Starting phenix.real_space_refine on Tue Nov 18 17:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g8z_4362/11_2025/6g8z_4362.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g8z_4362/11_2025/6g8z_4362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6g8z_4362/11_2025/6g8z_4362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g8z_4362/11_2025/6g8z_4362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6g8z_4362/11_2025/6g8z_4362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g8z_4362/11_2025/6g8z_4362.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 102 5.16 5 C 10530 2.51 5 N 2562 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.70, per 1000 atoms: 0.17 Number of scatterers: 15966 At special positions: 0 Unit cell: (104.275, 104.275, 132.225, 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 102 16.00 O 2772 8.00 N 2562 7.00 C 10530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 864.6 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3708 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 74.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 22 through 50 Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.627A pdb=" N TYR A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.631A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 5.398A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 286 removed outlier: 4.188A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.736A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.773A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.627A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 146 removed outlier: 3.630A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 5.398A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 4.028A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 286 removed outlier: 4.189A pdb=" N ARG B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 404 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.627A pdb=" N TYR C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.630A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 5.399A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.982A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 removed outlier: 4.028A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 4.189A pdb=" N ARG C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.686A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 50 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.626A pdb=" N TYR D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.631A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.399A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.982A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 4.188A pdb=" N ARG D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 395 removed outlier: 3.773A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 404 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 50 Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.628A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.632A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 5.398A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.560A pdb=" N GLU E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 4.189A pdb=" N ARG E 262 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU E 394 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 404 " --> pdb=" O ASN E 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 50 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.626A pdb=" N TYR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.631A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 5.398A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 removed outlier: 3.560A pdb=" N GLU F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 286 removed outlier: 4.190A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.738A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU F 394 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 removed outlier: 3.676A pdb=" N GLU F 399 " --> pdb=" O SER F 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 404 " --> pdb=" O ASN F 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 8.829A pdb=" N ARG A 306 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 297 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 8.828A pdb=" N ARG B 306 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 297 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 removed outlier: 8.828A pdb=" N ARG C 306 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 297 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 removed outlier: 8.827A pdb=" N ARG D 306 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 297 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 56 removed outlier: 8.828A pdb=" N ARG E 306 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL E 297 " --> pdb=" O ARG E 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 removed outlier: 8.829A pdb=" N ARG F 306 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL F 297 " --> pdb=" O ARG F 306 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4752 1.34 - 1.46: 4260 1.46 - 1.58: 7260 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 16416 Sorted by residual: bond pdb=" N ASP B 50 " pdb=" CA ASP B 50 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.00e+00 bond pdb=" N ASP E 50 " pdb=" CA ASP E 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.91e+00 bond pdb=" N ASP F 50 " pdb=" CA ASP F 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.88e+00 bond pdb=" N ASP D 50 " pdb=" CA ASP D 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.82e+00 bond pdb=" N ASP C 50 " pdb=" CA ASP C 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.81e+00 ... (remaining 16411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 21201 1.62 - 3.25: 854 3.25 - 4.87: 151 4.87 - 6.49: 12 6.49 - 8.12: 12 Bond angle restraints: 22230 Sorted by residual: angle pdb=" N ASP E 371 " pdb=" CA ASP E 371 " pdb=" CB ASP E 371 " ideal model delta sigma weight residual 114.17 110.18 3.99 1.14e+00 7.69e-01 1.22e+01 angle pdb=" N ASP C 371 " pdb=" CA ASP C 371 " pdb=" CB ASP C 371 " ideal model delta sigma weight residual 114.17 110.20 3.97 1.14e+00 7.69e-01 1.21e+01 angle pdb=" N ASP D 371 " pdb=" CA ASP D 371 " pdb=" CB ASP D 371 " ideal model delta sigma weight residual 114.17 110.22 3.95 1.14e+00 7.69e-01 1.20e+01 angle pdb=" N ASP B 371 " pdb=" CA ASP B 371 " pdb=" CB ASP B 371 " ideal model delta sigma weight residual 114.17 110.23 3.94 1.14e+00 7.69e-01 1.19e+01 angle pdb=" N ASP F 371 " pdb=" CA ASP F 371 " pdb=" CB ASP F 371 " ideal model delta sigma weight residual 114.17 110.24 3.93 1.14e+00 7.69e-01 1.19e+01 ... (remaining 22225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 9252 16.16 - 32.31: 342 32.31 - 48.47: 78 48.47 - 64.63: 0 64.63 - 80.79: 6 Dihedral angle restraints: 9678 sinusoidal: 3948 harmonic: 5730 Sorted by residual: dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 65 " pdb=" CB CYS A 65 " ideal model delta sinusoidal sigma weight residual 93.00 173.76 -80.76 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2078 0.061 - 0.123: 340 0.123 - 0.184: 24 0.184 - 0.245: 0 0.245 - 0.307: 6 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CB THR D 92 " pdb=" CA THR D 92 " pdb=" OG1 THR D 92 " pdb=" CG2 THR D 92 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB THR F 92 " pdb=" CA THR F 92 " pdb=" OG1 THR F 92 " pdb=" CG2 THR F 92 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB THR B 92 " pdb=" CA THR B 92 " pdb=" OG1 THR B 92 " pdb=" CG2 THR B 92 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2445 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 21 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO E 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 22 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 22 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO D 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO F 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.033 5.00e-02 4.00e+02 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5319 2.87 - 3.38: 16657 3.38 - 3.88: 24681 3.88 - 4.39: 26984 4.39 - 4.90: 47089 Nonbonded interactions: 120730 Sorted by model distance: nonbonded pdb=" OE2 GLU A 115 " pdb=" OG1 THR B 316 " model vdw 2.362 3.040 nonbonded pdb=" O PHE B 324 " pdb=" OG SER B 327 " model vdw 2.403 3.040 nonbonded pdb=" O PHE D 324 " pdb=" OG SER D 327 " model vdw 2.404 3.040 nonbonded pdb=" O PHE A 324 " pdb=" OG SER A 327 " model vdw 2.404 3.040 nonbonded pdb=" O PHE E 324 " pdb=" OG SER E 327 " model vdw 2.404 3.040 ... (remaining 120725 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.005 0.039 16434 Z= 0.233 Angle : 0.774 8.118 22266 Z= 0.432 Chirality : 0.045 0.307 2448 Planarity : 0.005 0.060 2688 Dihedral : 8.701 44.834 5916 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.18), residues: 1872 helix: -0.18 (0.12), residues: 1266 sheet: 1.28 (0.47), residues: 96 loop : -1.02 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 262 TYR 0.010 0.002 TYR C 106 PHE 0.040 0.003 PHE E 136 TRP 0.025 0.002 TRP E 24 HIS 0.011 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00516 (16416) covalent geometry : angle 0.77352 (22230) SS BOND : bond 0.00274 ( 18) SS BOND : angle 0.97668 ( 36) hydrogen bonds : bond 0.13840 ( 1038) hydrogen bonds : angle 5.19829 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 ASP cc_start: 0.7993 (t70) cc_final: 0.7793 (t0) REVERT: B 383 ASP cc_start: 0.7829 (t0) cc_final: 0.7401 (p0) REVERT: C 154 GLU cc_start: 0.7389 (pp20) cc_final: 0.7173 (pp20) REVERT: C 383 ASP cc_start: 0.8136 (t0) cc_final: 0.7300 (p0) REVERT: D 154 GLU cc_start: 0.7433 (pp20) cc_final: 0.7123 (pp20) REVERT: D 383 ASP cc_start: 0.8050 (t0) cc_final: 0.7288 (p0) REVERT: E 33 ILE cc_start: 0.8471 (mm) cc_final: 0.8181 (mm) REVERT: E 102 ASP cc_start: 0.7869 (m-30) cc_final: 0.7588 (p0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1042 time to fit residues: 41.4314 Evaluate side-chains 128 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 267 GLN A 404 GLN A 406 ASN B 267 GLN B 404 GLN C 267 GLN C 404 GLN D 267 GLN D 406 ASN E 267 GLN E 406 ASN F 239 GLN F 267 GLN F 404 GLN F 406 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099671 restraints weight = 28882.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102734 restraints weight = 12031.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104580 restraints weight = 6796.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105689 restraints weight = 4870.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106296 restraints weight = 4056.678| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16434 Z= 0.125 Angle : 0.508 5.271 22266 Z= 0.288 Chirality : 0.039 0.151 2448 Planarity : 0.004 0.054 2688 Dihedral : 4.283 19.342 2112 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 5.03 % Favored : 94.07 % 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 (0.19), residues: 1872 helix: 1.51 (0.14), residues: 1290 sheet: 1.50 (0.52), residues: 102 loop : -1.18 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.018 0.001 TYR E 281 PHE 0.021 0.002 PHE A 136 TRP 0.020 0.002 TRP F 24 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00245 (16416) covalent geometry : angle 0.50742 (22230) SS BOND : bond 0.00187 ( 18) SS BOND : angle 0.91647 ( 36) hydrogen bonds : bond 0.04678 ( 1038) hydrogen bonds : angle 3.90144 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7540 (mm110) REVERT: A 353 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6275 (t80) REVERT: B 353 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6659 (t80) REVERT: B 404 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8502 (mm110) REVERT: C 110 ASP cc_start: 0.7911 (t0) cc_final: 0.7691 (t0) REVERT: C 154 GLU cc_start: 0.7457 (pp20) cc_final: 0.7184 (pp20) REVERT: C 353 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6551 (t80) REVERT: D 154 GLU cc_start: 0.7442 (pp20) cc_final: 0.7167 (pp20) REVERT: E 404 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8391 (mm110) REVERT: F 110 ASP cc_start: 0.7840 (t0) cc_final: 0.7591 (t0) outliers start: 16 outliers final: 4 residues processed: 186 average time/residue: 0.0997 time to fit residues: 30.3533 Evaluate side-chains 133 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 404 GLN E 288 ASN F 288 ASN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096454 restraints weight = 29316.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099513 restraints weight = 12276.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101385 restraints weight = 6974.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102475 restraints weight = 4999.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103077 restraints weight = 4174.967| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16434 Z= 0.112 Angle : 0.462 5.015 22266 Z= 0.260 Chirality : 0.037 0.154 2448 Planarity : 0.003 0.052 2688 Dihedral : 4.006 18.049 2112 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.02 % Allowed : 9.32 % Favored : 89.66 % 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: 1.88 (0.20), residues: 1872 helix: 1.98 (0.14), residues: 1302 sheet: 1.91 (0.55), residues: 102 loop : -1.05 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 403 TYR 0.017 0.001 TYR E 281 PHE 0.015 0.001 PHE A 136 TRP 0.015 0.001 TRP C 24 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00224 (16416) covalent geometry : angle 0.46173 (22230) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.70324 ( 36) hydrogen bonds : bond 0.04250 ( 1038) hydrogen bonds : angle 3.70646 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7575 (mm110) REVERT: A 353 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6436 (t80) REVERT: B 353 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7055 (t80) REVERT: C 154 GLU cc_start: 0.7572 (pp20) cc_final: 0.7320 (pp20) REVERT: C 353 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6773 (t80) REVERT: D 154 GLU cc_start: 0.7502 (pp20) cc_final: 0.7245 (pp20) REVERT: E 353 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6763 (t80) REVERT: F 37 MET cc_start: 0.8203 (mtp) cc_final: 0.7996 (ttm) REVERT: F 353 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6978 (t80) outliers start: 18 outliers final: 6 residues processed: 171 average time/residue: 0.1030 time to fit residues: 28.5861 Evaluate side-chains 148 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 175 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN D 267 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084936 restraints weight = 30312.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087858 restraints weight = 13383.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089652 restraints weight = 7865.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090730 restraints weight = 5727.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091188 restraints weight = 4815.151| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16434 Z= 0.173 Angle : 0.526 7.889 22266 Z= 0.294 Chirality : 0.040 0.153 2448 Planarity : 0.004 0.050 2688 Dihedral : 4.150 19.777 2112 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.15 % Allowed : 11.41 % Favored : 86.44 % 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: 1.98 (0.20), residues: 1872 helix: 2.02 (0.14), residues: 1308 sheet: 1.53 (0.55), residues: 108 loop : -0.87 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 266 TYR 0.015 0.002 TYR B 281 PHE 0.018 0.002 PHE F 353 TRP 0.022 0.002 TRP F 143 HIS 0.006 0.002 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.00394 (16416) covalent geometry : angle 0.52491 (22230) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.82743 ( 36) hydrogen bonds : bond 0.05523 ( 1038) hydrogen bonds : angle 3.89412 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.648 Fit side-chains REVERT: A 265 MET cc_start: 0.8366 (mmm) cc_final: 0.7718 (mmm) REVERT: A 343 MET cc_start: 0.9031 (ttp) cc_final: 0.8597 (ttm) REVERT: A 353 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 104 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.7589 (t-90) REVERT: B 353 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7257 (t80) REVERT: C 353 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6967 (t80) REVERT: D 265 MET cc_start: 0.8293 (mmm) cc_final: 0.7571 (mmm) REVERT: D 343 MET cc_start: 0.9002 (ttp) cc_final: 0.8578 (ttm) REVERT: D 353 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.6657 (t80) REVERT: E 104 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.7862 (t-90) REVERT: E 238 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8245 (tm-30) REVERT: E 239 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7489 (mm110) REVERT: E 353 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7384 (t80) REVERT: F 353 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6947 (t80) outliers start: 38 outliers final: 14 residues processed: 173 average time/residue: 0.1046 time to fit residues: 29.5845 Evaluate side-chains 140 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 174 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN D 267 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081251 restraints weight = 30785.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.084053 restraints weight = 13733.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.085845 restraints weight = 8183.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.086898 restraints weight = 5987.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087458 restraints weight = 5045.696| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16434 Z= 0.209 Angle : 0.574 9.420 22266 Z= 0.311 Chirality : 0.041 0.153 2448 Planarity : 0.003 0.048 2688 Dihedral : 4.239 19.542 2112 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.09 % Allowed : 13.95 % Favored : 83.95 % 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: 1.87 (0.19), residues: 1872 helix: 1.94 (0.14), residues: 1302 sheet: 1.52 (0.53), residues: 108 loop : -0.88 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 262 TYR 0.015 0.002 TYR E 281 PHE 0.019 0.002 PHE F 353 TRP 0.019 0.002 TRP D 143 HIS 0.006 0.002 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.00487 (16416) covalent geometry : angle 0.57337 (22230) SS BOND : bond 0.00214 ( 18) SS BOND : angle 0.86072 ( 36) hydrogen bonds : bond 0.05713 ( 1038) hydrogen bonds : angle 4.00764 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 265 MET cc_start: 0.8384 (mmm) cc_final: 0.7453 (mmm) REVERT: A 343 MET cc_start: 0.9030 (ttp) cc_final: 0.8455 (ttm) REVERT: A 353 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.6808 (t80) REVERT: B 104 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.7604 (t-90) REVERT: B 353 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7549 (t80) REVERT: C 353 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7159 (t80) REVERT: C 375 MET cc_start: 0.8384 (mtt) cc_final: 0.8184 (mtt) REVERT: D 265 MET cc_start: 0.8353 (mmm) cc_final: 0.7430 (mmm) REVERT: D 343 MET cc_start: 0.9036 (ttp) cc_final: 0.8507 (ttm) REVERT: D 353 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.6886 (t80) REVERT: E 104 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.7702 (t-90) REVERT: E 238 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8457 (tm-30) REVERT: E 239 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7745 (mm110) REVERT: E 353 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7433 (t80) REVERT: F 353 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7088 (t80) outliers start: 37 outliers final: 26 residues processed: 159 average time/residue: 0.1050 time to fit residues: 27.2600 Evaluate side-chains 150 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN E 404 GLN F 239 GLN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085198 restraints weight = 30555.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088128 restraints weight = 13419.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089962 restraints weight = 7918.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.091017 restraints weight = 5764.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091496 restraints weight = 4858.222| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16434 Z= 0.118 Angle : 0.493 8.907 22266 Z= 0.268 Chirality : 0.038 0.147 2448 Planarity : 0.003 0.048 2688 Dihedral : 4.004 17.370 2112 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.36 % Allowed : 15.54 % Favored : 83.11 % 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: 2.06 (0.19), residues: 1872 helix: 2.09 (0.14), residues: 1302 sheet: 1.60 (0.53), residues: 108 loop : -0.85 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 306 TYR 0.011 0.001 TYR B 281 PHE 0.014 0.001 PHE F 353 TRP 0.012 0.001 TRP F 341 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00250 (16416) covalent geometry : angle 0.49248 (22230) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.65947 ( 36) hydrogen bonds : bond 0.04458 ( 1038) hydrogen bonds : angle 3.73135 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6481 (t80) REVERT: B 104 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.7163 (t-90) REVERT: B 353 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7460 (t80) REVERT: C 353 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7071 (t80) REVERT: D 353 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.6801 (t80) REVERT: E 104 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: E 238 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8345 (tm-30) REVERT: E 239 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7728 (mm110) REVERT: E 353 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7391 (t80) REVERT: F 37 MET cc_start: 0.8353 (mtp) cc_final: 0.8132 (ttm) REVERT: F 239 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7859 (mm110) REVERT: F 353 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7003 (t80) outliers start: 24 outliers final: 14 residues processed: 165 average time/residue: 0.1032 time to fit residues: 27.9879 Evaluate side-chains 150 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 124 optimal weight: 0.0980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 404 GLN C 288 ASN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084770 restraints weight = 30432.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087675 restraints weight = 13307.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.089477 restraints weight = 7822.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.090518 restraints weight = 5705.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090859 restraints weight = 4812.395| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16434 Z= 0.128 Angle : 0.496 8.567 22266 Z= 0.271 Chirality : 0.038 0.144 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.938 16.999 2112 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.47 % Allowed : 16.16 % Favored : 82.37 % 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: 2.16 (0.19), residues: 1872 helix: 2.10 (0.14), residues: 1308 sheet: 2.29 (0.51), residues: 102 loop : -0.75 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 306 TYR 0.011 0.001 TYR B 281 PHE 0.017 0.001 PHE D 136 TRP 0.011 0.001 TRP F 341 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00281 (16416) covalent geometry : angle 0.49589 (22230) SS BOND : bond 0.00184 ( 18) SS BOND : angle 0.67329 ( 36) hydrogen bonds : bond 0.04513 ( 1038) hydrogen bonds : angle 3.72230 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.6602 (t80) REVERT: B 104 HIS cc_start: 0.8653 (OUTLIER) cc_final: 0.7186 (t-90) REVERT: B 353 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7512 (t80) REVERT: C 37 MET cc_start: 0.8354 (mtp) cc_final: 0.8079 (ttm) REVERT: C 353 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7132 (t80) REVERT: D 265 MET cc_start: 0.8311 (mmm) cc_final: 0.7668 (mmm) REVERT: D 343 MET cc_start: 0.9025 (ttp) cc_final: 0.8634 (ttm) REVERT: D 353 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.6752 (t80) REVERT: D 371 ASP cc_start: 0.7712 (t0) cc_final: 0.7392 (t0) REVERT: E 104 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.7283 (t-90) REVERT: E 353 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7502 (t80) REVERT: F 37 MET cc_start: 0.8349 (mtp) cc_final: 0.8034 (ttm) REVERT: F 239 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7896 (mm110) REVERT: F 353 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7101 (t80) outliers start: 26 outliers final: 18 residues processed: 152 average time/residue: 0.0997 time to fit residues: 25.1984 Evaluate side-chains 149 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 62 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 0.0980 chunk 161 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085854 restraints weight = 30859.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088708 restraints weight = 13843.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090505 restraints weight = 8245.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.091376 restraints weight = 6055.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092044 restraints weight = 5187.008| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16434 Z= 0.106 Angle : 0.474 8.082 22266 Z= 0.259 Chirality : 0.037 0.148 2448 Planarity : 0.003 0.047 2688 Dihedral : 3.812 17.081 2112 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.64 % Allowed : 16.38 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.19), residues: 1872 helix: 2.21 (0.14), residues: 1308 sheet: 2.35 (0.51), residues: 102 loop : -0.72 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 345 TYR 0.009 0.001 TYR E 281 PHE 0.013 0.001 PHE D 136 TRP 0.010 0.001 TRP E 24 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00220 (16416) covalent geometry : angle 0.47382 (22230) SS BOND : bond 0.00175 ( 18) SS BOND : angle 0.57510 ( 36) hydrogen bonds : bond 0.03880 ( 1038) hydrogen bonds : angle 3.60662 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6569 (t80) REVERT: A 371 ASP cc_start: 0.7444 (t0) cc_final: 0.7185 (t0) REVERT: B 104 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.6971 (t-90) REVERT: B 353 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7447 (t80) REVERT: C 353 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7141 (t80) REVERT: D 265 MET cc_start: 0.8197 (mmm) cc_final: 0.7571 (mmm) REVERT: D 343 MET cc_start: 0.8983 (ttp) cc_final: 0.8554 (ttm) REVERT: D 353 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.6760 (t80) REVERT: D 371 ASP cc_start: 0.7458 (t0) cc_final: 0.7165 (t0) REVERT: E 104 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7065 (t-90) REVERT: E 353 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7573 (t80) REVERT: F 239 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7847 (mm110) REVERT: F 353 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7035 (t80) outliers start: 29 outliers final: 18 residues processed: 182 average time/residue: 0.1030 time to fit residues: 30.6510 Evaluate side-chains 159 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087579 restraints weight = 30469.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090399 restraints weight = 13579.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092155 restraints weight = 8056.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093192 restraints weight = 5904.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093506 restraints weight = 4976.595| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16434 Z= 0.111 Angle : 0.501 11.753 22266 Z= 0.272 Chirality : 0.037 0.181 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.748 17.494 2112 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.86 % Allowed : 17.12 % Favored : 81.02 % 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: 2.37 (0.19), residues: 1872 helix: 2.28 (0.14), residues: 1308 sheet: 2.44 (0.51), residues: 102 loop : -0.77 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 403 TYR 0.015 0.001 TYR E 281 PHE 0.013 0.001 PHE F 353 TRP 0.010 0.001 TRP F 24 HIS 0.008 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00232 (16416) covalent geometry : angle 0.50057 (22230) SS BOND : bond 0.00177 ( 18) SS BOND : angle 0.58551 ( 36) hydrogen bonds : bond 0.03854 ( 1038) hydrogen bonds : angle 3.55920 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6601 (t80) REVERT: A 371 ASP cc_start: 0.7423 (t0) cc_final: 0.7181 (t0) REVERT: B 104 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.7048 (t-90) REVERT: B 353 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 353 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7157 (t80) REVERT: D 265 MET cc_start: 0.8214 (mmm) cc_final: 0.7707 (mmm) REVERT: D 343 MET cc_start: 0.8968 (ttp) cc_final: 0.8618 (ttm) REVERT: D 353 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.6764 (t80) REVERT: D 371 ASP cc_start: 0.7427 (t0) cc_final: 0.7161 (t0) REVERT: E 104 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.7115 (t-90) REVERT: E 353 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7541 (t80) REVERT: F 239 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8014 (mm110) REVERT: F 353 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7076 (t80) outliers start: 33 outliers final: 19 residues processed: 171 average time/residue: 0.1011 time to fit residues: 28.3870 Evaluate side-chains 161 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 143 optimal weight: 3.9990 chunk 149 optimal weight: 0.0010 chunk 14 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 253 HIS B 404 GLN C 404 GLN D 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086428 restraints weight = 31085.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089274 restraints weight = 14013.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091041 restraints weight = 8384.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091976 restraints weight = 6191.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.092609 restraints weight = 5302.060| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16434 Z= 0.113 Angle : 0.507 9.083 22266 Z= 0.275 Chirality : 0.037 0.142 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.735 17.506 2112 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.69 % Allowed : 17.12 % Favored : 81.19 % 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: 2.41 (0.19), residues: 1872 helix: 2.31 (0.14), residues: 1308 sheet: 2.45 (0.51), residues: 102 loop : -0.75 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 306 TYR 0.013 0.001 TYR E 281 PHE 0.019 0.001 PHE A 136 TRP 0.010 0.001 TRP F 24 HIS 0.009 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00242 (16416) covalent geometry : angle 0.50706 (22230) SS BOND : bond 0.00175 ( 18) SS BOND : angle 0.57594 ( 36) hydrogen bonds : bond 0.03891 ( 1038) hydrogen bonds : angle 3.54833 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.6710 (t80) REVERT: A 371 ASP cc_start: 0.7411 (t0) cc_final: 0.7150 (t0) REVERT: B 104 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.7124 (t-90) REVERT: B 353 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7433 (t80) REVERT: C 353 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7166 (t80) REVERT: D 265 MET cc_start: 0.8210 (mmm) cc_final: 0.7674 (mmm) REVERT: D 343 MET cc_start: 0.8954 (ttp) cc_final: 0.8587 (ttm) REVERT: D 353 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6783 (t80) REVERT: D 371 ASP cc_start: 0.7409 (t0) cc_final: 0.7145 (t0) REVERT: E 104 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.7201 (t-90) REVERT: E 353 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7577 (t80) REVERT: F 239 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8046 (mm-40) REVERT: F 353 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7118 (t80) outliers start: 30 outliers final: 20 residues processed: 164 average time/residue: 0.1008 time to fit residues: 27.4865 Evaluate side-chains 163 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 404 GLN C 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.083564 restraints weight = 30858.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086364 restraints weight = 13978.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088164 restraints weight = 8418.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089179 restraints weight = 6230.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.089637 restraints weight = 5286.064| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16434 Z= 0.136 Angle : 0.525 9.480 22266 Z= 0.285 Chirality : 0.038 0.145 2448 Planarity : 0.003 0.045 2688 Dihedral : 3.840 20.439 2112 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.64 % Allowed : 17.46 % Favored : 80.90 % 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: 2.37 (0.19), residues: 1872 helix: 2.24 (0.14), residues: 1320 sheet: 2.44 (0.51), residues: 102 loop : -0.73 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 266 TYR 0.014 0.001 TYR E 281 PHE 0.016 0.001 PHE A 136 TRP 0.010 0.001 TRP F 143 HIS 0.009 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00308 (16416) covalent geometry : angle 0.52474 (22230) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.65787 ( 36) hydrogen bonds : bond 0.04451 ( 1038) hydrogen bonds : angle 3.62867 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.62 seconds wall clock time: 37 minutes 36.54 seconds (2256.54 seconds total)