Starting phenix.real_space_refine on Thu Feb 5 14:51:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hez_52102/02_2026/9hez_52102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hez_52102/02_2026/9hez_52102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hez_52102/02_2026/9hez_52102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hez_52102/02_2026/9hez_52102.map" model { file = "/net/cci-nas-00/data/ceres_data/9hez_52102/02_2026/9hez_52102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hez_52102/02_2026/9hez_52102.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 98 5.16 5 C 11977 2.51 5 N 2730 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17934 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2562 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.02, per 1000 atoms: 0.11 Number of scatterers: 17934 At special positions: 0 Unit cell: (115.5, 113.85, 114.675, 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 98 16.00 O 3129 8.00 N 2730 7.00 C 11977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 583.6 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 7 sheets defined 74.7% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.119A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.534A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 89 through 92 removed outlier: 6.915A pdb=" N SER A 92 " --> pdb=" O GLN A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 100 through 131 removed outlier: 3.667A pdb=" N TRP A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 155 removed outlier: 3.793A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 206 through 236 removed outlier: 3.520A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 249 through 255 removed outlier: 4.037A pdb=" N ASN A 254 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.575A pdb=" N LEU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.768A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.904A pdb=" N GLN A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.690A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.004A pdb=" N THR A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 4.118A pdb=" N LEU B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.534A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 89 through 92 removed outlier: 6.914A pdb=" N SER B 92 " --> pdb=" O GLN B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 100 through 131 removed outlier: 3.666A pdb=" N TRP B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 155 removed outlier: 3.794A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 206 through 236 removed outlier: 3.520A pdb=" N MET B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 4.037A pdb=" N ASN B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.575A pdb=" N LEU B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.767A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.904A pdb=" N GLN B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.690A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 363 through 369 removed outlier: 4.004A pdb=" N THR B 367 " --> pdb=" O MET B 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 4.118A pdb=" N LEU C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.533A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 89 through 92 removed outlier: 6.914A pdb=" N SER C 92 " --> pdb=" O GLN C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 100 through 131 removed outlier: 3.666A pdb=" N TRP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 155 removed outlier: 3.793A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 Processing helix chain 'C' and resid 206 through 236 removed outlier: 3.521A pdb=" N MET C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 249 through 255 removed outlier: 4.037A pdb=" N ASN C 254 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 294 removed outlier: 3.574A pdb=" N LEU C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.767A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.903A pdb=" N GLN C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.691A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 332 " --> pdb=" O SER C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 363 through 369 removed outlier: 4.004A pdb=" N THR C 367 " --> pdb=" O MET C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 4.119A pdb=" N LEU D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.535A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 89 through 92 removed outlier: 6.914A pdb=" N SER D 92 " --> pdb=" O GLN D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 100 through 131 removed outlier: 3.667A pdb=" N TRP D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 155 removed outlier: 3.793A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'D' and resid 206 through 236 removed outlier: 3.521A pdb=" N MET D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.037A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 294 removed outlier: 3.575A pdb=" N LEU D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.767A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.903A pdb=" N GLN D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.691A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 363 through 369 removed outlier: 4.004A pdb=" N THR D 367 " --> pdb=" O MET D 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 4.118A pdb=" N LEU E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.535A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 89 through 92 removed outlier: 6.914A pdb=" N SER E 92 " --> pdb=" O GLN E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 100 through 131 removed outlier: 3.667A pdb=" N TRP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 155 removed outlier: 3.794A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 206 through 236 removed outlier: 3.521A pdb=" N MET E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 249 through 255 removed outlier: 4.038A pdb=" N ASN E 254 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 294 removed outlier: 3.575A pdb=" N LEU E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.767A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 removed outlier: 3.905A pdb=" N GLN E 300 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.691A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 332 " --> pdb=" O SER E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 363 through 369 removed outlier: 4.005A pdb=" N THR E 367 " --> pdb=" O MET E 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 4.118A pdb=" N LEU F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.535A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 89 through 92 removed outlier: 6.914A pdb=" N SER F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 100 through 131 removed outlier: 3.667A pdb=" N TRP F 104 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 155 removed outlier: 3.794A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 203 Processing helix chain 'F' and resid 206 through 236 removed outlier: 3.521A pdb=" N MET F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 249 through 255 removed outlier: 4.037A pdb=" N ASN F 254 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 294 removed outlier: 3.575A pdb=" N LEU F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.767A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 removed outlier: 3.904A pdb=" N GLN F 300 " --> pdb=" O ILE F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.690A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 332 " --> pdb=" O SER F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 363 through 369 removed outlier: 4.004A pdb=" N THR F 367 " --> pdb=" O MET F 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 4.118A pdb=" N LEU G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.534A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 89 through 92 removed outlier: 6.914A pdb=" N SER G 92 " --> pdb=" O GLN G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 100 through 131 removed outlier: 3.667A pdb=" N TRP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 155 removed outlier: 3.794A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 203 Processing helix chain 'G' and resid 206 through 236 removed outlier: 3.521A pdb=" N MET G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 249 through 255 removed outlier: 4.036A pdb=" N ASN G 254 " --> pdb=" O VAL G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 294 removed outlier: 3.575A pdb=" N LEU G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.768A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 removed outlier: 3.904A pdb=" N GLN G 300 " --> pdb=" O ILE G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.691A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 332 " --> pdb=" O SER G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 354 Processing helix chain 'G' and resid 363 through 369 removed outlier: 4.004A pdb=" N THR G 367 " --> pdb=" O MET G 363 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1102 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5243 1.35 - 1.46: 4562 1.46 - 1.58: 8423 1.58 - 1.70: 0 1.70 - 1.82: 133 Bond restraints: 18361 Sorted by residual: bond pdb=" CB CYS B 245 " pdb=" SG CYS B 245 " ideal model delta sigma weight residual 1.808 1.787 0.021 3.30e-02 9.18e+02 4.10e-01 bond pdb=" CB CYS D 245 " pdb=" SG CYS D 245 " ideal model delta sigma weight residual 1.808 1.787 0.021 3.30e-02 9.18e+02 4.04e-01 bond pdb=" CB CYS F 245 " pdb=" SG CYS F 245 " ideal model delta sigma weight residual 1.808 1.787 0.021 3.30e-02 9.18e+02 4.03e-01 bond pdb=" CB CYS E 245 " pdb=" SG CYS E 245 " ideal model delta sigma weight residual 1.808 1.787 0.021 3.30e-02 9.18e+02 4.01e-01 bond pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.88e-01 ... (remaining 18356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 23193 1.02 - 2.04: 1420 2.04 - 3.06: 195 3.06 - 4.08: 35 4.08 - 5.10: 56 Bond angle restraints: 24899 Sorted by residual: angle pdb=" N ILE F 296 " pdb=" CA ILE F 296 " pdb=" C ILE F 296 " ideal model delta sigma weight residual 108.88 113.79 -4.91 2.16e+00 2.14e-01 5.16e+00 angle pdb=" N ILE B 296 " pdb=" CA ILE B 296 " pdb=" C ILE B 296 " ideal model delta sigma weight residual 108.88 113.77 -4.89 2.16e+00 2.14e-01 5.13e+00 angle pdb=" N ILE E 296 " pdb=" CA ILE E 296 " pdb=" C ILE E 296 " ideal model delta sigma weight residual 108.88 113.76 -4.88 2.16e+00 2.14e-01 5.11e+00 angle pdb=" N ILE D 296 " pdb=" CA ILE D 296 " pdb=" C ILE D 296 " ideal model delta sigma weight residual 108.88 113.76 -4.88 2.16e+00 2.14e-01 5.11e+00 angle pdb=" N ILE G 296 " pdb=" CA ILE G 296 " pdb=" C ILE G 296 " ideal model delta sigma weight residual 108.88 113.75 -4.87 2.16e+00 2.14e-01 5.08e+00 ... (remaining 24894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 10212 15.68 - 31.36: 561 31.36 - 47.04: 105 47.04 - 62.72: 63 62.72 - 78.40: 28 Dihedral angle restraints: 10969 sinusoidal: 4298 harmonic: 6671 Sorted by residual: dihedral pdb=" CA SER C 98 " pdb=" C SER C 98 " pdb=" N GLY C 99 " pdb=" CA GLY C 99 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER E 98 " pdb=" C SER E 98 " pdb=" N GLY E 99 " pdb=" CA GLY E 99 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA SER G 98 " pdb=" C SER G 98 " pdb=" N GLY G 99 " pdb=" CA GLY G 99 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 10966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1784 0.031 - 0.061: 855 0.061 - 0.092: 230 0.092 - 0.122: 83 0.122 - 0.153: 9 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA ILE G 258 " pdb=" N ILE G 258 " pdb=" C ILE G 258 " pdb=" CB ILE G 258 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE D 258 " pdb=" N ILE D 258 " pdb=" C ILE D 258 " pdb=" CB ILE D 258 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 2958 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 10 " -0.002 2.00e-02 2.50e+03 2.31e-02 1.06e+01 pdb=" CG TYR G 10 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR G 10 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR G 10 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 10 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR G 10 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 10 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR G 10 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 10 " -0.002 2.00e-02 2.50e+03 2.31e-02 1.06e+01 pdb=" CG TYR F 10 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR F 10 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR F 10 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 10 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR F 10 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 10 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR F 10 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 10 " -0.003 2.00e-02 2.50e+03 2.30e-02 1.06e+01 pdb=" CG TYR B 10 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR B 10 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 10 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 10 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 10 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 10 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR B 10 " -0.034 2.00e-02 2.50e+03 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4207 2.79 - 3.32: 18073 3.32 - 3.85: 28907 3.85 - 4.37: 34479 4.37 - 4.90: 59429 Nonbonded interactions: 145095 Sorted by model distance: nonbonded pdb=" NZ LYS B 148 " pdb=" O LEU C 369 " model vdw 2.268 3.120 nonbonded pdb=" NZ LYS F 148 " pdb=" O LEU G 369 " model vdw 2.282 3.120 nonbonded pdb=" NZ LYS D 148 " pdb=" O LEU E 369 " model vdw 2.289 3.120 nonbonded pdb=" NZ LYS C 148 " pdb=" O LEU D 369 " model vdw 2.294 3.120 nonbonded pdb=" O LEU A 369 " pdb=" NZ LYS G 148 " model vdw 2.298 3.120 ... (remaining 145090 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 : 0.003 0.022 18375 Z= 0.122 Angle : 0.590 5.097 24927 Z= 0.347 Chirality : 0.039 0.153 2961 Planarity : 0.005 0.058 2975 Dihedral : 12.137 78.402 6573 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.55 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2170 helix: -0.08 (0.13), residues: 1477 sheet: None (None), residues: 0 loop : -0.84 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG F 216 TYR 0.034 0.004 TYR B 10 PHE 0.010 0.001 PHE D 295 TRP 0.019 0.002 TRP F 104 HIS 0.005 0.002 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00265 (18361) covalent geometry : angle 0.58691 (24899) SS BOND : bond 0.00062 ( 14) SS BOND : angle 1.81032 ( 28) hydrogen bonds : bond 0.19942 ( 1102) hydrogen bonds : angle 7.11853 ( 3201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9170 (mt0) cc_final: 0.8779 (tm130) REVERT: A 59 SER cc_start: 0.9374 (t) cc_final: 0.9156 (t) REVERT: A 74 TRP cc_start: 0.8925 (t-100) cc_final: 0.8707 (t60) REVERT: A 134 HIS cc_start: 0.8766 (t70) cc_final: 0.8355 (t-170) REVERT: A 296 ILE cc_start: 0.9446 (mt) cc_final: 0.9235 (mp) REVERT: A 298 PHE cc_start: 0.8886 (m-80) cc_final: 0.8674 (t80) REVERT: A 301 LYS cc_start: 0.8244 (mttt) cc_final: 0.7498 (tptp) REVERT: A 331 ASN cc_start: 0.9730 (m-40) cc_final: 0.9414 (m-40) REVERT: A 344 TYR cc_start: 0.9279 (t80) cc_final: 0.9042 (t80) REVERT: B 74 TRP cc_start: 0.8901 (t-100) cc_final: 0.8687 (t60) REVERT: B 134 HIS cc_start: 0.8694 (t70) cc_final: 0.8303 (t-170) REVERT: B 136 CYS cc_start: 0.9031 (t) cc_final: 0.8783 (p) REVERT: B 261 ARG cc_start: 0.8771 (mmt-90) cc_final: 0.8563 (mmt180) REVERT: B 298 PHE cc_start: 0.8897 (m-80) cc_final: 0.8693 (t80) REVERT: B 301 LYS cc_start: 0.8278 (mttt) cc_final: 0.7504 (tptp) REVERT: B 331 ASN cc_start: 0.9718 (m-40) cc_final: 0.9405 (m-40) REVERT: B 344 TYR cc_start: 0.9270 (t80) cc_final: 0.9033 (t80) REVERT: C 59 SER cc_start: 0.9410 (t) cc_final: 0.9059 (p) REVERT: C 74 TRP cc_start: 0.8955 (t-100) cc_final: 0.8728 (t60) REVERT: C 134 HIS cc_start: 0.8701 (t70) cc_final: 0.8306 (t-170) REVERT: C 301 LYS cc_start: 0.8278 (mttt) cc_final: 0.7416 (tptp) REVERT: C 331 ASN cc_start: 0.9728 (m-40) cc_final: 0.9407 (m-40) REVERT: D 56 GLN cc_start: 0.9155 (mt0) cc_final: 0.8787 (tm130) REVERT: D 59 SER cc_start: 0.9363 (t) cc_final: 0.9147 (t) REVERT: D 74 TRP cc_start: 0.8948 (t-100) cc_final: 0.8710 (t60) REVERT: D 134 HIS cc_start: 0.8717 (t70) cc_final: 0.8245 (t-170) REVERT: D 298 PHE cc_start: 0.8928 (m-80) cc_final: 0.8597 (t80) REVERT: D 301 LYS cc_start: 0.8246 (mttt) cc_final: 0.7847 (tptp) REVERT: D 331 ASN cc_start: 0.9722 (m-40) cc_final: 0.9375 (m-40) REVERT: D 348 LYS cc_start: 0.9374 (tptt) cc_final: 0.9134 (pttp) REVERT: E 56 GLN cc_start: 0.9189 (mt0) cc_final: 0.8764 (tm130) REVERT: E 134 HIS cc_start: 0.8715 (t70) cc_final: 0.8232 (t-170) REVERT: E 296 ILE cc_start: 0.9431 (mt) cc_final: 0.9218 (mp) REVERT: E 301 LYS cc_start: 0.8311 (mttt) cc_final: 0.7508 (tptp) REVERT: E 331 ASN cc_start: 0.9732 (m-40) cc_final: 0.9407 (m-40) REVERT: F 134 HIS cc_start: 0.8695 (t70) cc_final: 0.8276 (t-170) REVERT: F 151 ASN cc_start: 0.9462 (m-40) cc_final: 0.9223 (m110) REVERT: F 261 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8540 (mmt180) REVERT: F 301 LYS cc_start: 0.8272 (mttt) cc_final: 0.7875 (tptp) REVERT: F 331 ASN cc_start: 0.9721 (m-40) cc_final: 0.9403 (m-40) REVERT: G 74 TRP cc_start: 0.8925 (t-100) cc_final: 0.8704 (t60) REVERT: G 134 HIS cc_start: 0.8716 (t70) cc_final: 0.8255 (t-170) REVERT: G 151 ASN cc_start: 0.9480 (m-40) cc_final: 0.9212 (m110) REVERT: G 301 LYS cc_start: 0.8250 (mttt) cc_final: 0.7522 (tptp) REVERT: G 331 ASN cc_start: 0.9732 (m-40) cc_final: 0.9402 (m-40) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.5057 time to fit residues: 306.8765 Evaluate side-chains 329 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 151 ASN A 279 ASN A 352 ASN A 368 ASN B 5 HIS B 90 GLN B 151 ASN B 368 ASN C 151 ASN C 279 ASN C 368 ASN D 89 GLN D 151 ASN D 279 ASN D 368 ASN E 151 ASN E 368 ASN F 90 GLN F 100 ASN F 352 ASN F 368 ASN G 368 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.067011 restraints weight = 33702.352| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.93 r_work: 0.2722 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18375 Z= 0.214 Angle : 0.667 6.441 24927 Z= 0.338 Chirality : 0.043 0.209 2961 Planarity : 0.004 0.032 2975 Dihedral : 4.388 14.729 2359 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.73 % Allowed : 11.58 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2170 helix: 1.32 (0.13), residues: 1498 sheet: None (None), residues: 0 loop : -0.53 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 216 TYR 0.018 0.002 TYR C 344 PHE 0.021 0.002 PHE A 141 TRP 0.012 0.002 TRP C 104 HIS 0.006 0.002 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00508 (18361) covalent geometry : angle 0.66605 (24899) SS BOND : bond 0.00287 ( 14) SS BOND : angle 1.36613 ( 28) hydrogen bonds : bond 0.05538 ( 1102) hydrogen bonds : angle 4.95618 ( 3201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 352 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8375 (tttt) cc_final: 0.8135 (tptt) REVERT: A 56 GLN cc_start: 0.9234 (mt0) cc_final: 0.8943 (tm-30) REVERT: A 134 HIS cc_start: 0.8781 (t70) cc_final: 0.8270 (t-170) REVERT: A 151 ASN cc_start: 0.9351 (m-40) cc_final: 0.9109 (m110) REVERT: A 298 PHE cc_start: 0.8982 (m-80) cc_final: 0.8623 (t80) REVERT: A 300 GLN cc_start: 0.7543 (pm20) cc_final: 0.7194 (pp30) REVERT: A 325 ASN cc_start: 0.8976 (p0) cc_final: 0.8626 (p0) REVERT: A 331 ASN cc_start: 0.9550 (m-40) cc_final: 0.9329 (m110) REVERT: B 74 TRP cc_start: 0.8693 (t-100) cc_final: 0.8486 (t60) REVERT: B 128 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8165 (tpt-90) REVERT: B 134 HIS cc_start: 0.8791 (t70) cc_final: 0.8397 (t-170) REVERT: B 194 ILE cc_start: 0.9068 (mt) cc_final: 0.8762 (mm) REVERT: B 298 PHE cc_start: 0.8975 (m-80) cc_final: 0.8599 (t80) REVERT: B 300 GLN cc_start: 0.7535 (pm20) cc_final: 0.7169 (pp30) REVERT: B 301 LYS cc_start: 0.8077 (mttt) cc_final: 0.7753 (tptp) REVERT: B 352 ASN cc_start: 0.9627 (m-40) cc_final: 0.9407 (m110) REVERT: C 30 LEU cc_start: 0.9260 (mt) cc_final: 0.9052 (mm) REVERT: C 134 HIS cc_start: 0.8740 (t70) cc_final: 0.8322 (t-170) REVERT: C 194 ILE cc_start: 0.9017 (mt) cc_final: 0.8679 (mm) REVERT: C 298 PHE cc_start: 0.8526 (t80) cc_final: 0.8288 (t80) REVERT: C 300 GLN cc_start: 0.7513 (pm20) cc_final: 0.7272 (pp30) REVERT: C 301 LYS cc_start: 0.8193 (mttt) cc_final: 0.7889 (tptp) REVERT: C 325 ASN cc_start: 0.9020 (p0) cc_final: 0.8696 (p0) REVERT: C 331 ASN cc_start: 0.9559 (m-40) cc_final: 0.9325 (m110) REVERT: C 348 LYS cc_start: 0.9237 (pttp) cc_final: 0.8976 (pptt) REVERT: C 349 VAL cc_start: 0.9774 (t) cc_final: 0.9279 (t) REVERT: D 56 GLN cc_start: 0.9224 (mt0) cc_final: 0.8843 (tm130) REVERT: D 74 TRP cc_start: 0.8681 (t-100) cc_final: 0.8467 (t60) REVERT: D 134 HIS cc_start: 0.8723 (t70) cc_final: 0.8173 (t-170) REVERT: D 151 ASN cc_start: 0.9341 (m-40) cc_final: 0.9136 (m110) REVERT: D 194 ILE cc_start: 0.9119 (mt) cc_final: 0.8778 (mm) REVERT: D 298 PHE cc_start: 0.8950 (m-80) cc_final: 0.8583 (t80) REVERT: D 301 LYS cc_start: 0.8405 (mttt) cc_final: 0.7807 (tptp) REVERT: D 331 ASN cc_start: 0.9519 (m-40) cc_final: 0.9290 (m110) REVERT: D 349 VAL cc_start: 0.9783 (t) cc_final: 0.9466 (t) REVERT: E 56 GLN cc_start: 0.9263 (mt0) cc_final: 0.8979 (tm-30) REVERT: E 134 HIS cc_start: 0.8787 (t70) cc_final: 0.8283 (t-170) REVERT: E 151 ASN cc_start: 0.9381 (m-40) cc_final: 0.8956 (m110) REVERT: E 194 ILE cc_start: 0.9089 (mt) cc_final: 0.8731 (mm) REVERT: E 298 PHE cc_start: 0.8859 (m-80) cc_final: 0.8590 (t80) REVERT: E 300 GLN cc_start: 0.7406 (pm20) cc_final: 0.7168 (pp30) REVERT: E 301 LYS cc_start: 0.8215 (mttt) cc_final: 0.7898 (mmtt) REVERT: E 325 ASN cc_start: 0.9066 (p0) cc_final: 0.8690 (p0) REVERT: E 331 ASN cc_start: 0.9580 (m-40) cc_final: 0.9376 (m110) REVERT: E 352 ASN cc_start: 0.9650 (m-40) cc_final: 0.9408 (m110) REVERT: F 95 GLN cc_start: 0.6520 (mp10) cc_final: 0.6034 (mp10) REVERT: F 100 ASN cc_start: 0.8951 (m-40) cc_final: 0.8745 (m110) REVERT: F 128 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8189 (tpt-90) REVERT: F 134 HIS cc_start: 0.8717 (t70) cc_final: 0.8201 (t-170) REVERT: F 261 ARG cc_start: 0.8954 (mmt-90) cc_final: 0.8687 (mmt90) REVERT: F 301 LYS cc_start: 0.8336 (mttt) cc_final: 0.7700 (tptp) REVERT: F 325 ASN cc_start: 0.9035 (p0) cc_final: 0.8710 (p0) REVERT: F 331 ASN cc_start: 0.9555 (m-40) cc_final: 0.9349 (m110) REVERT: G 74 TRP cc_start: 0.8810 (t-100) cc_final: 0.8570 (t60) REVERT: G 134 HIS cc_start: 0.8752 (t70) cc_final: 0.8231 (t-170) REVERT: G 151 ASN cc_start: 0.9425 (m-40) cc_final: 0.9224 (m110) REVERT: G 194 ILE cc_start: 0.9069 (mt) cc_final: 0.8683 (mm) REVERT: G 300 GLN cc_start: 0.7516 (pm20) cc_final: 0.7142 (pp30) REVERT: G 331 ASN cc_start: 0.9577 (m-40) cc_final: 0.9336 (m110) outliers start: 96 outliers final: 40 residues processed: 410 average time/residue: 0.4760 time to fit residues: 221.6299 Evaluate side-chains 353 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 313 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 287 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 192 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 213 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 100 ASN A 197 GLN A 279 ASN B 5 HIS B 89 GLN B 100 ASN B 151 ASN B 279 ASN D 89 GLN D 263 GLN D 279 ASN F 151 ASN F 197 GLN F 352 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.070029 restraints weight = 33373.810| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.96 r_work: 0.2805 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18375 Z= 0.125 Angle : 0.581 6.319 24927 Z= 0.292 Chirality : 0.040 0.252 2961 Planarity : 0.003 0.031 2975 Dihedral : 4.157 19.247 2359 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.69 % Allowed : 14.58 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2170 helix: 1.53 (0.13), residues: 1498 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 261 TYR 0.019 0.001 TYR G 344 PHE 0.021 0.001 PHE C 141 TRP 0.010 0.001 TRP F 104 HIS 0.007 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00260 (18361) covalent geometry : angle 0.58019 (24899) SS BOND : bond 0.00143 ( 14) SS BOND : angle 1.12777 ( 28) hydrogen bonds : bond 0.04488 ( 1102) hydrogen bonds : angle 4.43049 ( 3201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9252 (mt0) cc_final: 0.8807 (tm130) REVERT: A 128 ARG cc_start: 0.8581 (tpt-90) cc_final: 0.8002 (ttp-170) REVERT: A 134 HIS cc_start: 0.8767 (t70) cc_final: 0.8199 (t-170) REVERT: A 298 PHE cc_start: 0.8980 (m-80) cc_final: 0.8552 (t80) REVERT: A 300 GLN cc_start: 0.7495 (pm20) cc_final: 0.7113 (pp30) REVERT: A 325 ASN cc_start: 0.8901 (p0) cc_final: 0.8455 (p0) REVERT: A 331 ASN cc_start: 0.9541 (m-40) cc_final: 0.9295 (m110) REVERT: B 95 GLN cc_start: 0.6484 (mp-120) cc_final: 0.6150 (mp10) REVERT: B 128 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8106 (tpt-90) REVERT: B 134 HIS cc_start: 0.8783 (t70) cc_final: 0.8356 (t-170) REVERT: B 151 ASN cc_start: 0.9320 (m-40) cc_final: 0.8936 (m110) REVERT: B 298 PHE cc_start: 0.8958 (m-80) cc_final: 0.8691 (t80) REVERT: B 338 ILE cc_start: 0.9065 (pp) cc_final: 0.8799 (tp) REVERT: C 95 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7401 (mm-40) REVERT: C 134 HIS cc_start: 0.8784 (t70) cc_final: 0.8370 (t-170) REVERT: C 298 PHE cc_start: 0.8599 (t80) cc_final: 0.8285 (t80) REVERT: C 300 GLN cc_start: 0.7495 (pm20) cc_final: 0.7087 (pp30) REVERT: C 301 LYS cc_start: 0.8150 (mttt) cc_final: 0.7897 (tptp) REVERT: C 325 ASN cc_start: 0.8937 (p0) cc_final: 0.8473 (p0) REVERT: C 331 ASN cc_start: 0.9522 (m-40) cc_final: 0.9263 (m-40) REVERT: C 348 LYS cc_start: 0.9257 (pttp) cc_final: 0.9028 (pptt) REVERT: D 56 GLN cc_start: 0.9217 (mt0) cc_final: 0.8824 (tm130) REVERT: D 95 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7373 (mm-40) REVERT: D 100 ASN cc_start: 0.8946 (m110) cc_final: 0.8702 (m110) REVERT: D 134 HIS cc_start: 0.8711 (t70) cc_final: 0.8121 (t-170) REVERT: D 151 ASN cc_start: 0.9398 (m-40) cc_final: 0.9106 (m110) REVERT: D 298 PHE cc_start: 0.8963 (m-80) cc_final: 0.8532 (t80) REVERT: D 299 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8168 (mtp180) REVERT: D 301 LYS cc_start: 0.8346 (mttt) cc_final: 0.7784 (mmtt) REVERT: D 331 ASN cc_start: 0.9518 (m-40) cc_final: 0.9253 (m110) REVERT: E 95 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7465 (mm-40) REVERT: E 134 HIS cc_start: 0.8797 (t70) cc_final: 0.8291 (t-170) REVERT: E 151 ASN cc_start: 0.9390 (m-40) cc_final: 0.9176 (m110) REVERT: E 298 PHE cc_start: 0.8852 (m-80) cc_final: 0.8528 (t80) REVERT: E 300 GLN cc_start: 0.7375 (pm20) cc_final: 0.7115 (pp30) REVERT: E 301 LYS cc_start: 0.8154 (mttt) cc_final: 0.7878 (mmtt) REVERT: E 325 ASN cc_start: 0.8970 (p0) cc_final: 0.8449 (p0) REVERT: E 352 ASN cc_start: 0.9623 (m-40) cc_final: 0.9397 (m110) REVERT: F 100 ASN cc_start: 0.8845 (m-40) cc_final: 0.8544 (m110) REVERT: F 125 LEU cc_start: 0.8980 (tp) cc_final: 0.8771 (tp) REVERT: F 134 HIS cc_start: 0.8691 (t70) cc_final: 0.8190 (t-170) REVERT: F 151 ASN cc_start: 0.9224 (m-40) cc_final: 0.8870 (m110) REVERT: F 301 LYS cc_start: 0.8432 (mttt) cc_final: 0.7512 (tptp) REVERT: F 325 ASN cc_start: 0.8960 (p0) cc_final: 0.8525 (p0) REVERT: G 94 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8591 (mp) REVERT: G 95 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6692 (mp10) REVERT: G 125 LEU cc_start: 0.8969 (tp) cc_final: 0.8752 (tp) REVERT: G 134 HIS cc_start: 0.8755 (t70) cc_final: 0.8247 (t-170) REVERT: G 298 PHE cc_start: 0.8518 (t80) cc_final: 0.8261 (t80) REVERT: G 300 GLN cc_start: 0.7503 (pm20) cc_final: 0.7075 (pp30) REVERT: G 352 ASN cc_start: 0.9600 (m-40) cc_final: 0.9393 (m110) outliers start: 75 outliers final: 31 residues processed: 393 average time/residue: 0.5139 time to fit residues: 227.9394 Evaluate side-chains 338 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 287 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 198 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 214 optimal weight: 1.9990 chunk 213 optimal weight: 0.4980 chunk 128 optimal weight: 0.0170 chunk 168 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 279 ASN B 89 GLN B 279 ASN C 279 ASN D 89 GLN D 279 ASN E 5 HIS E 263 GLN E 279 ASN F 5 HIS F 95 GLN F 331 ASN F 352 ASN G 89 GLN G 100 ASN G 151 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071190 restraints weight = 33497.663| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.92 r_work: 0.2834 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18375 Z= 0.116 Angle : 0.575 12.809 24927 Z= 0.284 Chirality : 0.040 0.319 2961 Planarity : 0.003 0.034 2975 Dihedral : 4.013 15.207 2359 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.45 % Allowed : 17.04 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 2170 helix: 1.66 (0.14), residues: 1498 sheet: -1.15 (0.61), residues: 70 loop : -0.24 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 152 TYR 0.014 0.001 TYR A 344 PHE 0.013 0.001 PHE A 141 TRP 0.011 0.001 TRP E 74 HIS 0.007 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00238 (18361) covalent geometry : angle 0.57451 (24899) SS BOND : bond 0.00125 ( 14) SS BOND : angle 0.95670 ( 28) hydrogen bonds : bond 0.03924 ( 1102) hydrogen bonds : angle 4.25487 ( 3201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9253 (mt0) cc_final: 0.8926 (tm130) REVERT: A 128 ARG cc_start: 0.8546 (tpt-90) cc_final: 0.8015 (ttp-170) REVERT: A 134 HIS cc_start: 0.8733 (t70) cc_final: 0.8186 (t-170) REVERT: A 298 PHE cc_start: 0.8967 (m-80) cc_final: 0.8633 (t80) REVERT: A 325 ASN cc_start: 0.8787 (p0) cc_final: 0.8244 (p0) REVERT: A 331 ASN cc_start: 0.9526 (m-40) cc_final: 0.9309 (m110) REVERT: B 95 GLN cc_start: 0.6529 (mp-120) cc_final: 0.6198 (mp10) REVERT: B 100 ASN cc_start: 0.8895 (m110) cc_final: 0.8569 (m110) REVERT: B 134 HIS cc_start: 0.8779 (t70) cc_final: 0.8355 (t-170) REVERT: B 151 ASN cc_start: 0.9392 (m-40) cc_final: 0.9191 (m-40) REVERT: B 298 PHE cc_start: 0.8925 (m-80) cc_final: 0.8663 (t80) REVERT: B 338 ILE cc_start: 0.9066 (pp) cc_final: 0.8801 (tp) REVERT: B 352 ASN cc_start: 0.9602 (m-40) cc_final: 0.9384 (m110) REVERT: C 36 LYS cc_start: 0.8295 (tttt) cc_final: 0.8044 (tptt) REVERT: C 56 GLN cc_start: 0.8556 (pp30) cc_final: 0.8144 (tm130) REVERT: C 134 HIS cc_start: 0.8807 (t70) cc_final: 0.8386 (t-170) REVERT: C 301 LYS cc_start: 0.8137 (mttt) cc_final: 0.7485 (tptp) REVERT: C 325 ASN cc_start: 0.8775 (p0) cc_final: 0.8368 (p0) REVERT: C 331 ASN cc_start: 0.9523 (m-40) cc_final: 0.9249 (m110) REVERT: C 348 LYS cc_start: 0.9298 (pttp) cc_final: 0.9032 (pptt) REVERT: D 30 LEU cc_start: 0.9451 (mt) cc_final: 0.9120 (mm) REVERT: D 56 GLN cc_start: 0.9214 (mt0) cc_final: 0.8809 (tm130) REVERT: D 95 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7288 (mm-40) REVERT: D 100 ASN cc_start: 0.8893 (m110) cc_final: 0.8619 (m110) REVERT: D 134 HIS cc_start: 0.8772 (t70) cc_final: 0.8195 (t-170) REVERT: D 151 ASN cc_start: 0.9421 (m-40) cc_final: 0.9077 (m110) REVERT: D 261 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8650 (mmm-85) REVERT: D 298 PHE cc_start: 0.8945 (m-80) cc_final: 0.8496 (t80) REVERT: D 301 LYS cc_start: 0.8323 (mttt) cc_final: 0.7759 (mmtt) REVERT: D 331 ASN cc_start: 0.9506 (m-40) cc_final: 0.9259 (m110) REVERT: E 95 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7408 (mm-40) REVERT: E 134 HIS cc_start: 0.8816 (t70) cc_final: 0.8309 (t-170) REVERT: E 151 ASN cc_start: 0.9389 (m-40) cc_final: 0.9144 (m110) REVERT: E 298 PHE cc_start: 0.8843 (m-80) cc_final: 0.8641 (t80) REVERT: E 301 LYS cc_start: 0.8107 (mttt) cc_final: 0.7401 (mmtt) REVERT: E 325 ASN cc_start: 0.8730 (p0) cc_final: 0.8189 (p0) REVERT: F 95 GLN cc_start: 0.6655 (mp10) cc_final: 0.6058 (mp10) REVERT: F 100 ASN cc_start: 0.8767 (m-40) cc_final: 0.8422 (m110) REVERT: F 125 LEU cc_start: 0.8959 (tp) cc_final: 0.8750 (tp) REVERT: F 134 HIS cc_start: 0.8703 (t70) cc_final: 0.8196 (t-170) REVERT: F 151 ASN cc_start: 0.9297 (m-40) cc_final: 0.8993 (m110) REVERT: F 210 MET cc_start: 0.8326 (tpt) cc_final: 0.8105 (tpp) REVERT: F 261 ARG cc_start: 0.9058 (mmt-90) cc_final: 0.8765 (mmt90) REVERT: F 301 LYS cc_start: 0.8048 (mttt) cc_final: 0.7532 (tptp) REVERT: F 325 ASN cc_start: 0.8757 (p0) cc_final: 0.8281 (p0) REVERT: F 331 ASN cc_start: 0.9581 (m-40) cc_final: 0.9345 (m110) REVERT: G 56 GLN cc_start: 0.8505 (pp30) cc_final: 0.8113 (tm130) REVERT: G 134 HIS cc_start: 0.8761 (t70) cc_final: 0.8266 (t-170) REVERT: G 151 ASN cc_start: 0.9184 (m-40) cc_final: 0.8905 (m110) REVERT: G 210 MET cc_start: 0.8358 (tpt) cc_final: 0.8073 (tpp) REVERT: G 352 ASN cc_start: 0.9598 (m-40) cc_final: 0.9378 (m110) outliers start: 70 outliers final: 23 residues processed: 389 average time/residue: 0.5191 time to fit residues: 228.0212 Evaluate side-chains 331 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 279 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 81 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 89 GLN B 100 ASN B 279 ASN C 279 ASN D 89 GLN D 279 ASN E 263 GLN F 5 HIS G 89 GLN G 100 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070636 restraints weight = 33171.968| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.95 r_work: 0.2815 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18375 Z= 0.121 Angle : 0.570 6.900 24927 Z= 0.280 Chirality : 0.039 0.481 2961 Planarity : 0.003 0.035 2975 Dihedral : 3.928 14.869 2359 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.10 % Allowed : 17.88 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 2170 helix: 1.76 (0.14), residues: 1498 sheet: -1.10 (0.62), residues: 70 loop : -0.20 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 152 TYR 0.014 0.001 TYR G 344 PHE 0.022 0.001 PHE G 298 TRP 0.011 0.001 TRP E 74 HIS 0.008 0.001 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.00276 (18361) covalent geometry : angle 0.56917 (24899) SS BOND : bond 0.00134 ( 14) SS BOND : angle 0.82208 ( 28) hydrogen bonds : bond 0.03835 ( 1102) hydrogen bonds : angle 4.19946 ( 3201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 325 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9257 (mt0) cc_final: 0.8941 (tm130) REVERT: A 95 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6516 (mp10) REVERT: A 128 ARG cc_start: 0.8576 (tpt-90) cc_final: 0.8062 (ttp-170) REVERT: A 134 HIS cc_start: 0.8753 (t70) cc_final: 0.8218 (t-170) REVERT: A 298 PHE cc_start: 0.8989 (m-80) cc_final: 0.8525 (t80) REVERT: A 300 GLN cc_start: 0.7470 (pm20) cc_final: 0.6867 (pp30) REVERT: A 325 ASN cc_start: 0.8728 (p0) cc_final: 0.8168 (p0) REVERT: A 331 ASN cc_start: 0.9526 (m-40) cc_final: 0.9310 (m110) REVERT: B 56 GLN cc_start: 0.8352 (tm130) cc_final: 0.8132 (tm130) REVERT: B 95 GLN cc_start: 0.6626 (mp-120) cc_final: 0.6295 (mp10) REVERT: B 100 ASN cc_start: 0.8845 (m-40) cc_final: 0.8560 (m110) REVERT: B 134 HIS cc_start: 0.8767 (t70) cc_final: 0.8362 (t-170) REVERT: B 151 ASN cc_start: 0.9392 (m-40) cc_final: 0.9190 (m-40) REVERT: B 261 ARG cc_start: 0.9172 (mmt90) cc_final: 0.8940 (mmt90) REVERT: B 298 PHE cc_start: 0.8922 (m-80) cc_final: 0.8669 (t80) REVERT: B 299 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8152 (mtp180) REVERT: B 338 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8749 (tp) REVERT: B 352 ASN cc_start: 0.9596 (m-40) cc_final: 0.9348 (m110) REVERT: C 30 LEU cc_start: 0.9444 (mt) cc_final: 0.9203 (mm) REVERT: C 36 LYS cc_start: 0.8312 (tttt) cc_final: 0.8060 (tptt) REVERT: C 56 GLN cc_start: 0.8593 (pp30) cc_final: 0.8183 (tm130) REVERT: C 95 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6722 (mp10) REVERT: C 134 HIS cc_start: 0.8827 (t70) cc_final: 0.8431 (t-170) REVERT: C 300 GLN cc_start: 0.7566 (pm20) cc_final: 0.7083 (pp30) REVERT: C 301 LYS cc_start: 0.8120 (mttt) cc_final: 0.7851 (tptp) REVERT: C 325 ASN cc_start: 0.8810 (p0) cc_final: 0.8180 (p0) REVERT: C 331 ASN cc_start: 0.9517 (m-40) cc_final: 0.9266 (m110) REVERT: C 348 LYS cc_start: 0.9362 (pttp) cc_final: 0.9067 (pptt) REVERT: D 30 LEU cc_start: 0.9479 (mt) cc_final: 0.9151 (mm) REVERT: D 56 GLN cc_start: 0.9207 (mt0) cc_final: 0.8826 (tm130) REVERT: D 74 TRP cc_start: 0.8656 (t-100) cc_final: 0.8417 (t60) REVERT: D 95 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7430 (mm-40) REVERT: D 100 ASN cc_start: 0.8874 (m110) cc_final: 0.8620 (m110) REVERT: D 134 HIS cc_start: 0.8788 (t70) cc_final: 0.8229 (t-170) REVERT: D 151 ASN cc_start: 0.9416 (m-40) cc_final: 0.9092 (m110) REVERT: D 298 PHE cc_start: 0.8917 (m-80) cc_final: 0.8488 (t80) REVERT: D 301 LYS cc_start: 0.8303 (mttt) cc_final: 0.7752 (mmtt) REVERT: E 95 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7361 (mm-40) REVERT: E 134 HIS cc_start: 0.8817 (t70) cc_final: 0.8297 (t-170) REVERT: E 151 ASN cc_start: 0.9411 (m-40) cc_final: 0.9142 (m110) REVERT: E 298 PHE cc_start: 0.8821 (m-80) cc_final: 0.8468 (t80) REVERT: E 300 GLN cc_start: 0.7479 (pm20) cc_final: 0.6942 (pp30) REVERT: E 301 LYS cc_start: 0.8092 (mttt) cc_final: 0.7858 (mmtt) REVERT: E 325 ASN cc_start: 0.8656 (p0) cc_final: 0.7997 (p0) REVERT: F 56 GLN cc_start: 0.8489 (tm130) cc_final: 0.8188 (tm130) REVERT: F 95 GLN cc_start: 0.6663 (mp10) cc_final: 0.6355 (mp10) REVERT: F 100 ASN cc_start: 0.8774 (m-40) cc_final: 0.8420 (m110) REVERT: F 125 LEU cc_start: 0.8972 (tp) cc_final: 0.8763 (tp) REVERT: F 134 HIS cc_start: 0.8719 (t70) cc_final: 0.8174 (t-170) REVERT: F 151 ASN cc_start: 0.9322 (m-40) cc_final: 0.8997 (m110) REVERT: F 210 MET cc_start: 0.8319 (tpt) cc_final: 0.8095 (tpp) REVERT: F 261 ARG cc_start: 0.9109 (mmt-90) cc_final: 0.8868 (mmt90) REVERT: F 301 LYS cc_start: 0.8026 (mttt) cc_final: 0.7519 (tptp) REVERT: F 325 ASN cc_start: 0.8647 (p0) cc_final: 0.8176 (p0) REVERT: F 331 ASN cc_start: 0.9619 (m-40) cc_final: 0.9399 (m110) REVERT: G 30 LEU cc_start: 0.9439 (mt) cc_final: 0.9123 (mt) REVERT: G 56 GLN cc_start: 0.8550 (pp30) cc_final: 0.8137 (tm130) REVERT: G 95 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6594 (mp10) REVERT: G 128 ARG cc_start: 0.8543 (tpt-90) cc_final: 0.8093 (ttp-170) REVERT: G 134 HIS cc_start: 0.8797 (t70) cc_final: 0.8307 (t-170) REVERT: G 151 ASN cc_start: 0.9284 (m-40) cc_final: 0.8934 (m110) REVERT: G 210 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8090 (tpp) REVERT: G 300 GLN cc_start: 0.7496 (pm20) cc_final: 0.7032 (pp30) REVERT: G 352 ASN cc_start: 0.9595 (m-40) cc_final: 0.9354 (m110) outliers start: 63 outliers final: 28 residues processed: 357 average time/residue: 0.5422 time to fit residues: 217.9257 Evaluate side-chains 321 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 279 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 279 ASN B 89 GLN B 279 ASN C 279 ASN D 279 ASN E 5 HIS E 279 ASN F 5 HIS F 352 ASN G 100 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069447 restraints weight = 33184.703| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.90 r_work: 0.2794 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18375 Z= 0.137 Angle : 0.582 11.782 24927 Z= 0.284 Chirality : 0.040 0.336 2961 Planarity : 0.003 0.040 2975 Dihedral : 3.906 15.196 2359 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.81 % Allowed : 18.28 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2170 helix: 1.84 (0.14), residues: 1498 sheet: -1.05 (0.64), residues: 70 loop : -0.15 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 152 TYR 0.014 0.001 TYR A 344 PHE 0.019 0.001 PHE G 298 TRP 0.014 0.001 TRP E 74 HIS 0.008 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00320 (18361) covalent geometry : angle 0.58208 (24899) SS BOND : bond 0.00189 ( 14) SS BOND : angle 0.82373 ( 28) hydrogen bonds : bond 0.03925 ( 1102) hydrogen bonds : angle 4.18401 ( 3201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9257 (mt0) cc_final: 0.8892 (tm130) REVERT: A 95 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6675 (mm-40) REVERT: A 128 ARG cc_start: 0.8586 (tpt-90) cc_final: 0.8105 (ttp-170) REVERT: A 134 HIS cc_start: 0.8760 (t70) cc_final: 0.8253 (t-170) REVERT: A 298 PHE cc_start: 0.8960 (m-80) cc_final: 0.8534 (t80) REVERT: A 300 GLN cc_start: 0.7570 (pm20) cc_final: 0.6835 (pp30) REVERT: A 325 ASN cc_start: 0.8585 (p0) cc_final: 0.8111 (p0) REVERT: A 331 ASN cc_start: 0.9506 (m-40) cc_final: 0.9288 (m110) REVERT: A 347 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9441 (mm) REVERT: B 56 GLN cc_start: 0.8392 (tm130) cc_final: 0.8156 (tm130) REVERT: B 95 GLN cc_start: 0.6740 (mp-120) cc_final: 0.6280 (mp10) REVERT: B 100 ASN cc_start: 0.8841 (m-40) cc_final: 0.8521 (m110) REVERT: B 128 ARG cc_start: 0.8502 (ttp-170) cc_final: 0.8084 (tpt-90) REVERT: B 134 HIS cc_start: 0.8806 (t70) cc_final: 0.8399 (t-170) REVERT: B 151 ASN cc_start: 0.9406 (m-40) cc_final: 0.9197 (m-40) REVERT: B 197 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8953 (mm-40) REVERT: B 261 ARG cc_start: 0.9168 (mmt90) cc_final: 0.8900 (mmt90) REVERT: B 298 PHE cc_start: 0.8900 (m-80) cc_final: 0.8597 (t80) REVERT: B 352 ASN cc_start: 0.9583 (m-40) cc_final: 0.9363 (m110) REVERT: C 36 LYS cc_start: 0.8350 (tttt) cc_final: 0.8113 (tptt) REVERT: C 56 GLN cc_start: 0.8617 (pp30) cc_final: 0.8192 (tm130) REVERT: C 95 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7122 (mm-40) REVERT: C 134 HIS cc_start: 0.8805 (t70) cc_final: 0.8388 (t-170) REVERT: C 200 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8971 (mtmm) REVERT: C 300 GLN cc_start: 0.7557 (pm20) cc_final: 0.7035 (pp30) REVERT: C 301 LYS cc_start: 0.8131 (mttt) cc_final: 0.7886 (tptp) REVERT: C 325 ASN cc_start: 0.8756 (p0) cc_final: 0.8139 (p0) REVERT: C 331 ASN cc_start: 0.9512 (m-40) cc_final: 0.9272 (m110) REVERT: C 348 LYS cc_start: 0.9368 (pttp) cc_final: 0.9066 (pptt) REVERT: D 30 LEU cc_start: 0.9486 (mt) cc_final: 0.9164 (mm) REVERT: D 56 GLN cc_start: 0.9220 (mt0) cc_final: 0.8847 (tm130) REVERT: D 95 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7459 (mm-40) REVERT: D 100 ASN cc_start: 0.8883 (m110) cc_final: 0.8657 (m110) REVERT: D 134 HIS cc_start: 0.8824 (t70) cc_final: 0.8276 (t-170) REVERT: D 151 ASN cc_start: 0.9424 (m-40) cc_final: 0.9160 (m110) REVERT: D 298 PHE cc_start: 0.8898 (m-80) cc_final: 0.8480 (t80) REVERT: D 301 LYS cc_start: 0.8262 (mttt) cc_final: 0.7748 (mmtt) REVERT: D 331 ASN cc_start: 0.9498 (m-40) cc_final: 0.9222 (m110) REVERT: E 1 MET cc_start: 0.6936 (mmp) cc_final: 0.6646 (tpt) REVERT: E 95 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7479 (mm-40) REVERT: E 134 HIS cc_start: 0.8845 (t70) cc_final: 0.8333 (t-170) REVERT: E 151 ASN cc_start: 0.9390 (m-40) cc_final: 0.9168 (m110) REVERT: E 298 PHE cc_start: 0.8815 (m-80) cc_final: 0.8496 (t80) REVERT: E 299 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8258 (mtp180) REVERT: E 300 GLN cc_start: 0.7481 (pm20) cc_final: 0.6860 (pp30) REVERT: E 301 LYS cc_start: 0.8094 (mttt) cc_final: 0.7853 (mmtt) REVERT: F 56 GLN cc_start: 0.8505 (tm130) cc_final: 0.8211 (tm130) REVERT: F 95 GLN cc_start: 0.6603 (mp10) cc_final: 0.6169 (mp10) REVERT: F 100 ASN cc_start: 0.8772 (m-40) cc_final: 0.8429 (m110) REVERT: F 125 LEU cc_start: 0.9007 (tp) cc_final: 0.8799 (tp) REVERT: F 134 HIS cc_start: 0.8742 (t70) cc_final: 0.8200 (t-170) REVERT: F 151 ASN cc_start: 0.9344 (m-40) cc_final: 0.9012 (m110) REVERT: F 210 MET cc_start: 0.8320 (tpt) cc_final: 0.8094 (tpp) REVERT: F 261 ARG cc_start: 0.9097 (mmt-90) cc_final: 0.8805 (mmt90) REVERT: F 301 LYS cc_start: 0.8075 (mttt) cc_final: 0.7533 (tptp) REVERT: F 325 ASN cc_start: 0.8606 (p0) cc_final: 0.8118 (p0) REVERT: F 331 ASN cc_start: 0.9632 (m-40) cc_final: 0.9405 (m110) REVERT: G 30 LEU cc_start: 0.9456 (mt) cc_final: 0.9126 (mt) REVERT: G 95 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6622 (mp10) REVERT: G 128 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8181 (ttp-170) REVERT: G 134 HIS cc_start: 0.8830 (t70) cc_final: 0.8344 (t-170) REVERT: G 151 ASN cc_start: 0.9349 (m-40) cc_final: 0.9009 (m110) REVERT: G 210 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8115 (tpp) REVERT: G 331 ASN cc_start: 0.9484 (m-40) cc_final: 0.9272 (m-40) outliers start: 57 outliers final: 33 residues processed: 335 average time/residue: 0.5369 time to fit residues: 202.0289 Evaluate side-chains 329 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 279 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 184 optimal weight: 0.4980 chunk 206 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 0.0270 chunk 211 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.2840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 279 ASN B 89 GLN B 279 ASN C 279 ASN D 279 ASN E 352 ASN F 5 HIS F 352 ASN G 100 ASN G 352 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.069463 restraints weight = 33635.748| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.93 r_work: 0.2788 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18375 Z= 0.126 Angle : 0.582 8.671 24927 Z= 0.285 Chirality : 0.039 0.293 2961 Planarity : 0.003 0.041 2975 Dihedral : 3.890 15.255 2359 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.20 % Allowed : 18.52 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 2170 helix: 1.90 (0.14), residues: 1498 sheet: -1.05 (0.64), residues: 70 loop : -0.07 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 152 TYR 0.021 0.001 TYR A 344 PHE 0.017 0.001 PHE G 298 TRP 0.015 0.001 TRP E 74 HIS 0.009 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00292 (18361) covalent geometry : angle 0.58181 (24899) SS BOND : bond 0.00168 ( 14) SS BOND : angle 0.80180 ( 28) hydrogen bonds : bond 0.03828 ( 1102) hydrogen bonds : angle 4.12546 ( 3201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 311 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9257 (mt0) cc_final: 0.8845 (tm130) REVERT: A 95 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6666 (mm-40) REVERT: A 128 ARG cc_start: 0.8574 (tpt-90) cc_final: 0.8115 (ttp-170) REVERT: A 134 HIS cc_start: 0.8771 (t70) cc_final: 0.8259 (t-170) REVERT: A 298 PHE cc_start: 0.8954 (m-80) cc_final: 0.8523 (t80) REVERT: A 300 GLN cc_start: 0.7531 (pm20) cc_final: 0.6783 (pp30) REVERT: A 325 ASN cc_start: 0.8497 (p0) cc_final: 0.7962 (p0) REVERT: A 352 ASN cc_start: 0.9578 (m-40) cc_final: 0.9371 (m110) REVERT: B 56 GLN cc_start: 0.8405 (tm130) cc_final: 0.8159 (tm130) REVERT: B 95 GLN cc_start: 0.6810 (mp-120) cc_final: 0.6506 (mp-120) REVERT: B 134 HIS cc_start: 0.8831 (t70) cc_final: 0.8402 (t-170) REVERT: B 210 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8229 (tpp) REVERT: B 261 ARG cc_start: 0.9161 (mmt90) cc_final: 0.8958 (mmt90) REVERT: B 298 PHE cc_start: 0.8890 (m-80) cc_final: 0.8552 (t80) REVERT: B 352 ASN cc_start: 0.9591 (m-40) cc_final: 0.9372 (m110) REVERT: C 36 LYS cc_start: 0.8332 (tttt) cc_final: 0.8093 (tptt) REVERT: C 56 GLN cc_start: 0.8617 (pp30) cc_final: 0.8189 (tm130) REVERT: C 95 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7184 (mm-40) REVERT: C 128 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8185 (ttp-170) REVERT: C 134 HIS cc_start: 0.8824 (t70) cc_final: 0.8402 (t-170) REVERT: C 300 GLN cc_start: 0.7548 (pm20) cc_final: 0.6972 (pp30) REVERT: C 325 ASN cc_start: 0.8651 (p0) cc_final: 0.7978 (p0) REVERT: C 331 ASN cc_start: 0.9507 (m-40) cc_final: 0.9301 (m110) REVERT: C 348 LYS cc_start: 0.9369 (pttp) cc_final: 0.9052 (pptt) REVERT: D 1 MET cc_start: 0.6877 (mmp) cc_final: 0.6649 (tpt) REVERT: D 56 GLN cc_start: 0.9228 (mt0) cc_final: 0.8829 (tm130) REVERT: D 95 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7413 (mm-40) REVERT: D 100 ASN cc_start: 0.8876 (m110) cc_final: 0.8674 (m110) REVERT: D 134 HIS cc_start: 0.8842 (t70) cc_final: 0.8297 (t-170) REVERT: D 151 ASN cc_start: 0.9441 (m-40) cc_final: 0.9176 (m110) REVERT: D 298 PHE cc_start: 0.8884 (m-80) cc_final: 0.8448 (t80) REVERT: D 301 LYS cc_start: 0.8269 (mttt) cc_final: 0.7759 (mmtt) REVERT: D 331 ASN cc_start: 0.9493 (m-40) cc_final: 0.9205 (m110) REVERT: E 95 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7395 (mm-40) REVERT: E 128 ARG cc_start: 0.8602 (tpt-90) cc_final: 0.8229 (ttp-170) REVERT: E 134 HIS cc_start: 0.8846 (t70) cc_final: 0.8353 (t-170) REVERT: E 301 LYS cc_start: 0.8064 (mttt) cc_final: 0.7346 (mmtt) REVERT: F 56 GLN cc_start: 0.8508 (tm130) cc_final: 0.8219 (tm130) REVERT: F 95 GLN cc_start: 0.6632 (mp10) cc_final: 0.6347 (mp10) REVERT: F 100 ASN cc_start: 0.8766 (m-40) cc_final: 0.8404 (m110) REVERT: F 125 LEU cc_start: 0.9012 (tp) cc_final: 0.8805 (tp) REVERT: F 134 HIS cc_start: 0.8758 (t70) cc_final: 0.8201 (t-170) REVERT: F 210 MET cc_start: 0.8297 (tpt) cc_final: 0.8079 (tpp) REVERT: F 261 ARG cc_start: 0.9070 (mmt-90) cc_final: 0.8788 (mmt90) REVERT: F 298 PHE cc_start: 0.8645 (m-80) cc_final: 0.8040 (t80) REVERT: F 301 LYS cc_start: 0.8063 (mttt) cc_final: 0.7504 (tptp) REVERT: F 331 ASN cc_start: 0.9617 (m-40) cc_final: 0.9396 (m110) REVERT: G 30 LEU cc_start: 0.9444 (mt) cc_final: 0.9116 (mt) REVERT: G 95 GLN cc_start: 0.7313 (mm-40) cc_final: 0.6721 (mm-40) REVERT: G 128 ARG cc_start: 0.8562 (tpt-90) cc_final: 0.8186 (ttp-170) REVERT: G 134 HIS cc_start: 0.8834 (t70) cc_final: 0.8349 (t-170) REVERT: G 151 ASN cc_start: 0.9372 (m-40) cc_final: 0.8997 (m110) REVERT: G 210 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8087 (tpp) REVERT: G 300 GLN cc_start: 0.7470 (pm20) cc_final: 0.7008 (pp30) REVERT: G 331 ASN cc_start: 0.9460 (m-40) cc_final: 0.9196 (m-40) outliers start: 65 outliers final: 32 residues processed: 345 average time/residue: 0.5366 time to fit residues: 208.2751 Evaluate side-chains 325 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 5 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 279 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 185 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 121 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 279 ASN A 331 ASN B 5 HIS B 89 GLN B 279 ASN C 279 ASN D 263 GLN D 279 ASN E 5 HIS E 352 ASN F 5 HIS F 151 ASN F 352 ASN G 5 HIS G 352 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.109480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071039 restraints weight = 33296.643| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.95 r_work: 0.2828 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18375 Z= 0.115 Angle : 0.614 12.030 24927 Z= 0.298 Chirality : 0.039 0.226 2961 Planarity : 0.003 0.042 2975 Dihedral : 3.868 17.919 2359 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.46 % Allowed : 19.95 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2170 helix: 1.93 (0.14), residues: 1491 sheet: -1.02 (0.63), residues: 70 loop : 0.04 (0.28), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 152 TYR 0.018 0.001 TYR B 344 PHE 0.016 0.001 PHE C 141 TRP 0.016 0.001 TRP E 74 HIS 0.012 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00250 (18361) covalent geometry : angle 0.61355 (24899) SS BOND : bond 0.00102 ( 14) SS BOND : angle 0.74892 ( 28) hydrogen bonds : bond 0.03606 ( 1102) hydrogen bonds : angle 4.08904 ( 3201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 321 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6985 (mmp) cc_final: 0.6751 (mmm) REVERT: A 36 LYS cc_start: 0.8412 (tttt) cc_final: 0.8138 (tttt) REVERT: A 56 GLN cc_start: 0.9249 (mt0) cc_final: 0.8851 (tm130) REVERT: A 95 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6729 (mm-40) REVERT: A 128 ARG cc_start: 0.8598 (tpt-90) cc_final: 0.8188 (ttp-170) REVERT: A 134 HIS cc_start: 0.8764 (t70) cc_final: 0.8256 (t-170) REVERT: A 298 PHE cc_start: 0.8963 (m-80) cc_final: 0.8683 (t80) REVERT: A 331 ASN cc_start: 0.9482 (m-40) cc_final: 0.9226 (m-40) REVERT: B 56 GLN cc_start: 0.8421 (tm130) cc_final: 0.8168 (tm130) REVERT: B 95 GLN cc_start: 0.6924 (mp-120) cc_final: 0.6154 (mp10) REVERT: B 134 HIS cc_start: 0.8824 (t70) cc_final: 0.8356 (t-170) REVERT: B 151 ASN cc_start: 0.9330 (m-40) cc_final: 0.9119 (m110) REVERT: B 261 ARG cc_start: 0.9171 (mmt90) cc_final: 0.8675 (mmt90) REVERT: B 298 PHE cc_start: 0.8871 (m-80) cc_final: 0.8526 (t80) REVERT: B 352 ASN cc_start: 0.9593 (m-40) cc_final: 0.9369 (m110) REVERT: C 36 LYS cc_start: 0.8353 (tttt) cc_final: 0.8105 (tptt) REVERT: C 56 GLN cc_start: 0.8610 (pp30) cc_final: 0.8257 (tm130) REVERT: C 59 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9016 (m) REVERT: C 95 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7172 (mm-40) REVERT: C 128 ARG cc_start: 0.8619 (tpt-90) cc_final: 0.8229 (ttp-170) REVERT: C 134 HIS cc_start: 0.8806 (t70) cc_final: 0.8413 (t-170) REVERT: C 300 GLN cc_start: 0.7495 (pm20) cc_final: 0.6902 (pp30) REVERT: C 348 LYS cc_start: 0.9372 (pttp) cc_final: 0.9053 (pptt) REVERT: D 56 GLN cc_start: 0.9227 (mt0) cc_final: 0.8848 (tm130) REVERT: D 95 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7533 (mm-40) REVERT: D 100 ASN cc_start: 0.8865 (m110) cc_final: 0.8655 (m110) REVERT: D 128 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.8172 (ttp-170) REVERT: D 134 HIS cc_start: 0.8834 (t70) cc_final: 0.8287 (t-170) REVERT: D 151 ASN cc_start: 0.9463 (m-40) cc_final: 0.9177 (m110) REVERT: D 298 PHE cc_start: 0.8881 (m-80) cc_final: 0.8449 (t80) REVERT: D 299 ARG cc_start: 0.8533 (mtp180) cc_final: 0.8252 (mtp180) REVERT: D 301 LYS cc_start: 0.8278 (mttt) cc_final: 0.7735 (mmtt) REVERT: D 331 ASN cc_start: 0.9507 (m-40) cc_final: 0.9199 (m110) REVERT: E 56 GLN cc_start: 0.8471 (pp30) cc_final: 0.8203 (tm-30) REVERT: E 95 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7402 (mm-40) REVERT: E 128 ARG cc_start: 0.8614 (tpt-90) cc_final: 0.8263 (ttp-170) REVERT: E 134 HIS cc_start: 0.8854 (t70) cc_final: 0.8372 (t-170) REVERT: E 151 ASN cc_start: 0.9402 (m-40) cc_final: 0.9172 (m110) REVERT: E 300 GLN cc_start: 0.7486 (pm20) cc_final: 0.6838 (pp30) REVERT: E 301 LYS cc_start: 0.8109 (mttt) cc_final: 0.7873 (mmtt) REVERT: E 331 ASN cc_start: 0.9391 (m-40) cc_final: 0.9188 (m-40) REVERT: F 56 GLN cc_start: 0.8519 (tm130) cc_final: 0.8233 (tm130) REVERT: F 95 GLN cc_start: 0.6643 (mp10) cc_final: 0.6336 (mp10) REVERT: F 100 ASN cc_start: 0.8755 (m-40) cc_final: 0.8378 (m110) REVERT: F 125 LEU cc_start: 0.9020 (tp) cc_final: 0.8811 (tp) REVERT: F 134 HIS cc_start: 0.8737 (t70) cc_final: 0.8208 (t-170) REVERT: F 210 MET cc_start: 0.8294 (tpt) cc_final: 0.8085 (tpp) REVERT: F 261 ARG cc_start: 0.9066 (mmt-90) cc_final: 0.8789 (mmt90) REVERT: F 298 PHE cc_start: 0.8664 (m-80) cc_final: 0.8042 (t80) REVERT: F 301 LYS cc_start: 0.8063 (mttt) cc_final: 0.7509 (tptp) REVERT: F 331 ASN cc_start: 0.9619 (m-40) cc_final: 0.9400 (m110) REVERT: G 30 LEU cc_start: 0.9463 (mt) cc_final: 0.9126 (mt) REVERT: G 95 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6824 (mm-40) REVERT: G 100 ASN cc_start: 0.8889 (m110) cc_final: 0.8583 (m110) REVERT: G 128 ARG cc_start: 0.8556 (tpt-90) cc_final: 0.8199 (ttp-170) REVERT: G 134 HIS cc_start: 0.8850 (t70) cc_final: 0.8350 (t-170) REVERT: G 151 ASN cc_start: 0.9393 (m-40) cc_final: 0.9009 (m110) REVERT: G 210 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8085 (tpp) outliers start: 50 outliers final: 25 residues processed: 344 average time/residue: 0.5242 time to fit residues: 202.6782 Evaluate side-chains 322 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 294 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 348 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 212 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 82 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 352 ASN B 89 GLN B 279 ASN C 279 ASN C 331 ASN D 263 GLN D 279 ASN E 5 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070995 restraints weight = 33099.118| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.92 r_work: 0.2848 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18375 Z= 0.120 Angle : 0.628 11.036 24927 Z= 0.304 Chirality : 0.040 0.201 2961 Planarity : 0.004 0.045 2975 Dihedral : 3.880 22.760 2359 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.46 % Allowed : 19.85 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.19), residues: 2170 helix: 1.94 (0.14), residues: 1491 sheet: -0.93 (0.65), residues: 70 loop : 0.06 (0.28), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 152 TYR 0.022 0.001 TYR G 344 PHE 0.014 0.001 PHE G 298 TRP 0.016 0.001 TRP E 74 HIS 0.009 0.001 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.00270 (18361) covalent geometry : angle 0.62764 (24899) SS BOND : bond 0.00126 ( 14) SS BOND : angle 0.73165 ( 28) hydrogen bonds : bond 0.03615 ( 1102) hydrogen bonds : angle 4.11053 ( 3201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8396 (tttt) cc_final: 0.8121 (tttt) REVERT: A 56 GLN cc_start: 0.9225 (mt0) cc_final: 0.8829 (tm130) REVERT: A 95 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6741 (mm-40) REVERT: A 128 ARG cc_start: 0.8581 (tpt-90) cc_final: 0.8175 (ttp-170) REVERT: A 134 HIS cc_start: 0.8766 (t70) cc_final: 0.8252 (t-170) REVERT: A 152 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8482 (ttp80) REVERT: A 298 PHE cc_start: 0.8905 (m-80) cc_final: 0.8428 (t80) REVERT: A 300 GLN cc_start: 0.7582 (pm20) cc_final: 0.6779 (pp30) REVERT: A 331 ASN cc_start: 0.9534 (m-40) cc_final: 0.9264 (m-40) REVERT: B 56 GLN cc_start: 0.8420 (tm130) cc_final: 0.8164 (tm130) REVERT: B 95 GLN cc_start: 0.6945 (mp-120) cc_final: 0.6594 (mp-120) REVERT: B 134 HIS cc_start: 0.8810 (t70) cc_final: 0.8375 (t-170) REVERT: B 151 ASN cc_start: 0.9333 (m-40) cc_final: 0.9072 (m110) REVERT: B 261 ARG cc_start: 0.9153 (mmt90) cc_final: 0.8926 (mmt90) REVERT: B 352 ASN cc_start: 0.9599 (m-40) cc_final: 0.9372 (m110) REVERT: C 36 LYS cc_start: 0.8338 (tttt) cc_final: 0.8083 (tptt) REVERT: C 59 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9106 (m) REVERT: C 94 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8650 (mt) REVERT: C 95 GLN cc_start: 0.7453 (mm-40) cc_final: 0.6705 (mp10) REVERT: C 128 ARG cc_start: 0.8582 (tpt-90) cc_final: 0.8227 (ttp-170) REVERT: C 134 HIS cc_start: 0.8812 (t70) cc_final: 0.8429 (t-170) REVERT: C 152 ARG cc_start: 0.8894 (ttm-80) cc_final: 0.8516 (ttp80) REVERT: C 298 PHE cc_start: 0.8462 (t80) cc_final: 0.8254 (t80) REVERT: C 331 ASN cc_start: 0.9474 (m-40) cc_final: 0.9268 (m-40) REVERT: C 348 LYS cc_start: 0.9395 (pttp) cc_final: 0.9078 (pptt) REVERT: D 56 GLN cc_start: 0.9189 (mt0) cc_final: 0.8816 (tm130) REVERT: D 95 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7536 (mm-40) REVERT: D 100 ASN cc_start: 0.8858 (m110) cc_final: 0.8642 (m110) REVERT: D 128 ARG cc_start: 0.8615 (tpt-90) cc_final: 0.8171 (ttp-170) REVERT: D 134 HIS cc_start: 0.8802 (t70) cc_final: 0.8289 (t-170) REVERT: D 151 ASN cc_start: 0.9472 (m-40) cc_final: 0.9165 (m110) REVERT: D 152 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8526 (ttp80) REVERT: D 298 PHE cc_start: 0.8853 (m-80) cc_final: 0.8411 (t80) REVERT: D 299 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8227 (mtp180) REVERT: D 301 LYS cc_start: 0.8265 (mttt) cc_final: 0.7723 (mmtt) REVERT: D 331 ASN cc_start: 0.9510 (m-40) cc_final: 0.9200 (m110) REVERT: E 56 GLN cc_start: 0.8486 (pp30) cc_final: 0.8201 (tm-30) REVERT: E 95 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7397 (mm-40) REVERT: E 128 ARG cc_start: 0.8598 (tpt-90) cc_final: 0.8236 (ttp-170) REVERT: E 134 HIS cc_start: 0.8853 (t70) cc_final: 0.8375 (t-170) REVERT: E 299 ARG cc_start: 0.8611 (mtp180) cc_final: 0.8156 (mtp180) REVERT: E 300 GLN cc_start: 0.7454 (pm20) cc_final: 0.6932 (pp30) REVERT: E 301 LYS cc_start: 0.8107 (mttt) cc_final: 0.7895 (mmtt) REVERT: E 331 ASN cc_start: 0.9419 (m-40) cc_final: 0.9180 (m-40) REVERT: F 56 GLN cc_start: 0.8524 (tm130) cc_final: 0.8231 (tm130) REVERT: F 95 GLN cc_start: 0.6663 (mp10) cc_final: 0.6332 (mp10) REVERT: F 100 ASN cc_start: 0.8733 (m-40) cc_final: 0.8357 (m110) REVERT: F 125 LEU cc_start: 0.9007 (tp) cc_final: 0.8807 (tp) REVERT: F 134 HIS cc_start: 0.8749 (t70) cc_final: 0.8223 (t-170) REVERT: F 210 MET cc_start: 0.8280 (tpt) cc_final: 0.8064 (tpp) REVERT: F 261 ARG cc_start: 0.9046 (mmt-90) cc_final: 0.8758 (mmt90) REVERT: F 298 PHE cc_start: 0.8640 (m-80) cc_final: 0.7955 (t80) REVERT: F 299 ARG cc_start: 0.8441 (mtp180) cc_final: 0.8208 (mmm-85) REVERT: F 301 LYS cc_start: 0.8108 (mttt) cc_final: 0.7450 (tptp) REVERT: F 331 ASN cc_start: 0.9624 (m-40) cc_final: 0.9400 (m110) REVERT: F 352 ASN cc_start: 0.9442 (m110) cc_final: 0.9058 (p0) REVERT: G 30 LEU cc_start: 0.9425 (mt) cc_final: 0.9081 (mt) REVERT: G 95 GLN cc_start: 0.7443 (mm-40) cc_final: 0.6860 (mm-40) REVERT: G 100 ASN cc_start: 0.8899 (m110) cc_final: 0.8590 (m110) REVERT: G 128 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.8165 (ttp-170) REVERT: G 134 HIS cc_start: 0.8850 (t70) cc_final: 0.8321 (t-170) REVERT: G 151 ASN cc_start: 0.9424 (m-40) cc_final: 0.9049 (m110) REVERT: G 210 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (tpp) outliers start: 50 outliers final: 35 residues processed: 331 average time/residue: 0.5592 time to fit residues: 207.8458 Evaluate side-chains 334 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 295 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 348 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 143 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 91 optimal weight: 0.0270 chunk 106 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 89 GLN B 279 ASN C 279 ASN D 279 ASN E 151 ASN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 ASN ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.069133 restraints weight = 33153.207| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.93 r_work: 0.2785 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18375 Z= 0.163 Angle : 0.661 10.726 24927 Z= 0.319 Chirality : 0.041 0.186 2961 Planarity : 0.004 0.045 2975 Dihedral : 3.907 26.163 2359 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.17 % Allowed : 20.69 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.19), residues: 2170 helix: 1.91 (0.14), residues: 1491 sheet: -0.94 (0.66), residues: 70 loop : 0.07 (0.28), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 152 TYR 0.023 0.001 TYR B 344 PHE 0.015 0.001 PHE G 298 TRP 0.020 0.001 TRP A 74 HIS 0.010 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00390 (18361) covalent geometry : angle 0.66097 (24899) SS BOND : bond 0.00210 ( 14) SS BOND : angle 0.75839 ( 28) hydrogen bonds : bond 0.03832 ( 1102) hydrogen bonds : angle 4.19572 ( 3201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8444 (tttt) cc_final: 0.8167 (tttt) REVERT: A 56 GLN cc_start: 0.9255 (mt0) cc_final: 0.8861 (tm130) REVERT: A 95 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6810 (mm-40) REVERT: A 128 ARG cc_start: 0.8617 (tpt-90) cc_final: 0.8203 (ttp-170) REVERT: A 134 HIS cc_start: 0.8791 (t70) cc_final: 0.8278 (t-170) REVERT: A 152 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.8495 (ttp80) REVERT: A 298 PHE cc_start: 0.8943 (m-80) cc_final: 0.8450 (t80) REVERT: A 300 GLN cc_start: 0.7570 (pm20) cc_final: 0.6784 (pp30) REVERT: A 331 ASN cc_start: 0.9544 (m-40) cc_final: 0.9278 (m-40) REVERT: B 56 GLN cc_start: 0.8470 (tm130) cc_final: 0.8233 (tm130) REVERT: B 95 GLN cc_start: 0.7012 (mp-120) cc_final: 0.6303 (mp10) REVERT: B 134 HIS cc_start: 0.8835 (t70) cc_final: 0.8391 (t-170) REVERT: B 151 ASN cc_start: 0.9321 (m-40) cc_final: 0.9068 (m110) REVERT: B 261 ARG cc_start: 0.9147 (mmt90) cc_final: 0.8694 (mmt90) REVERT: B 298 PHE cc_start: 0.8832 (m-80) cc_final: 0.8475 (t80) REVERT: B 352 ASN cc_start: 0.9601 (m-40) cc_final: 0.9378 (m110) REVERT: C 36 LYS cc_start: 0.8372 (tttt) cc_final: 0.8095 (tptt) REVERT: C 59 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9104 (m) REVERT: C 95 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7217 (mm-40) REVERT: C 128 ARG cc_start: 0.8641 (tpt-90) cc_final: 0.8299 (ttp-170) REVERT: C 134 HIS cc_start: 0.8833 (t70) cc_final: 0.8452 (t-170) REVERT: C 152 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8514 (ttp80) REVERT: C 298 PHE cc_start: 0.8452 (t80) cc_final: 0.7910 (t80) REVERT: C 300 GLN cc_start: 0.7447 (pm20) cc_final: 0.6912 (pp30) REVERT: C 348 LYS cc_start: 0.9415 (pttp) cc_final: 0.9037 (pptt) REVERT: C 352 ASN cc_start: 0.9499 (m-40) cc_final: 0.9139 (p0) REVERT: D 56 GLN cc_start: 0.9227 (mt0) cc_final: 0.8844 (tm130) REVERT: D 74 TRP cc_start: 0.8755 (t-100) cc_final: 0.8479 (t60) REVERT: D 95 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7579 (mm-40) REVERT: D 128 ARG cc_start: 0.8659 (tpt-90) cc_final: 0.8206 (ttp-170) REVERT: D 134 HIS cc_start: 0.8840 (t70) cc_final: 0.8326 (t-170) REVERT: D 151 ASN cc_start: 0.9469 (m-40) cc_final: 0.9160 (m110) REVERT: D 152 ARG cc_start: 0.8896 (ttm-80) cc_final: 0.8535 (ttp80) REVERT: D 298 PHE cc_start: 0.8852 (m-80) cc_final: 0.8433 (t80) REVERT: D 299 ARG cc_start: 0.8560 (mtp180) cc_final: 0.8276 (mtp180) REVERT: D 301 LYS cc_start: 0.8285 (mttt) cc_final: 0.7742 (mmtt) REVERT: E 56 GLN cc_start: 0.8560 (pp30) cc_final: 0.8260 (tm-30) REVERT: E 95 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7449 (mm-40) REVERT: E 128 ARG cc_start: 0.8635 (tpt-90) cc_final: 0.8283 (ttp-170) REVERT: E 134 HIS cc_start: 0.8879 (t70) cc_final: 0.8417 (t-170) REVERT: E 300 GLN cc_start: 0.7497 (pm20) cc_final: 0.6902 (pp30) REVERT: E 331 ASN cc_start: 0.9423 (m-40) cc_final: 0.9194 (m-40) REVERT: F 56 GLN cc_start: 0.8547 (tm130) cc_final: 0.8264 (tm130) REVERT: F 95 GLN cc_start: 0.6692 (mp10) cc_final: 0.6301 (mp-120) REVERT: F 100 ASN cc_start: 0.8785 (m-40) cc_final: 0.8443 (m110) REVERT: F 125 LEU cc_start: 0.9034 (tp) cc_final: 0.8828 (tp) REVERT: F 134 HIS cc_start: 0.8759 (t70) cc_final: 0.8227 (t-170) REVERT: F 210 MET cc_start: 0.8262 (tpt) cc_final: 0.8033 (tpp) REVERT: F 261 ARG cc_start: 0.9058 (mmt-90) cc_final: 0.8826 (mmt-90) REVERT: F 298 PHE cc_start: 0.8637 (m-80) cc_final: 0.8003 (t80) REVERT: F 331 ASN cc_start: 0.9628 (m-40) cc_final: 0.9406 (m110) REVERT: F 352 ASN cc_start: 0.9446 (m110) cc_final: 0.9079 (p0) REVERT: G 30 LEU cc_start: 0.9434 (mt) cc_final: 0.9101 (mt) REVERT: G 56 GLN cc_start: 0.8546 (pp30) cc_final: 0.8124 (tm130) REVERT: G 95 GLN cc_start: 0.7497 (mm-40) cc_final: 0.6901 (mm-40) REVERT: G 128 ARG cc_start: 0.8572 (tpt-90) cc_final: 0.8211 (ttp-170) REVERT: G 134 HIS cc_start: 0.8863 (t70) cc_final: 0.8347 (t-170) REVERT: G 151 ASN cc_start: 0.9424 (m-40) cc_final: 0.9041 (m110) REVERT: G 210 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8098 (tpp) outliers start: 44 outliers final: 35 residues processed: 314 average time/residue: 0.5363 time to fit residues: 188.8185 Evaluate side-chains 332 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 348 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 0 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 141 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 207 optimal weight: 0.0670 chunk 212 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 89 GLN B 279 ASN B 318 HIS C 279 ASN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.071224 restraints weight = 33126.482| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.98 r_work: 0.2836 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18375 Z= 0.120 Angle : 0.658 12.221 24927 Z= 0.317 Chirality : 0.040 0.221 2961 Planarity : 0.004 0.042 2975 Dihedral : 3.920 25.303 2359 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.07 % Allowed : 21.13 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2170 helix: 1.89 (0.14), residues: 1463 sheet: -0.95 (0.65), residues: 70 loop : -0.04 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 152 TYR 0.026 0.001 TYR C 344 PHE 0.014 0.001 PHE B 141 TRP 0.018 0.001 TRP E 74 HIS 0.010 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00263 (18361) covalent geometry : angle 0.65775 (24899) SS BOND : bond 0.00097 ( 14) SS BOND : angle 0.75022 ( 28) hydrogen bonds : bond 0.03566 ( 1102) hydrogen bonds : angle 4.14129 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5971.68 seconds wall clock time: 102 minutes 30.88 seconds (6150.88 seconds total)