Starting phenix.real_space_refine on Sat Sep 12 05:02:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wy_68061/09_2026/21wy_68061.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wy_68061/09_2026/21wy_68061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21wy_68061/09_2026/21wy_68061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wy_68061/09_2026/21wy_68061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21wy_68061/09_2026/21wy_68061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wy_68061/09_2026/21wy_68061.map" } resolution = 3.0 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8785 2.51 5 N 2250 2.21 5 O 2380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13485 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2697 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain breaks: 3 Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.95, per 1000 atoms: 0.22 Number of scatterers: 13485 At special positions: 0 Unit cell: (103.455, 100.89, 129.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2380 8.00 N 2250 7.00 C 8785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 252 " - pdb=" SG CYS E 263 " 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: 1.04 Conformation dependent library (CDL) restraints added in 720.1 milliseconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3170 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 39.9% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 126 through 129 removed outlier: 3.617A pdb=" N GLN A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.619A pdb=" N ILE A 148 " --> pdb=" O HIS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.518A pdb=" N PHE A 296 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 298 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.510A pdb=" N SER A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 326 Processing helix chain 'A' and resid 334 through 363 removed outlier: 3.622A pdb=" N LEU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 412 removed outlier: 3.588A pdb=" N VAL A 385 " --> pdb=" O HIS A 381 " (cutoff:3.500A) Proline residue: A 398 - end of helix Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 126 through 129 removed outlier: 3.618A pdb=" N GLN B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 129' Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.618A pdb=" N ILE B 148 " --> pdb=" O HIS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.518A pdb=" N PHE B 296 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 298 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.511A pdb=" N SER B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 326 Processing helix chain 'B' and resid 334 through 363 removed outlier: 3.623A pdb=" N LEU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 363 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 412 removed outlier: 3.588A pdb=" N VAL B 385 " --> pdb=" O HIS B 381 " (cutoff:3.500A) Proline residue: B 398 - end of helix Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 126 through 129 removed outlier: 3.617A pdb=" N GLN C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.620A pdb=" N ILE C 148 " --> pdb=" O HIS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.518A pdb=" N PHE C 296 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 298 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.510A pdb=" N SER C 307 " --> pdb=" O VAL C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 326 Processing helix chain 'C' and resid 334 through 363 removed outlier: 3.622A pdb=" N LEU C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 363 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 412 removed outlier: 3.589A pdb=" N VAL C 385 " --> pdb=" O HIS C 381 " (cutoff:3.500A) Proline residue: C 398 - end of helix Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 126 through 129 removed outlier: 3.618A pdb=" N GLN D 129 " --> pdb=" O PRO D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 129' Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.618A pdb=" N ILE D 148 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 281 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.518A pdb=" N PHE D 296 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 298 " --> pdb=" O THR D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.511A pdb=" N SER D 307 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 326 Processing helix chain 'D' and resid 334 through 363 removed outlier: 3.622A pdb=" N LEU D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 363 " --> pdb=" O ASN D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 412 removed outlier: 3.588A pdb=" N VAL D 385 " --> pdb=" O HIS D 381 " (cutoff:3.500A) Proline residue: D 398 - end of helix Processing helix chain 'E' and resid 42 through 51 Processing helix chain 'E' and resid 126 through 129 removed outlier: 3.618A pdb=" N GLN E 129 " --> pdb=" O PRO E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 126 through 129' Processing helix chain 'E' and resid 144 through 148 removed outlier: 3.618A pdb=" N ILE E 148 " --> pdb=" O HIS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 281 Processing helix chain 'E' and resid 281 through 292 Processing helix chain 'E' and resid 293 through 298 removed outlier: 3.518A pdb=" N PHE E 296 " --> pdb=" O PHE E 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.510A pdb=" N SER E 307 " --> pdb=" O VAL E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 326 Processing helix chain 'E' and resid 334 through 363 removed outlier: 3.621A pdb=" N LEU E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 363 " --> pdb=" O ASN E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 412 removed outlier: 3.588A pdb=" N VAL E 385 " --> pdb=" O HIS E 381 " (cutoff:3.500A) Proline residue: E 398 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.747A pdb=" N SER A 102 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 118 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 100 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 120 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 98 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN A 122 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 96 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN A 124 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL A 94 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 92 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 223 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL A 94 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.747A pdb=" N SER A 102 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 118 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 100 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 120 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 98 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN A 122 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 96 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN A 124 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL A 94 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N THR A 238 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 101 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU A 240 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.746A pdb=" N SER B 102 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 118 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU B 100 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN B 120 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL B 98 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 122 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 96 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 124 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL B 94 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 92 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 223 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL B 94 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 removed outlier: 3.746A pdb=" N SER B 102 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 118 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU B 100 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN B 120 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL B 98 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 122 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 96 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 124 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL B 94 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N THR B 238 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 101 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU B 240 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 156 Processing sheet with id=AA7, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.747A pdb=" N SER C 102 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 100 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL C 98 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN C 122 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C 96 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN C 124 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL C 94 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 92 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C 223 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL C 94 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 170 through 173 removed outlier: 3.747A pdb=" N SER C 102 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 100 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL C 98 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN C 122 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C 96 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN C 124 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL C 94 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N THR C 238 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 101 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU C 240 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.748A pdb=" N SER D 102 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU D 118 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU D 100 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN D 120 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL D 98 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN D 122 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL D 96 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN D 124 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL D 94 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU D 92 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL D 223 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL D 94 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 170 through 173 removed outlier: 3.748A pdb=" N SER D 102 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU D 118 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU D 100 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN D 120 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL D 98 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN D 122 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL D 96 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN D 124 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL D 94 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N THR D 238 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 101 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU D 240 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 103 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AB4, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.747A pdb=" N SER E 102 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 118 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU E 100 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN E 120 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL E 98 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN E 122 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL E 96 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 124 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL E 94 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 92 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL E 223 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL E 94 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 170 through 173 removed outlier: 3.747A pdb=" N SER E 102 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 118 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU E 100 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN E 120 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL E 98 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN E 122 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL E 96 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 124 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL E 94 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N THR E 238 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 101 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU E 240 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 103 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 153 through 156 676 hydrogen bonds defined for protein. 1983 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: 2.42 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4162 1.34 - 1.46: 3004 1.46 - 1.58: 6589 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 13860 Sorted by residual: bond pdb=" CA ARG E 258 " pdb=" C ARG E 258 " ideal model delta sigma weight residual 1.520 1.543 -0.023 1.37e-02 5.33e+03 2.79e+00 bond pdb=" CA ARG C 258 " pdb=" C ARG C 258 " ideal model delta sigma weight residual 1.520 1.543 -0.023 1.37e-02 5.33e+03 2.76e+00 bond pdb=" CA ARG A 258 " pdb=" C ARG A 258 " ideal model delta sigma weight residual 1.520 1.542 -0.022 1.37e-02 5.33e+03 2.68e+00 bond pdb=" CA ARG D 258 " pdb=" C ARG D 258 " ideal model delta sigma weight residual 1.520 1.542 -0.022 1.37e-02 5.33e+03 2.65e+00 bond pdb=" CA ARG B 258 " pdb=" C ARG B 258 " ideal model delta sigma weight residual 1.520 1.542 -0.022 1.37e-02 5.33e+03 2.53e+00 ... (remaining 13855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 18520 2.21 - 4.41: 249 4.41 - 6.62: 46 6.62 - 8.82: 5 8.82 - 11.03: 5 Bond angle restraints: 18825 Sorted by residual: angle pdb=" C ARG B 258 " pdb=" N GLY B 259 " pdb=" CA GLY B 259 " ideal model delta sigma weight residual 121.83 128.56 -6.73 1.30e+00 5.92e-01 2.68e+01 angle pdb=" C ARG C 258 " pdb=" N GLY C 259 " pdb=" CA GLY C 259 " ideal model delta sigma weight residual 121.83 128.55 -6.72 1.30e+00 5.92e-01 2.67e+01 angle pdb=" C ARG A 258 " pdb=" N GLY A 259 " pdb=" CA GLY A 259 " ideal model delta sigma weight residual 121.83 128.52 -6.69 1.30e+00 5.92e-01 2.65e+01 angle pdb=" C ARG D 258 " pdb=" N GLY D 259 " pdb=" CA GLY D 259 " ideal model delta sigma weight residual 121.83 128.50 -6.67 1.30e+00 5.92e-01 2.63e+01 angle pdb=" C ARG E 258 " pdb=" N GLY E 259 " pdb=" CA GLY E 259 " ideal model delta sigma weight residual 121.83 128.50 -6.67 1.30e+00 5.92e-01 2.63e+01 ... (remaining 18820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 6986 16.55 - 33.10: 779 33.10 - 49.65: 290 49.65 - 66.20: 55 66.20 - 82.75: 35 Dihedral angle restraints: 8145 sinusoidal: 3275 harmonic: 4870 Sorted by residual: dihedral pdb=" CA ASN C 255 " pdb=" C ASN C 255 " pdb=" N SER C 256 " pdb=" CA SER C 256 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN D 255 " pdb=" C ASN D 255 " pdb=" N SER D 256 " pdb=" CA SER D 256 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN E 255 " pdb=" C ASN E 255 " pdb=" N SER E 256 " pdb=" CA SER E 256 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.061: 591 0.061 - 0.092: 181 0.092 - 0.123: 62 0.123 - 0.154: 10 Chirality restraints: 2105 Sorted by residual: chirality pdb=" CA ILE D 189 " pdb=" N ILE D 189 " pdb=" C ILE D 189 " pdb=" CB ILE D 189 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2102 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 150 " 0.067 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO C 151 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 150 " 0.067 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO D 151 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 150 " 0.067 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO A 151 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.054 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 360 2.70 - 3.25: 12498 3.25 - 3.80: 20107 3.80 - 4.35: 25931 4.35 - 4.90: 44237 Nonbonded interactions: 103133 Sorted by model distance: nonbonded pdb=" OH TYR A 243 " pdb=" OG SER B 332 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR D 243 " pdb=" OG SER E 332 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR B 243 " pdb=" OG SER C 332 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR C 243 " pdb=" OG SER D 332 " model vdw 2.180 3.040 nonbonded pdb=" OG1 THR E 153 " pdb=" OH TYR E 222 " model vdw 2.263 3.040 ... (remaining 103128 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.640 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.066 13870 Z= 0.154 Angle : 0.675 11.028 18845 Z= 0.380 Chirality : 0.040 0.154 2105 Planarity : 0.007 0.100 2340 Dihedral : 16.828 82.748 4945 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.26 % Allowed : 24.32 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.33 (0.21), residues: 1605 helix: 2.69 (0.22), residues: 530 sheet: 1.05 (0.27), residues: 390 loop : -2.50 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 265 TYR 0.009 0.001 TYR C 130 PHE 0.039 0.002 PHE D 170 TRP 0.012 0.002 TRP A 257 HIS 0.002 0.000 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (13860) covalent geometry : angle 0.67516 / 0.38 (18825) SS BOND : bond 0.00181 / 0.11 ( 10) SS BOND : angle 0.47512 / 0.32 ( 20) hydrogen bonds : bond 0.12829 / 8.37 ( 601) hydrogen bonds : angle 5.40294 / 3.73 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 381 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.7929 (p90) cc_final: 0.7561 (p90) REVERT: A 155 PHE cc_start: 0.8505 (m-80) cc_final: 0.8185 (m-80) REVERT: A 232 ARG cc_start: 0.7577 (ttm170) cc_final: 0.7230 (mtt-85) REVERT: A 260 ASN cc_start: 0.8100 (m110) cc_final: 0.7895 (m110) REVERT: A 261 TYR cc_start: 0.8121 (m-10) cc_final: 0.7815 (m-10) REVERT: A 265 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7972 (ttm170) REVERT: B 59 LEU cc_start: 0.8623 (tt) cc_final: 0.8411 (tp) REVERT: B 176 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7615 (mtt90) REVERT: B 246 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8126 (tttp) REVERT: B 282 PHE cc_start: 0.8357 (m-80) cc_final: 0.7889 (m-80) REVERT: B 359 ASN cc_start: 0.7976 (t0) cc_final: 0.7473 (t0) REVERT: B 360 TYR cc_start: 0.8542 (t80) cc_final: 0.8146 (t80) REVERT: C 59 LEU cc_start: 0.8660 (tt) cc_final: 0.8450 (tt) REVERT: C 125 ASP cc_start: 0.8458 (t0) cc_final: 0.8251 (t0) REVERT: C 246 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: C 311 VAL cc_start: 0.7673 (m) cc_final: 0.7439 (t) REVERT: C 330 VAL cc_start: 0.8506 (p) cc_final: 0.8304 (t) REVERT: C 341 ASP cc_start: 0.7917 (m-30) cc_final: 0.7571 (m-30) REVERT: D 59 LEU cc_start: 0.8664 (tt) cc_final: 0.8459 (tm) REVERT: D 99 LEU cc_start: 0.8447 (tp) cc_final: 0.8221 (tt) REVERT: D 125 ASP cc_start: 0.8337 (t0) cc_final: 0.7983 (t70) REVERT: D 154 TYR cc_start: 0.7920 (p90) cc_final: 0.7650 (p90) REVERT: D 177 ASN cc_start: 0.7100 (p0) cc_final: 0.6879 (p0) REVERT: D 214 SER cc_start: 0.8457 (t) cc_final: 0.8250 (m) REVERT: D 246 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8028 (tttp) REVERT: D 274 ARG cc_start: 0.8471 (tpp80) cc_final: 0.8265 (tpp80) REVERT: E 260 ASN cc_start: 0.7957 (m110) cc_final: 0.7749 (m-40) REVERT: E 359 ASN cc_start: 0.7986 (t0) cc_final: 0.7398 (t0) outliers start: 49 outliers final: 26 residues processed: 409 average time/residue: 0.5404 time to fit residues: 243.2254 Evaluate side-chains 383 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 240 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN A 226 ASN A 241 ASN A 247 ASN A 301 ASN C 301 ASN D 120 ASN D 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104643 restraints weight = 18485.451| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.12 r_work: 0.3151 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13870 Z= 0.133 Angle : 0.564 7.806 18845 Z= 0.293 Chirality : 0.042 0.171 2105 Planarity : 0.005 0.063 2340 Dihedral : 6.409 57.132 1852 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.25 % Allowed : 23.32 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.57 (0.21), residues: 1605 helix: 2.78 (0.22), residues: 535 sheet: 1.75 (0.27), residues: 370 loop : -2.57 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 325 TYR 0.017 0.001 TYR C 130 PHE 0.023 0.002 PHE B 170 TRP 0.017 0.002 TRP D 123 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13860) covalent geometry : angle 0.56385 / 0.29 (18825) SS BOND : bond 0.00438 / 0.24 ( 10) SS BOND : angle 0.57091 / 0.28 ( 20) hydrogen bonds : bond 0.05126 / 3.32 ( 601) hydrogen bonds : angle 4.03896 / 2.79 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 371 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.8607 (m-80) cc_final: 0.8375 (m-80) REVERT: A 182 TYR cc_start: 0.7979 (t80) cc_final: 0.7692 (t80) REVERT: A 205 LYS cc_start: 0.8138 (mtpm) cc_final: 0.7757 (tttm) REVERT: A 217 GLU cc_start: 0.7484 (tp30) cc_final: 0.7254 (tp30) REVERT: A 232 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7693 (mtt180) REVERT: A 260 ASN cc_start: 0.7994 (m110) cc_final: 0.7748 (m-40) REVERT: A 354 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 56 ASP cc_start: 0.7888 (p0) cc_final: 0.7564 (p0) REVERT: B 176 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7936 (mtt90) REVERT: B 238 THR cc_start: 0.8292 (m) cc_final: 0.7867 (p) REVERT: B 282 PHE cc_start: 0.8309 (m-80) cc_final: 0.7997 (m-80) REVERT: B 360 TYR cc_start: 0.8725 (t80) cc_final: 0.8413 (t80) REVERT: C 107 ASP cc_start: 0.7305 (t0) cc_final: 0.6986 (t0) REVERT: C 116 GLU cc_start: 0.8196 (tt0) cc_final: 0.7959 (tt0) REVERT: C 125 ASP cc_start: 0.8412 (t0) cc_final: 0.8149 (t0) REVERT: C 232 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7416 (mtm180) REVERT: C 341 ASP cc_start: 0.7828 (m-30) cc_final: 0.7525 (m-30) REVERT: D 99 LEU cc_start: 0.8458 (tp) cc_final: 0.8230 (tt) REVERT: D 125 ASP cc_start: 0.8332 (t0) cc_final: 0.7987 (t0) REVERT: D 177 ASN cc_start: 0.7108 (p0) cc_final: 0.6906 (m110) REVERT: D 182 TYR cc_start: 0.8251 (t80) cc_final: 0.7892 (t80) REVERT: D 214 SER cc_start: 0.8524 (t) cc_final: 0.8236 (m) REVERT: D 238 THR cc_start: 0.8258 (m) cc_final: 0.7782 (p) REVERT: D 316 ASN cc_start: 0.8116 (t0) cc_final: 0.7900 (t160) REVERT: E 46 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7797 (mp) REVERT: E 59 LEU cc_start: 0.8415 (tp) cc_final: 0.8158 (tt) REVERT: E 238 THR cc_start: 0.8239 (m) cc_final: 0.7821 (p) outliers start: 64 outliers final: 37 residues processed: 407 average time/residue: 0.5195 time to fit residues: 233.3081 Evaluate side-chains 403 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 364 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 184 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 ASN A 301 ASN C 301 ASN D 120 ASN D 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102628 restraints weight = 18478.913| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.08 r_work: 0.3124 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13870 Z= 0.155 Angle : 0.549 7.832 18845 Z= 0.288 Chirality : 0.042 0.160 2105 Planarity : 0.005 0.057 2340 Dihedral : 4.735 36.648 1822 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.72 % Allowed : 24.65 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.58 (0.21), residues: 1605 helix: 2.77 (0.21), residues: 530 sheet: 1.50 (0.27), residues: 390 loop : -2.46 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.016 0.001 TYR C 130 PHE 0.026 0.002 PHE C 170 TRP 0.014 0.002 TRP D 123 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (13860) covalent geometry : angle 0.54876 / 0.29 (18825) SS BOND : bond 0.00226 / 0.15 ( 10) SS BOND : angle 0.84403 / 0.69 ( 20) hydrogen bonds : bond 0.05751 / 3.76 ( 601) hydrogen bonds : angle 3.97836 / 2.75 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8132 (mtpm) cc_final: 0.7712 (tttm) REVERT: A 210 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8131 (mtm) REVERT: A 213 ILE cc_start: 0.8313 (tt) cc_final: 0.8054 (tt) REVERT: A 217 GLU cc_start: 0.7461 (tp30) cc_final: 0.7246 (tp30) REVERT: A 232 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7660 (mtt180) REVERT: B 56 ASP cc_start: 0.7940 (p0) cc_final: 0.7640 (p0) REVERT: B 176 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7823 (mtt90) REVERT: B 210 MET cc_start: 0.8352 (mtp) cc_final: 0.8131 (mtm) REVERT: B 238 THR cc_start: 0.8331 (m) cc_final: 0.7909 (p) REVERT: C 107 ASP cc_start: 0.7477 (t0) cc_final: 0.7114 (t0) REVERT: C 125 ASP cc_start: 0.8409 (t0) cc_final: 0.8179 (t0) REVERT: C 238 THR cc_start: 0.8248 (m) cc_final: 0.7838 (p) REVERT: C 241 ASN cc_start: 0.8075 (t0) cc_final: 0.7818 (t0) REVERT: C 341 ASP cc_start: 0.7925 (m-30) cc_final: 0.7613 (m-30) REVERT: C 384 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7745 (mtp180) REVERT: D 99 LEU cc_start: 0.8603 (tp) cc_final: 0.8382 (tt) REVERT: D 125 ASP cc_start: 0.8382 (t0) cc_final: 0.8033 (t0) REVERT: D 214 SER cc_start: 0.8570 (t) cc_final: 0.8287 (m) REVERT: D 223 VAL cc_start: 0.8199 (p) cc_final: 0.7886 (m) REVERT: D 233 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.2043 (ttmm) REVERT: D 238 THR cc_start: 0.8275 (m) cc_final: 0.7818 (p) REVERT: D 247 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7983 (p0) REVERT: E 46 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7779 (mp) REVERT: E 59 LEU cc_start: 0.8432 (tp) cc_final: 0.8182 (tt) REVERT: E 107 ASP cc_start: 0.7518 (t0) cc_final: 0.7225 (t0) REVERT: E 238 THR cc_start: 0.8289 (m) cc_final: 0.7883 (p) REVERT: E 265 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.8173 (ttp-110) outliers start: 56 outliers final: 32 residues processed: 389 average time/residue: 0.5203 time to fit residues: 223.4207 Evaluate side-chains 393 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 357 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 184 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 142 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN C 301 ASN D 120 ASN E 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103208 restraints weight = 18368.442| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.09 r_work: 0.3133 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13870 Z= 0.123 Angle : 0.534 8.225 18845 Z= 0.280 Chirality : 0.041 0.160 2105 Planarity : 0.005 0.053 2340 Dihedral : 3.875 23.651 1796 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.32 % Allowed : 24.58 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.70 (0.21), residues: 1605 helix: 2.86 (0.21), residues: 530 sheet: 1.58 (0.27), residues: 390 loop : -2.39 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 54 TYR 0.020 0.001 TYR E 130 PHE 0.029 0.002 PHE C 170 TRP 0.012 0.001 TRP E 257 HIS 0.004 0.000 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13860) covalent geometry : angle 0.53441 / 0.28 (18825) SS BOND : bond 0.00168 / 0.11 ( 10) SS BOND : angle 0.50946 / 0.42 ( 20) hydrogen bonds : bond 0.04986 / 3.25 ( 601) hydrogen bonds : angle 3.89094 / 2.69 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.8629 (m-80) cc_final: 0.8371 (m-80) REVERT: A 176 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7996 (mtt90) REVERT: A 205 LYS cc_start: 0.8125 (mtpm) cc_final: 0.7761 (tttm) REVERT: A 210 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8136 (mtm) REVERT: A 213 ILE cc_start: 0.8250 (tt) cc_final: 0.8014 (tt) REVERT: A 232 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7639 (mtt180) REVERT: A 354 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8134 (tm-30) REVERT: B 56 ASP cc_start: 0.7968 (p0) cc_final: 0.7654 (p0) REVERT: B 238 THR cc_start: 0.8324 (m) cc_final: 0.7914 (p) REVERT: C 107 ASP cc_start: 0.7506 (t0) cc_final: 0.7101 (t0) REVERT: C 125 ASP cc_start: 0.8371 (t0) cc_final: 0.8146 (t0) REVERT: C 238 THR cc_start: 0.8258 (m) cc_final: 0.7851 (p) REVERT: C 243 TYR cc_start: 0.7282 (m-80) cc_final: 0.7026 (m-80) REVERT: C 337 MET cc_start: 0.7829 (mmm) cc_final: 0.7438 (mmm) REVERT: C 341 ASP cc_start: 0.7853 (m-30) cc_final: 0.7513 (m-30) REVERT: C 384 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7679 (mtp180) REVERT: D 99 LEU cc_start: 0.8553 (tp) cc_final: 0.8304 (tt) REVERT: D 107 ASP cc_start: 0.7418 (t0) cc_final: 0.7100 (t0) REVERT: D 125 ASP cc_start: 0.8338 (t0) cc_final: 0.8035 (t0) REVERT: D 214 SER cc_start: 0.8572 (t) cc_final: 0.8275 (m) REVERT: D 223 VAL cc_start: 0.8205 (p) cc_final: 0.7929 (m) REVERT: D 238 THR cc_start: 0.8272 (m) cc_final: 0.7811 (p) REVERT: D 258 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7661 (mtm180) REVERT: D 358 VAL cc_start: 0.8137 (t) cc_final: 0.7927 (t) REVERT: E 46 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7727 (mp) REVERT: E 107 ASP cc_start: 0.7521 (t0) cc_final: 0.7174 (t0) REVERT: E 130 TYR cc_start: 0.8019 (p90) cc_final: 0.7784 (p90) REVERT: E 182 TYR cc_start: 0.8127 (t80) cc_final: 0.7911 (t80) REVERT: E 238 THR cc_start: 0.8302 (m) cc_final: 0.7882 (p) REVERT: E 265 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8169 (ttp-110) outliers start: 50 outliers final: 30 residues processed: 381 average time/residue: 0.5246 time to fit residues: 220.7153 Evaluate side-chains 395 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 363 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 134 optimal weight: 0.0770 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN A 301 ASN C 301 ASN D 97 ASN D 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103870 restraints weight = 18401.435| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.07 r_work: 0.3142 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13870 Z= 0.113 Angle : 0.517 8.199 18845 Z= 0.271 Chirality : 0.041 0.175 2105 Planarity : 0.004 0.050 2340 Dihedral : 3.751 23.173 1795 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.85 % Allowed : 23.79 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.77 (0.21), residues: 1605 helix: 2.92 (0.21), residues: 530 sheet: 1.59 (0.27), residues: 390 loop : -2.32 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.017 0.001 TYR C 130 PHE 0.031 0.002 PHE C 170 TRP 0.009 0.001 TRP E 257 HIS 0.004 0.000 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13860) covalent geometry : angle 0.51694 / 0.27 (18825) SS BOND : bond 0.00167 / 0.10 ( 10) SS BOND : angle 0.69921 / 0.37 ( 20) hydrogen bonds : bond 0.04728 / 3.09 ( 601) hydrogen bonds : angle 3.83049 / 2.65 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 361 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7782 (tttm) REVERT: A 210 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: A 213 ILE cc_start: 0.8246 (tt) cc_final: 0.8010 (tt) REVERT: A 232 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7587 (mtt180) REVERT: B 56 ASP cc_start: 0.7943 (p0) cc_final: 0.7654 (p0) REVERT: B 238 THR cc_start: 0.8341 (m) cc_final: 0.7932 (p) REVERT: C 107 ASP cc_start: 0.7578 (t0) cc_final: 0.7225 (t0) REVERT: C 125 ASP cc_start: 0.8339 (t0) cc_final: 0.8115 (t0) REVERT: C 176 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7641 (tpp-160) REVERT: C 223 VAL cc_start: 0.8407 (p) cc_final: 0.8157 (m) REVERT: C 232 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7657 (mtt-85) REVERT: C 238 THR cc_start: 0.8268 (m) cc_final: 0.7867 (p) REVERT: C 243 TYR cc_start: 0.7283 (m-80) cc_final: 0.6970 (m-80) REVERT: C 337 MET cc_start: 0.7787 (mmm) cc_final: 0.7404 (mmm) REVERT: C 341 ASP cc_start: 0.7815 (m-30) cc_final: 0.7467 (m-30) REVERT: D 99 LEU cc_start: 0.8581 (tp) cc_final: 0.8344 (tt) REVERT: D 107 ASP cc_start: 0.7462 (t0) cc_final: 0.7131 (t0) REVERT: D 214 SER cc_start: 0.8585 (t) cc_final: 0.8301 (m) REVERT: D 223 VAL cc_start: 0.8186 (p) cc_final: 0.7917 (m) REVERT: D 233 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.1960 (ttmm) REVERT: D 238 THR cc_start: 0.8278 (m) cc_final: 0.7825 (p) REVERT: D 265 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.8211 (ttp80) REVERT: D 358 VAL cc_start: 0.8134 (t) cc_final: 0.7924 (t) REVERT: E 107 ASP cc_start: 0.7557 (t0) cc_final: 0.7217 (t0) REVERT: E 182 TYR cc_start: 0.8077 (t80) cc_final: 0.7826 (t80) REVERT: E 238 THR cc_start: 0.8323 (m) cc_final: 0.7907 (p) REVERT: E 265 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.8183 (ttp-110) outliers start: 58 outliers final: 41 residues processed: 390 average time/residue: 0.5186 time to fit residues: 223.1979 Evaluate side-chains 400 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 357 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 308 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 47 optimal weight: 0.0010 chunk 153 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN A 301 ASN B 124 ASN C 301 ASN D 97 ASN D 120 ASN D 260 ASN D 301 ASN E 197 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102791 restraints weight = 18671.324| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.05 r_work: 0.3138 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13870 Z= 0.127 Angle : 0.533 8.856 18845 Z= 0.277 Chirality : 0.041 0.169 2105 Planarity : 0.004 0.051 2340 Dihedral : 3.779 23.869 1795 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.46 % Allowed : 24.58 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.77 (0.21), residues: 1605 helix: 2.90 (0.21), residues: 530 sheet: 1.55 (0.27), residues: 390 loop : -2.27 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.017 0.001 TYR A 130 PHE 0.032 0.002 PHE C 170 TRP 0.010 0.001 TRP C 257 HIS 0.005 0.000 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13860) covalent geometry : angle 0.53271 / 0.28 (18825) SS BOND : bond 0.00154 / 0.10 ( 10) SS BOND : angle 0.57364 / 0.33 ( 20) hydrogen bonds : bond 0.05052 / 3.31 ( 601) hydrogen bonds : angle 3.82093 / 2.64 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 371 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7972 (mtt90) REVERT: A 205 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7834 (tttm) REVERT: A 210 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8143 (mtm) REVERT: A 213 ILE cc_start: 0.8275 (tt) cc_final: 0.8055 (tt) REVERT: A 232 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7571 (mtt180) REVERT: B 56 ASP cc_start: 0.7961 (p0) cc_final: 0.7635 (p0) REVERT: B 107 ASP cc_start: 0.7680 (t0) cc_final: 0.7174 (t0) REVERT: B 238 THR cc_start: 0.8414 (m) cc_final: 0.8031 (p) REVERT: C 107 ASP cc_start: 0.7679 (t0) cc_final: 0.7326 (t0) REVERT: C 176 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7737 (tpp-160) REVERT: C 223 VAL cc_start: 0.8467 (p) cc_final: 0.8226 (m) REVERT: C 232 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7790 (mtt-85) REVERT: C 238 THR cc_start: 0.8340 (m) cc_final: 0.7961 (p) REVERT: C 243 TYR cc_start: 0.7293 (m-80) cc_final: 0.6945 (m-80) REVERT: C 341 ASP cc_start: 0.7906 (m-30) cc_final: 0.7540 (m-30) REVERT: D 99 LEU cc_start: 0.8643 (tp) cc_final: 0.8427 (tt) REVERT: D 107 ASP cc_start: 0.7481 (t0) cc_final: 0.7142 (t0) REVERT: D 214 SER cc_start: 0.8592 (t) cc_final: 0.8300 (m) REVERT: D 223 VAL cc_start: 0.8204 (p) cc_final: 0.7948 (m) REVERT: D 233 LYS cc_start: 0.5470 (OUTLIER) cc_final: 0.2148 (ttmm) REVERT: D 238 THR cc_start: 0.8337 (m) cc_final: 0.7894 (p) REVERT: D 265 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8173 (ttp80) REVERT: D 358 VAL cc_start: 0.8299 (t) cc_final: 0.8082 (t) REVERT: E 107 ASP cc_start: 0.7591 (t0) cc_final: 0.7259 (t0) REVERT: E 238 THR cc_start: 0.8349 (m) cc_final: 0.7947 (p) REVERT: E 265 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8136 (ttp-110) outliers start: 52 outliers final: 39 residues processed: 397 average time/residue: 0.5125 time to fit residues: 224.9619 Evaluate side-chains 405 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 364 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 262 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 HIS A 260 ASN A 301 ASN B 169 HIS B 197 HIS C 197 HIS C 301 ASN D 97 ASN D 120 ASN D 260 ASN D 301 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099792 restraints weight = 18902.286| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.02 r_work: 0.3078 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13870 Z= 0.235 Angle : 0.606 9.954 18845 Z= 0.316 Chirality : 0.045 0.174 2105 Planarity : 0.005 0.055 2340 Dihedral : 4.090 25.558 1795 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.99 % Allowed : 24.58 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.56 (0.21), residues: 1605 helix: 2.70 (0.21), residues: 520 sheet: 1.48 (0.27), residues: 390 loop : -2.33 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 176 TYR 0.026 0.002 TYR A 130 PHE 0.046 0.002 PHE A 138 TRP 0.014 0.002 TRP D 123 HIS 0.006 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.23 (13860) covalent geometry : angle 0.60579 / 0.32 (18825) SS BOND : bond 0.00224 / 0.14 ( 10) SS BOND : angle 0.61686 / 0.35 ( 20) hydrogen bonds : bond 0.06940 / 4.56 ( 601) hydrogen bonds : angle 4.00251 / 2.77 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 369 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8262 (mtm) REVERT: A 213 ILE cc_start: 0.8423 (tt) cc_final: 0.8180 (tt) REVERT: A 232 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7630 (mtt180) REVERT: A 243 TYR cc_start: 0.7359 (m-80) cc_final: 0.7053 (m-80) REVERT: B 56 ASP cc_start: 0.8023 (p0) cc_final: 0.7726 (p0) REVERT: B 107 ASP cc_start: 0.7709 (t0) cc_final: 0.7240 (t0) REVERT: B 238 THR cc_start: 0.8399 (m) cc_final: 0.8004 (p) REVERT: C 107 ASP cc_start: 0.7789 (t0) cc_final: 0.7471 (t0) REVERT: C 176 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7915 (mtt-85) REVERT: C 232 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7798 (mtt-85) REVERT: C 238 THR cc_start: 0.8382 (m) cc_final: 0.8005 (p) REVERT: C 243 TYR cc_start: 0.7289 (m-80) cc_final: 0.6946 (m-80) REVERT: C 258 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7680 (mtm-85) REVERT: C 337 MET cc_start: 0.8275 (mmm) cc_final: 0.8002 (mmm) REVERT: C 341 ASP cc_start: 0.8039 (m-30) cc_final: 0.7770 (m-30) REVERT: D 99 LEU cc_start: 0.8683 (tp) cc_final: 0.8463 (tt) REVERT: D 107 ASP cc_start: 0.7550 (t0) cc_final: 0.7217 (t0) REVERT: D 214 SER cc_start: 0.8625 (t) cc_final: 0.8323 (m) REVERT: D 223 VAL cc_start: 0.8174 (p) cc_final: 0.7949 (m) REVERT: D 233 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.2065 (ttmm) REVERT: D 238 THR cc_start: 0.8354 (m) cc_final: 0.7913 (p) REVERT: D 358 VAL cc_start: 0.8444 (t) cc_final: 0.8236 (t) REVERT: E 107 ASP cc_start: 0.7686 (t0) cc_final: 0.7383 (t0) REVERT: E 238 THR cc_start: 0.8364 (m) cc_final: 0.7963 (p) REVERT: E 260 ASN cc_start: 0.8374 (m110) cc_final: 0.8069 (m110) REVERT: E 265 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.8114 (ttp-110) outliers start: 60 outliers final: 45 residues processed: 392 average time/residue: 0.5542 time to fit residues: 238.3172 Evaluate side-chains 410 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 363 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 262 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 260 ASN A 301 ASN C 301 ASN D 97 ASN D 120 ASN E 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101492 restraints weight = 18706.890| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.02 r_work: 0.3107 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13870 Z= 0.149 Angle : 0.566 9.167 18845 Z= 0.294 Chirality : 0.042 0.167 2105 Planarity : 0.004 0.054 2340 Dihedral : 3.971 24.040 1795 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.92 % Allowed : 25.65 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.64 (0.21), residues: 1605 helix: 2.77 (0.21), residues: 525 sheet: 1.46 (0.27), residues: 390 loop : -2.27 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 54 TYR 0.018 0.001 TYR A 130 PHE 0.038 0.002 PHE A 138 TRP 0.011 0.001 TRP D 123 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (13860) covalent geometry : angle 0.56631 / 0.29 (18825) SS BOND : bond 0.00145 / 0.09 ( 10) SS BOND : angle 0.49389 / 0.30 ( 20) hydrogen bonds : bond 0.05546 / 3.63 ( 601) hydrogen bonds : angle 3.90060 / 2.70 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 368 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8262 (mtt90) cc_final: 0.8032 (mtt90) REVERT: A 210 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8180 (mtm) REVERT: A 213 ILE cc_start: 0.8346 (tt) cc_final: 0.8108 (tt) REVERT: A 232 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7588 (mtt180) REVERT: A 243 TYR cc_start: 0.7371 (m-80) cc_final: 0.7059 (m-80) REVERT: A 354 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 56 ASP cc_start: 0.8033 (p0) cc_final: 0.7717 (p0) REVERT: B 107 ASP cc_start: 0.7678 (t0) cc_final: 0.7212 (t0) REVERT: B 176 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.7990 (mtt90) REVERT: B 238 THR cc_start: 0.8399 (m) cc_final: 0.7998 (p) REVERT: C 107 ASP cc_start: 0.7750 (t0) cc_final: 0.7433 (t0) REVERT: C 176 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7780 (tpp-160) REVERT: C 223 VAL cc_start: 0.8431 (p) cc_final: 0.8204 (m) REVERT: C 232 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7792 (mtt-85) REVERT: C 238 THR cc_start: 0.8383 (m) cc_final: 0.7999 (p) REVERT: C 258 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7573 (mtm-85) REVERT: C 341 ASP cc_start: 0.7950 (m-30) cc_final: 0.7595 (m-30) REVERT: D 99 LEU cc_start: 0.8634 (tp) cc_final: 0.8404 (tt) REVERT: D 107 ASP cc_start: 0.7545 (t0) cc_final: 0.7222 (t0) REVERT: D 214 SER cc_start: 0.8604 (t) cc_final: 0.8298 (m) REVERT: D 223 VAL cc_start: 0.8164 (p) cc_final: 0.7953 (m) REVERT: D 233 LYS cc_start: 0.5392 (OUTLIER) cc_final: 0.2171 (ttmm) REVERT: D 238 THR cc_start: 0.8316 (m) cc_final: 0.7892 (p) REVERT: D 358 VAL cc_start: 0.8391 (t) cc_final: 0.8179 (t) REVERT: E 56 ASP cc_start: 0.7787 (p0) cc_final: 0.7459 (p0) REVERT: E 107 ASP cc_start: 0.7669 (t0) cc_final: 0.7375 (t0) REVERT: E 238 THR cc_start: 0.8348 (m) cc_final: 0.7924 (p) REVERT: E 260 ASN cc_start: 0.8365 (m110) cc_final: 0.8052 (m110) REVERT: E 265 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8134 (ttp-110) outliers start: 44 outliers final: 34 residues processed: 386 average time/residue: 0.5347 time to fit residues: 227.4936 Evaluate side-chains 399 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 363 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 262 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 144 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN A 301 ASN B 124 ASN C 301 ASN D 120 ASN D 301 ASN E 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102664 restraints weight = 18780.520| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.98 r_work: 0.3130 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13870 Z= 0.127 Angle : 0.550 9.656 18845 Z= 0.285 Chirality : 0.042 0.162 2105 Planarity : 0.004 0.054 2340 Dihedral : 3.853 22.463 1795 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.79 % Allowed : 26.25 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.72 (0.21), residues: 1605 helix: 2.81 (0.21), residues: 530 sheet: 1.50 (0.27), residues: 390 loop : -2.24 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.016 0.001 TYR E 130 PHE 0.035 0.002 PHE A 138 TRP 0.010 0.001 TRP E 340 HIS 0.004 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13860) covalent geometry : angle 0.55045 / 0.29 (18825) SS BOND : bond 0.00139 / 0.09 ( 10) SS BOND : angle 0.42524 / 0.26 ( 20) hydrogen bonds : bond 0.05033 / 3.29 ( 601) hydrogen bonds : angle 3.82822 / 2.65 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7470 (ttm110) REVERT: A 176 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7995 (mtt90) REVERT: A 213 ILE cc_start: 0.8333 (tt) cc_final: 0.8091 (tt) REVERT: A 232 ARG cc_start: 0.7800 (ttm170) cc_final: 0.7588 (mtt180) REVERT: A 243 TYR cc_start: 0.7380 (m-80) cc_final: 0.7075 (m-80) REVERT: B 56 ASP cc_start: 0.7952 (p0) cc_final: 0.7677 (p0) REVERT: B 107 ASP cc_start: 0.7722 (t0) cc_final: 0.7254 (t0) REVERT: B 130 TYR cc_start: 0.8066 (p90) cc_final: 0.7667 (p90) REVERT: B 176 ARG cc_start: 0.8350 (tpp-160) cc_final: 0.7999 (mtt90) REVERT: B 238 THR cc_start: 0.8430 (m) cc_final: 0.8041 (p) REVERT: C 42 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6521 (t70) REVERT: C 107 ASP cc_start: 0.7736 (t0) cc_final: 0.7413 (t0) REVERT: C 223 VAL cc_start: 0.8427 (p) cc_final: 0.8178 (m) REVERT: C 232 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7803 (mtt-85) REVERT: C 238 THR cc_start: 0.8367 (m) cc_final: 0.7999 (p) REVERT: C 258 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7616 (mtp180) REVERT: C 341 ASP cc_start: 0.7888 (m-30) cc_final: 0.7543 (m-30) REVERT: D 107 ASP cc_start: 0.7517 (t0) cc_final: 0.7188 (t0) REVERT: D 214 SER cc_start: 0.8572 (t) cc_final: 0.8301 (m) REVERT: D 233 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.2145 (ttmm) REVERT: D 238 THR cc_start: 0.8348 (m) cc_final: 0.7916 (p) REVERT: D 358 VAL cc_start: 0.8373 (t) cc_final: 0.8156 (t) REVERT: E 107 ASP cc_start: 0.7648 (t0) cc_final: 0.7355 (t0) REVERT: E 238 THR cc_start: 0.8365 (m) cc_final: 0.7950 (p) REVERT: E 260 ASN cc_start: 0.8375 (m110) cc_final: 0.8066 (m110) REVERT: E 265 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8125 (ttp-110) outliers start: 42 outliers final: 37 residues processed: 378 average time/residue: 0.5267 time to fit residues: 219.3690 Evaluate side-chains 393 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 354 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 262 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 136 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 102 optimal weight: 0.0970 chunk 118 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN A 301 ASN C 301 ASN D 120 ASN D 301 ASN E 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104371 restraints weight = 18754.515| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.97 r_work: 0.3160 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13870 Z= 0.107 Angle : 0.544 9.736 18845 Z= 0.279 Chirality : 0.041 0.158 2105 Planarity : 0.004 0.052 2340 Dihedral : 3.753 23.119 1795 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.26 % Allowed : 26.98 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.21), residues: 1605 helix: 2.93 (0.21), residues: 530 sheet: 1.60 (0.26), residues: 385 loop : -2.15 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 54 TYR 0.014 0.001 TYR E 130 PHE 0.043 0.001 PHE C 138 TRP 0.010 0.001 TRP C 257 HIS 0.004 0.000 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (13860) covalent geometry : angle 0.54455 / 0.28 (18825) SS BOND : bond 0.00119 / 0.08 ( 10) SS BOND : angle 0.36788 / 0.22 ( 20) hydrogen bonds : bond 0.04291 / 2.80 ( 601) hydrogen bonds : angle 3.74702 / 2.59 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 360 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7957 (mtt90) REVERT: A 213 ILE cc_start: 0.8275 (tt) cc_final: 0.8063 (tt) REVERT: A 243 TYR cc_start: 0.7401 (m-80) cc_final: 0.7084 (m-80) REVERT: A 314 MET cc_start: 0.8179 (mtp) cc_final: 0.7977 (ttp) REVERT: B 56 ASP cc_start: 0.7958 (p0) cc_final: 0.7670 (p0) REVERT: B 107 ASP cc_start: 0.7688 (t0) cc_final: 0.7205 (t0) REVERT: B 176 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.8034 (mtt90) REVERT: B 238 THR cc_start: 0.8421 (m) cc_final: 0.8029 (p) REVERT: C 42 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.6430 (t70) REVERT: C 107 ASP cc_start: 0.7660 (t0) cc_final: 0.7317 (t0) REVERT: C 125 ASP cc_start: 0.8463 (t0) cc_final: 0.8214 (t0) REVERT: C 176 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7821 (tpp-160) REVERT: C 202 ASP cc_start: 0.7941 (p0) cc_final: 0.7669 (p0) REVERT: C 213 ILE cc_start: 0.7931 (tt) cc_final: 0.7580 (pt) REVERT: C 223 VAL cc_start: 0.8434 (p) cc_final: 0.8173 (m) REVERT: C 232 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7770 (mtt-85) REVERT: C 238 THR cc_start: 0.8364 (m) cc_final: 0.8002 (p) REVERT: C 258 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7415 (mtp180) REVERT: D 107 ASP cc_start: 0.7492 (t0) cc_final: 0.7155 (t0) REVERT: D 214 SER cc_start: 0.8546 (t) cc_final: 0.8277 (m) REVERT: D 233 LYS cc_start: 0.5370 (OUTLIER) cc_final: 0.2129 (ttmm) REVERT: D 238 THR cc_start: 0.8345 (m) cc_final: 0.7899 (p) REVERT: D 265 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8188 (ttp80) REVERT: D 358 VAL cc_start: 0.8303 (t) cc_final: 0.8083 (t) REVERT: E 107 ASP cc_start: 0.7628 (t0) cc_final: 0.7322 (t0) REVERT: E 238 THR cc_start: 0.8366 (m) cc_final: 0.7958 (p) REVERT: E 260 ASN cc_start: 0.8360 (m110) cc_final: 0.8033 (m110) REVERT: E 265 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.7988 (ttp-110) outliers start: 34 outliers final: 33 residues processed: 376 average time/residue: 0.5189 time to fit residues: 215.2877 Evaluate side-chains 394 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 359 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 262 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 34 optimal weight: 0.0000 chunk 17 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN B 124 ASN C 169 HIS C 301 ASN D 120 ASN D 301 ASN E 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104279 restraints weight = 18776.588| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.98 r_work: 0.3158 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13870 Z= 0.113 Angle : 0.543 9.969 18845 Z= 0.280 Chirality : 0.041 0.160 2105 Planarity : 0.004 0.059 2340 Dihedral : 3.703 23.655 1794 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 26.58 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.21), residues: 1605 helix: 2.94 (0.21), residues: 530 sheet: 1.62 (0.27), residues: 385 loop : -2.11 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 54 TYR 0.017 0.001 TYR E 130 PHE 0.034 0.001 PHE C 138 TRP 0.010 0.001 TRP C 257 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (13860) covalent geometry : angle 0.54310 / 0.28 (18825) SS BOND : bond 0.00136 / 0.09 ( 10) SS BOND : angle 0.40386 / 0.26 ( 20) hydrogen bonds : bond 0.04500 / 2.94 ( 601) hydrogen bonds : angle 3.73310 / 2.58 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4956.72 seconds wall clock time: 85 minutes 13.00 seconds (5113.00 seconds total)