8791 (m-10) cc_final: 0.8374 (m-10) REVERT: F1 25 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.6717 (ptt90) REVERT: F1 36 MET cc_start: 0.7420 (ttm) cc_final: 0.7185 (ttm) REVERT: F1 76 LEU cc_start: 0.7952 (pt) cc_final: 0.7642 (pp) REVERT: F1 82 ASN cc_start: 0.7953 (m-40) cc_final: 0.7423 (m110) REVERT: F1 165 TYR cc_start: 0.8259 (t80) cc_final: 0.7989 (t80) REVERT: F1 175 TYR cc_start: 0.7654 (m-80) cc_final: 0.7314 (m-80) REVERT: F1 197 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: F1 301 GLU cc_start: 0.7890 (mp0) cc_final: 0.7654 (mp0) REVERT: F1 316 TYR cc_start: 0.8853 (m-80) cc_final: 0.8112 (m-10) REVERT: G1 25 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.6547 (ptm160) REVERT: G1 82 ASN cc_start: 0.8022 (m-40) cc_final: 0.7366 (m110) REVERT: G1 171 GLU cc_start: 0.8420 (pt0) cc_final: 0.7295 (pt0) REVERT: G1 197 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: G1 277 MET cc_start: 0.8385 (tpt) cc_final: 0.7926 (tpt) REVERT: G1 326 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7875 (pp20) REVERT: H1 21 MET cc_start: 0.8475 (mmt) cc_final: 0.8093 (mmt) REVERT: H1 82 ASN cc_start: 0.7634 (m-40) cc_final: 0.7343 (m110) REVERT: H1 171 GLU cc_start: 0.8188 (pt0) cc_final: 0.7443 (pt0) REVERT: H1 182 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8211 (mp0) REVERT: H1 197 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: H1 316 TYR cc_start: 0.8948 (m-10) cc_final: 0.8439 (m-10) REVERT: H1 326 GLU cc_start: 0.7993 (pp20) cc_final: 0.7758 (pp20) REVERT: I1 21 MET cc_start: 0.8412 (mmt) cc_final: 0.7974 (mmt) REVERT: I1 82 ASN cc_start: 0.8303 (m-40) cc_final: 0.7897 (m110) REVERT: I1 175 TYR cc_start: 0.8131 (m-80) cc_final: 0.7682 (m-80) REVERT: I1 197 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: I1 269 ASN cc_start: 0.8043 (t0) cc_final: 0.7765 (t0) REVERT: I1 326 GLU cc_start: 0.8267 (pp20) cc_final: 0.7950 (pp20) REVERT: J1 82 ASN cc_start: 0.8293 (m-40) cc_final: 0.7894 (m110) REVERT: J1 116 LEU cc_start: 0.8532 (mt) cc_final: 0.8244 (pp) REVERT: J1 128 LYS cc_start: 0.6944 (ttmt) cc_final: 0.6481 (mmtp) REVERT: J1 175 TYR cc_start: 0.7650 (m-80) cc_final: 0.6637 (m-80) REVERT: J1 182 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8023 (mp0) REVERT: J1 269 ASN cc_start: 0.8006 (t0) cc_final: 0.7792 (t0) REVERT: J1 274 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7825 (tpp80) REVERT: J1 316 TYR cc_start: 0.8708 (m-10) cc_final: 0.8333 (m-80) REVERT: K1 76 LEU cc_start: 0.8559 (pt) cc_final: 0.7902 (pp) REVERT: K1 187 TYR cc_start: 0.8573 (t80) cc_final: 0.8271 (t80) REVERT: K1 326 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7817 (pp20) REVERT: L1 73 LYS cc_start: 0.7731 (tttp) cc_final: 0.7486 (ttmm) REVERT: L1 82 ASN cc_start: 0.8421 (m-40) cc_final: 0.7965 (m110) REVERT: L1 92 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7525 (tpp80) REVERT: L1 180 MET cc_start: 0.7929 (tpp) cc_final: 0.7301 (tpp) REVERT: L1 182 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8478 (mm-30) REVERT: L1 197 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: L1 269 ASN cc_start: 0.8061 (t0) cc_final: 0.7849 (t0) REVERT: L1 307 ASP cc_start: 0.7968 (p0) cc_final: 0.7555 (t70) REVERT: A2 1 MET cc_start: 0.5728 (mmt) cc_final: 0.5157 (mmm) REVERT: A2 15 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: A2 90 SER cc_start: 0.8771 (t) cc_final: 0.8464 (t) REVERT: A2 107 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7698 (mtp) REVERT: B2 15 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: B2 41 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.5328 (t70) REVERT: B2 61 TYR cc_start: 0.8751 (t80) cc_final: 0.8517 (t80) REVERT: B2 90 SER cc_start: 0.8456 (t) cc_final: 0.8138 (t) REVERT: B2 117 PHE cc_start: 0.7996 (t80) cc_final: 0.7738 (t80) REVERT: C2 15 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: C2 28 ASN cc_start: 0.8061 (t0) cc_final: 0.7650 (t0) REVERT: C2 41 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5483 (t70) REVERT: C2 90 SER cc_start: 0.8516 (t) cc_final: 0.8190 (t) REVERT: C2 107 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: D2 1 MET cc_start: 0.5618 (mmt) cc_final: 0.5061 (mmm) REVERT: D2 15 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: D2 41 ASP cc_start: 0.5759 (OUTLIER) cc_final: 0.5344 (t70) REVERT: D2 90 SER cc_start: 0.8766 (t) cc_final: 0.8428 (t) REVERT: E2 15 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: E2 41 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5568 (t70) REVERT: E2 90 SER cc_start: 0.8441 (t) cc_final: 0.8125 (t) REVERT: E2 107 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7892 (mtp) REVERT: F2 1 MET cc_start: 0.6012 (mmt) cc_final: 0.5260 (mmm) REVERT: F2 15 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: F2 41 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5370 (t70) REVERT: F2 90 SER cc_start: 0.8528 (t) cc_final: 0.8191 (t) REVERT: F2 107 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7713 (mtp) REVERT: G2 1 MET cc_start: 0.5797 (mmt) cc_final: 0.5105 (mmm) REVERT: G2 15 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: G2 41 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5623 (t70) REVERT: G2 90 SER cc_start: 0.8846 (t) cc_final: 0.8557 (t) REVERT: H2 1 MET cc_start: 0.5527 (mmt) cc_final: 0.4897 (mmt) REVERT: H2 15 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: H2 41 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5576 (t70) REVERT: H2 90 SER cc_start: 0.8471 (t) cc_final: 0.8164 (t) REVERT: I2 1 MET cc_start: 0.6216 (mmt) cc_final: 0.5390 (mmm) REVERT: I2 15 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: I2 28 ASN cc_start: 0.8234 (t0) cc_final: 0.7857 (t0) REVERT: I2 41 ASP cc_start: 0.5650 (OUTLIER) cc_final: 0.5302 (t70) REVERT: I2 90 SER cc_start: 0.8615 (t) cc_final: 0.8313 (t) REVERT: J2 15 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: J2 41 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5519 (t70) REVERT: J2 90 SER cc_start: 0.8737 (t) cc_final: 0.8409 (t) REVERT: K2 15 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: K2 28 ASN cc_start: 0.7981 (t0) cc_final: 0.7660 (t0) REVERT: K2 41 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.5499 (t70) REVERT: K2 90 SER cc_start: 0.8413 (t) cc_final: 0.8108 (t) REVERT: K2 113 MET cc_start: 0.8187 (ttp) cc_final: 0.7889 (ttp) REVERT: L2 15 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: L2 28 ASN cc_start: 0.8379 (t0) cc_final: 0.8107 (t0) REVERT: L2 41 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5380 (t70) REVERT: L2 90 SER cc_start: 0.8535 (t) cc_final: 0.8225 (t) outliers start: 220 outliers final: 167 residues processed: 1489 average time/residue: 0.2468 time to fit residues: 627.7712 Evaluate side-chains 1547 residues out of total 5004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1343 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 87 MET Chi-restraints excluded: chain A1 residue 117 LEU Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 197 GLN Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 148 THR Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 197 GLN Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 287 ILE Chi-restraints excluded: chain D1 residue 40 TYR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 126 ILE Chi-restraints excluded: chain D1 residue 140 ARG Chi-restraints excluded: chain D1 residue 148 THR Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 197 GLN Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain D1 residue 332 PHE Chi-restraints excluded: chain E1 residue 24 ASN Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 117 LEU Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 163 THR Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 87 MET Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 156 TRP Chi-restraints excluded: chain F1 residue 157 THR Chi-restraints excluded: chain F1 residue 163 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 156 TRP Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 128 LYS Chi-restraints excluded: chain H1 residue 140 ARG Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain H1 residue 371 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 76 LEU Chi-restraints excluded: chain I1 residue 87 MET Chi-restraints excluded: chain I1 residue 94 VAL Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 148 THR Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 197 GLN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 242 ILE Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 78 LYS Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 140 ARG Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 88 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 148 THR Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 163 THR Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain K1 residue 326 GLU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 159 VAL Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 197 GLN Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 91 ASP Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 30 TYR Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 91 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 15 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 15 ASP Chi-restraints excluded: chain G2 residue 30 TYR Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 98 SER Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain I2 residue 15 ASP Chi-restraints excluded: chain I2 residue 30 TYR Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 30 TYR Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 15 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 79 VAL Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain K2 residue 107 MET Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [450, 359, 141, 496, 48, 384, 298, 437, 79, 129, 284] chunk 450 optimal weight: 3.9990 chunk 359 optimal weight: 0.0370 chunk 141 optimal weight: 6.9990 chunk 496 optimal weight: 0.9990 chunk 48 optimal weight: 0.0020 chunk 384 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 chunk 437 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 284 optimal weight: 0.3980 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1 24 ASN ** C1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 28 ASN ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2 112 ASN ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 112 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.163524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.124253 restraints weight = 63955.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.128414 restraints weight = 29846.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.130981 restraints weight = 17504.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.132604 restraints weight = 12145.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.133587 restraints weight = 9558.761| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.274 46368 Z= 0.193 Angle : 0.833 59.197 62544 Z= 0.429 Chirality : 0.046 0.727 6876 Planarity : 0.004 0.112 8064 Dihedral : 5.441 26.110 6336 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.28 % Allowed : 27.42 % Favored : 68.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.11), residues: 5676 helix: -0.11 (0.10), residues: 2520 sheet: 0.12 (0.30), residues: 312 loop : -1.71 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGG2 100 TYR 0.045 0.002 TYRE1 55 PHE 0.046 0.002 PHEF1 305 TRP 0.007 0.001 TRPG2 92 HIS 0.003 0.001 HISB1 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (46356) covalent geometry : angle 0.83279 / 0.43 (62520) SS BOND : bond 0.00102 / 0.05 ( 12) SS BOND : angle 1.57548 / 0.95 ( 24) hydrogen bonds : bond 0.03553 / 2.33 ( 1953) hydrogen bonds : angle 5.56645 / 3.86 ( 5541) =============================================================================== Job complete usr+sys time: 12414.83 seconds wall clock time: 213 minutes 30.40 seconds (12810.40 seconds total)