Starting phenix.real_space_refine on Sat Jun 14 08:26:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g8z_4362/06_2025/6g8z_4362.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g8z_4362/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6g8z_4362/06_2025/6g8z_4362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g8z_4362/06_2025/6g8z_4362.map" model { file = "/net/cci-nas-00/data/ceres_data/6g8z_4362/06_2025/6g8z_4362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g8z_4362/06_2025/6g8z_4362.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 6.43, per 1000 atoms: 0.40 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 C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 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: 3.82 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.46 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: 4.56 Time building geometry restraints manager: 4.56 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (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 TRP 0.025 0.002 TRP E 24 HIS 0.011 0.002 HIS E 132 PHE 0.040 0.003 PHE E 136 TYR 0.010 0.002 TYR C 106 ARG 0.008 0.001 ARG F 262 Details of bonding type rmsd hydrogen bonds : bond 0.13840 ( 1038) hydrogen bonds : angle 5.19829 ( 3096) SS BOND : bond 0.00274 ( 18) SS BOND : angle 0.97668 ( 36) covalent geometry : bond 0.00516 (16416) covalent geometry : angle 0.77352 (22230) *********************** 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 : 1.864 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: 0.2264 time to fit residues: 88.7101 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 : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN F 267 GLN F 404 GLN F 406 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096920 restraints weight = 29037.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099924 restraints weight = 12109.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101773 restraints weight = 6884.722| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16434 Z= 0.137 Angle : 0.522 5.332 22266 Z= 0.297 Chirality : 0.040 0.153 2448 Planarity : 0.004 0.055 2688 Dihedral : 4.329 19.815 2112 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1872 helix: 1.49 (0.14), residues: 1290 sheet: 2.12 (0.53), residues: 96 loop : -1.20 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 143 HIS 0.007 0.001 HIS B 253 PHE 0.021 0.002 PHE A 136 TYR 0.016 0.001 TYR E 281 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 1038) hydrogen bonds : angle 3.94143 ( 3096) SS BOND : bond 0.00430 ( 18) SS BOND : angle 0.86711 ( 36) covalent geometry : bond 0.00285 (16416) covalent geometry : angle 0.52161 (22230) *********************** 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 181 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8186 (mtp) cc_final: 0.7979 (ttm) REVERT: A 239 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7563 (mm110) REVERT: A 353 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6295 (t80) REVERT: A 404 GLN cc_start: 0.8746 (mm110) cc_final: 0.8428 (mm110) REVERT: B 353 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6751 (t80) REVERT: B 371 ASP cc_start: 0.7911 (t70) cc_final: 0.7639 (t0) REVERT: B 404 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8521 (mm110) REVERT: C 154 GLU cc_start: 0.7522 (pp20) cc_final: 0.7257 (pp20) REVERT: C 353 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6671 (t80) REVERT: D 154 GLU cc_start: 0.7458 (pp20) cc_final: 0.7183 (pp20) REVERT: E 404 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8442 (mm110) REVERT: F 353 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 16 outliers final: 4 residues processed: 174 average time/residue: 0.2225 time to fit residues: 62.8341 Evaluate side-chains 117 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 37 MET 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 74 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 114 optimal weight: 0.2980 chunk 127 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 267 GLN B 288 ASN C 288 ASN C 404 GLN D 288 ASN E 288 ASN F 288 ASN F 404 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094139 restraints weight = 29121.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097168 restraints weight = 12413.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099008 restraints weight = 7130.443| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3068 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= 0.114 Angle : 0.465 5.250 22266 Z= 0.261 Chirality : 0.037 0.150 2448 Planarity : 0.003 0.052 2688 Dihedral : 4.024 18.042 2112 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.13 % Allowed : 9.10 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 1872 helix: 1.98 (0.14), residues: 1302 sheet: 1.94 (0.55), residues: 102 loop : -1.03 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 24 HIS 0.006 0.001 HIS B 253 PHE 0.014 0.001 PHE D 136 TYR 0.016 0.001 TYR B 281 ARG 0.003 0.000 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 1038) hydrogen bonds : angle 3.72159 ( 3096) SS BOND : bond 0.00180 ( 18) SS BOND : angle 0.70419 ( 36) covalent geometry : bond 0.00234 (16416) covalent geometry : angle 0.46470 (22230) *********************** 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 171 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7660 (mm110) REVERT: A 353 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6545 (t80) REVERT: B 104 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.6749 (t-90) REVERT: B 353 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7012 (t80) REVERT: C 37 MET cc_start: 0.8196 (mtp) cc_final: 0.7917 (ttm) REVERT: C 154 GLU cc_start: 0.7678 (pp20) cc_final: 0.7445 (pp20) REVERT: C 353 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6876 (t80) REVERT: D 154 GLU cc_start: 0.7571 (pp20) cc_final: 0.7313 (pp20) REVERT: D 239 GLN cc_start: 0.7785 (mm110) cc_final: 0.7574 (mm-40) REVERT: D 353 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6841 (t80) REVERT: E 104 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: E 353 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6927 (t80) REVERT: E 404 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8569 (mm110) REVERT: F 353 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6975 (t80) outliers start: 20 outliers final: 11 residues processed: 170 average time/residue: 0.2211 time to fit residues: 61.2518 Evaluate side-chains 153 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 HIS 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 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 E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 234 LYS 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 98 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 404 GLN D 267 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083046 restraints weight = 30322.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085914 restraints weight = 13548.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087704 restraints weight = 8094.687| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16434 Z= 0.189 Angle : 0.545 8.293 22266 Z= 0.304 Chirality : 0.040 0.156 2448 Planarity : 0.004 0.051 2688 Dihedral : 4.196 20.344 2112 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.49 % Allowed : 11.58 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 1872 helix: 2.00 (0.14), residues: 1302 sheet: 1.79 (0.56), residues: 102 loop : -1.04 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 143 HIS 0.006 0.001 HIS B 253 PHE 0.018 0.002 PHE F 353 TYR 0.015 0.002 TYR E 281 ARG 0.004 0.000 ARG F 266 Details of bonding type rmsd hydrogen bonds : bond 0.05815 ( 1038) hydrogen bonds : angle 3.94299 ( 3096) SS BOND : bond 0.00255 ( 18) SS BOND : angle 0.89404 ( 36) covalent geometry : bond 0.00434 (16416) covalent geometry : angle 0.54466 (22230) *********************** 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 171 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 1.756 Fit side-chains REVERT: A 265 MET cc_start: 0.8387 (mmm) cc_final: 0.7959 (mmm) REVERT: A 353 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.6910 (t80) REVERT: B 104 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.7673 (t-90) REVERT: B 353 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7306 (t80) REVERT: C 353 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7097 (t80) REVERT: D 353 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.6700 (t80) REVERT: E 46 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8175 (tm-30) REVERT: E 104 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.7769 (t-90) REVERT: E 238 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8444 (tm-30) REVERT: E 239 GLN cc_start: 0.7911 (mm110) cc_final: 0.7546 (mm110) REVERT: E 265 MET cc_start: 0.8014 (mmm) cc_final: 0.7802 (tpt) REVERT: E 353 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7324 (t80) REVERT: F 265 MET cc_start: 0.8298 (mmm) cc_final: 0.7998 (mmm) REVERT: F 353 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7060 (t80) outliers start: 44 outliers final: 17 residues processed: 164 average time/residue: 0.2301 time to fit residues: 60.6751 Evaluate side-chains 138 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS 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 157 VAL 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 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 163 CYS Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 163 CYS 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 23 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3507 r_free = 0.3507 target = 0.108241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085900 restraints weight = 30582.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088799 restraints weight = 13698.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090594 restraints weight = 8128.587| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16434 Z= 0.124 Angle : 0.504 9.706 22266 Z= 0.269 Chirality : 0.038 0.150 2448 Planarity : 0.003 0.048 2688 Dihedral : 3.991 18.610 2112 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.64 % Allowed : 13.84 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 1872 helix: 2.15 (0.14), residues: 1302 sheet: 2.15 (0.50), residues: 102 loop : -0.96 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 341 HIS 0.007 0.001 HIS B 253 PHE 0.013 0.001 PHE F 353 TYR 0.012 0.001 TYR E 281 ARG 0.001 0.000 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 1038) hydrogen bonds : angle 3.73147 ( 3096) SS BOND : bond 0.00181 ( 18) SS BOND : angle 0.69048 ( 36) covalent geometry : bond 0.00268 (16416) covalent geometry : angle 0.50351 (22230) *********************** 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 158 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8083 (mm110) cc_final: 0.7620 (mm110) REVERT: A 353 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.6695 (t80) REVERT: B 104 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.7147 (t-90) REVERT: B 353 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7390 (t80) REVERT: C 353 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7086 (t80) REVERT: D 353 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6766 (t80) REVERT: E 104 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7319 (t-90) REVERT: E 353 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7357 (t80) REVERT: F 353 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7047 (t80) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 0.2428 time to fit residues: 62.6924 Evaluate side-chains 143 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS 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 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 163 CYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 163 CYS 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 157 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.086648 restraints weight = 30264.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.089543 restraints weight = 13357.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.091327 restraints weight = 7846.075| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4191 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= 0.115 Angle : 0.478 8.756 22266 Z= 0.259 Chirality : 0.038 0.147 2448 Planarity : 0.003 0.047 2688 Dihedral : 3.842 16.873 2112 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.53 % Allowed : 14.97 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 1872 helix: 2.24 (0.14), residues: 1302 sheet: 2.31 (0.51), residues: 102 loop : -0.88 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 341 HIS 0.006 0.001 HIS B 253 PHE 0.013 0.001 PHE F 353 TYR 0.011 0.001 TYR E 281 ARG 0.001 0.000 ARG E 306 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1038) hydrogen bonds : angle 3.63546 ( 3096) SS BOND : bond 0.00177 ( 18) SS BOND : angle 0.62338 ( 36) covalent geometry : bond 0.00246 (16416) covalent geometry : angle 0.47822 (22230) *********************** 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 161 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6626 (t80) REVERT: A 371 ASP cc_start: 0.7639 (t0) cc_final: 0.7405 (t0) REVERT: B 104 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: B 353 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7327 (t80) REVERT: C 37 MET cc_start: 0.8337 (mtp) cc_final: 0.8001 (ttm) REVERT: C 353 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6987 (t80) REVERT: D 353 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6790 (t80) REVERT: E 104 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7106 (t-90) REVERT: E 353 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7327 (t80) REVERT: F 37 MET cc_start: 0.8316 (mtp) cc_final: 0.8001 (ttm) REVERT: F 353 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7024 (t80) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 0.2243 time to fit residues: 57.7197 Evaluate side-chains 142 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU 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 327 SER 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 353 PHE Chi-restraints excluded: chain D residue 48 THR 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 163 CYS 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 405 LEU Chi-restraints excluded: chain F residue 163 CYS 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 153 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 404 GLN C 404 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082959 restraints weight = 31031.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085766 restraints weight = 14043.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087517 restraints weight = 8413.040| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16434 Z= 0.144 Angle : 0.517 9.881 22266 Z= 0.280 Chirality : 0.038 0.176 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.884 16.824 2112 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.81 % Allowed : 15.48 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1872 helix: 2.18 (0.14), residues: 1308 sheet: 2.39 (0.53), residues: 96 loop : -0.74 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 143 HIS 0.006 0.001 HIS B 253 PHE 0.015 0.001 PHE F 353 TYR 0.013 0.001 TYR E 281 ARG 0.001 0.000 ARG C 266 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1038) hydrogen bonds : angle 3.71688 ( 3096) SS BOND : bond 0.00183 ( 18) SS BOND : angle 0.67670 ( 36) covalent geometry : bond 0.00325 (16416) covalent geometry : angle 0.51693 (22230) *********************** 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 152 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 371 ASP cc_start: 0.7732 (t0) cc_final: 0.7458 (t0) REVERT: B 104 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7326 (t-90) REVERT: B 353 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7446 (t80) REVERT: C 37 MET cc_start: 0.8305 (mtp) cc_final: 0.7968 (ttm) REVERT: C 353 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7087 (t80) REVERT: D 353 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6832 (t80) REVERT: E 104 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.7364 (t-90) REVERT: E 353 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7427 (t80) REVERT: F 37 MET cc_start: 0.8300 (mtp) cc_final: 0.7988 (ttm) REVERT: F 239 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7786 (mm-40) REVERT: F 353 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7035 (t80) outliers start: 32 outliers final: 21 residues processed: 148 average time/residue: 0.2289 time to fit residues: 55.0091 Evaluate side-chains 144 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU 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 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 327 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 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 163 CYS 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 405 LEU Chi-restraints excluded: chain F residue 163 CYS 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 59 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 F 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084461 restraints weight = 30745.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087253 restraints weight = 14061.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088997 restraints weight = 8486.188| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16434 Z= 0.118 Angle : 0.483 7.883 22266 Z= 0.263 Chirality : 0.038 0.146 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.837 16.905 2112 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.15 % Allowed : 15.08 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 1872 helix: 2.22 (0.14), residues: 1308 sheet: 2.51 (0.51), residues: 102 loop : -0.65 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 341 HIS 0.007 0.001 HIS B 253 PHE 0.019 0.001 PHE D 136 TYR 0.010 0.001 TYR B 281 ARG 0.001 0.000 ARG D 266 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 1038) hydrogen bonds : angle 3.64221 ( 3096) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.61108 ( 36) covalent geometry : bond 0.00257 (16416) covalent geometry : angle 0.48276 (22230) *********************** 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 165 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.6584 (t80) REVERT: A 371 ASP cc_start: 0.7567 (t0) cc_final: 0.7281 (t0) REVERT: B 104 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.7120 (t-90) REVERT: B 353 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7475 (t80) REVERT: C 37 MET cc_start: 0.8282 (mtp) cc_final: 0.7976 (ttm) REVERT: C 239 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7673 (mm-40) REVERT: C 353 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7086 (t80) REVERT: D 353 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6806 (t80) REVERT: E 104 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7181 (t-90) REVERT: E 353 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7481 (t80) REVERT: F 37 MET cc_start: 0.8255 (mtp) cc_final: 0.7999 (ttm) REVERT: F 353 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7166 (t80) outliers start: 38 outliers final: 27 residues processed: 160 average time/residue: 0.2240 time to fit residues: 58.7487 Evaluate side-chains 158 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU 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 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 327 SER 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 281 TYR 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 163 CYS Chi-restraints excluded: chain E residue 281 TYR 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 405 LEU Chi-restraints excluded: chain F residue 163 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 = 0.107999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085607 restraints weight = 30412.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088425 restraints weight = 13761.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090195 restraints weight = 8293.935| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16434 Z= 0.113 Angle : 0.482 8.016 22266 Z= 0.261 Chirality : 0.037 0.149 2448 Planarity : 0.003 0.045 2688 Dihedral : 3.798 16.807 2112 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.32 % Allowed : 14.86 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.19), residues: 1872 helix: 2.26 (0.14), residues: 1308 sheet: 2.55 (0.51), residues: 102 loop : -0.63 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 24 HIS 0.007 0.001 HIS B 253 PHE 0.015 0.001 PHE D 136 TYR 0.009 0.001 TYR B 281 ARG 0.002 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1038) hydrogen bonds : angle 3.61546 ( 3096) SS BOND : bond 0.00180 ( 18) SS BOND : angle 0.59172 ( 36) covalent geometry : bond 0.00240 (16416) covalent geometry : angle 0.48168 (22230) *********************** 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 173 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.6613 (t80) REVERT: A 371 ASP cc_start: 0.7525 (t0) cc_final: 0.7308 (t0) REVERT: B 104 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7119 (t-90) REVERT: B 353 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7494 (t80) REVERT: C 37 MET cc_start: 0.8285 (mtp) cc_final: 0.8023 (ttm) REVERT: C 353 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7088 (t80) REVERT: D 353 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6845 (t80) REVERT: E 46 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 104 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7133 (t-90) REVERT: E 353 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7519 (t80) REVERT: F 353 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7104 (t80) outliers start: 41 outliers final: 29 residues processed: 164 average time/residue: 0.2176 time to fit residues: 58.1862 Evaluate side-chains 166 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU 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 234 LYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 MET 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 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 D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 281 TYR 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 F residue 163 CYS 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 9 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 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 239 GLN B 253 HIS B 404 GLN C 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 = 0.3493 r_free = 0.3493 target = 0.107683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.084614 restraints weight = 30809.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.087549 restraints weight = 13733.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089391 restraints weight = 8190.086| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16434 Z= 0.126 Angle : 0.499 8.229 22266 Z= 0.270 Chirality : 0.038 0.158 2448 Planarity : 0.003 0.045 2688 Dihedral : 3.809 17.333 2112 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.09 % Allowed : 15.37 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 1872 helix: 2.27 (0.14), residues: 1308 sheet: 2.45 (0.54), residues: 96 loop : -0.60 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 24 HIS 0.008 0.001 HIS E 253 PHE 0.014 0.001 PHE A 136 TYR 0.011 0.001 TYR B 281 ARG 0.001 0.000 ARG F 309 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1038) hydrogen bonds : angle 3.63496 ( 3096) SS BOND : bond 0.00183 ( 18) SS BOND : angle 0.61729 ( 36) covalent geometry : bond 0.00281 (16416) covalent geometry : angle 0.49894 (22230) ********************** 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 162 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.6771 (t80) REVERT: A 371 ASP cc_start: 0.7610 (t0) cc_final: 0.7405 (t0) REVERT: B 104 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7182 (t-90) REVERT: B 353 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7490 (t80) REVERT: C 37 MET cc_start: 0.8348 (mtp) cc_final: 0.8072 (ttm) REVERT: C 353 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7018 (t80) REVERT: D 353 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6974 (t80) REVERT: E 104 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.7184 (t-90) REVERT: E 353 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7467 (t80) REVERT: F 239 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7849 (mm-40) REVERT: F 353 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7213 (t80) outliers start: 37 outliers final: 27 residues processed: 154 average time/residue: 0.2222 time to fit residues: 56.3294 Evaluate side-chains 157 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 243 LEU 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 234 LYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 MET 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 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 D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 163 CYS 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 92 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 147 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085883 restraints weight = 30516.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088718 restraints weight = 13732.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090466 restraints weight = 8221.599| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16434 Z= 0.113 Angle : 0.481 7.630 22266 Z= 0.261 Chirality : 0.037 0.146 2448 Planarity : 0.003 0.045 2688 Dihedral : 3.764 17.288 2112 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.03 % Allowed : 15.42 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.19), residues: 1872 helix: 2.30 (0.14), residues: 1308 sheet: 2.42 (0.54), residues: 96 loop : -0.58 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 341 HIS 0.007 0.001 HIS E 253 PHE 0.014 0.001 PHE D 136 TYR 0.009 0.001 TYR B 281 ARG 0.001 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 1038) hydrogen bonds : angle 3.58887 ( 3096) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.57291 ( 36) covalent geometry : bond 0.00241 (16416) covalent geometry : angle 0.48124 (22230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4026.82 seconds wall clock time: 71 minutes 55.64 seconds (4315.64 seconds total)