Starting phenix.real_space_refine on Wed Mar 4 17:58:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0j_21000/03_2026/6v0j_21000.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0j_21000/03_2026/6v0j_21000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0j_21000/03_2026/6v0j_21000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0j_21000/03_2026/6v0j_21000.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0j_21000/03_2026/6v0j_21000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0j_21000/03_2026/6v0j_21000.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 42 5.16 5 C 9642 2.51 5 N 2580 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15252 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "D" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "E" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "F" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Time building chain proxies: 2.57, per 1000 atoms: 0.17 Number of scatterers: 15252 At special positions: 0 Unit cell: (113.97, 116.59, 108.73, 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 42 16.00 O 2988 8.00 N 2580 7.00 C 9642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.11 Conformation dependent library (CDL) restraints added in 679.5 milliseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 18 sheets defined 12.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.630A pdb=" N VAL A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 removed outlier: 3.662A pdb=" N THR A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.753A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.167A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 361' Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 removed outlier: 3.661A pdb=" N THR B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.753A pdb=" N LEU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.167A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 361' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.668A pdb=" N VAL C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 4.549A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.615A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.355A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 361' Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.523A pdb=" N ALA D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 212 removed outlier: 3.661A pdb=" N THR D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.752A pdb=" N LEU D 246 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.168A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 361' Processing helix chain 'E' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA E 101 " --> pdb=" O ASP E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 212 removed outlier: 3.662A pdb=" N THR E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 212' Processing helix chain 'E' and resid 242 through 249 removed outlier: 3.753A pdb=" N LEU E 246 " --> pdb=" O SER E 242 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.570A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.166A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 359 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 361' Processing helix chain 'F' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 212 removed outlier: 3.661A pdb=" N THR F 212 " --> pdb=" O ARG F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 209 through 212' Processing helix chain 'F' and resid 242 through 249 removed outlier: 3.752A pdb=" N LEU F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.167A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU F 359 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 354 through 361' Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 3.537A pdb=" N TRP A 109 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 131 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 134 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 87 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 88 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 167 removed outlier: 3.516A pdb=" N ILE A 163 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 220 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG A 340 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.536A pdb=" N TRP B 109 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR B 131 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET B 134 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 81 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS B 87 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 88 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 167 removed outlier: 3.516A pdb=" N ILE B 163 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 220 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG B 340 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 3.539A pdb=" N TRP C 109 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 131 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 134 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 81 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS C 87 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 88 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.144A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 220 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.569A pdb=" N ARG C 340 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 3.536A pdb=" N TRP D 109 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR D 131 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 134 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU D 81 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS D 87 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 88 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 161 through 167 removed outlier: 3.517A pdb=" N ILE D 163 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 220 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 340 through 344 removed outlier: 3.669A pdb=" N ARG D 340 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.537A pdb=" N TRP E 109 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR E 131 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET E 134 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU E 81 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS E 87 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 88 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 167 removed outlier: 3.516A pdb=" N ILE E 163 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG E 220 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG E 340 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 320 " --> pdb=" O ASN E 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 107 through 111 removed outlier: 3.537A pdb=" N TRP F 109 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR F 131 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET F 134 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU F 81 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS F 87 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 88 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 161 through 167 removed outlier: 3.517A pdb=" N ILE F 163 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 220 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG F 340 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1050 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: 2.47 Time building geometry restraints manager: 1.57 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: 5076 1.34 - 1.46: 2389 1.46 - 1.57: 7943 1.57 - 1.69: 6 1.69 - 1.81: 84 Bond restraints: 15498 Sorted by residual: bond pdb=" CA ARG C 63 " pdb=" CB ARG C 63 " ideal model delta sigma weight residual 1.531 1.611 -0.080 3.28e-02 9.30e+02 6.02e+00 bond pdb=" CA ARG E 63 " pdb=" CB ARG E 63 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.70e+00 bond pdb=" CA ARG F 63 " pdb=" CB ARG F 63 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.67e+00 bond pdb=" CA ARG A 63 " pdb=" CB ARG A 63 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.67e+00 bond pdb=" CA ARG B 63 " pdb=" CB ARG B 63 " ideal model delta sigma weight residual 1.531 1.601 -0.071 3.28e-02 9.30e+02 4.63e+00 ... (remaining 15493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 20413 2.27 - 4.54: 498 4.54 - 6.81: 69 6.81 - 9.08: 8 9.08 - 11.35: 12 Bond angle restraints: 21000 Sorted by residual: angle pdb=" C SER D 82 " pdb=" N ASP D 83 " pdb=" CA ASP D 83 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C SER B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C SER E 82 " pdb=" N ASP E 83 " pdb=" CA ASP E 83 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C SER A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 121.54 131.15 -9.61 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C SER F 82 " pdb=" N ASP F 83 " pdb=" CA ASP F 83 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 ... (remaining 20995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 9012 15.07 - 30.15: 308 30.15 - 45.22: 70 45.22 - 60.29: 12 60.29 - 75.36: 30 Dihedral angle restraints: 9432 sinusoidal: 3756 harmonic: 5676 Sorted by residual: dihedral pdb=" CA GLU C 263 " pdb=" C GLU C 263 " pdb=" N ALA C 264 " pdb=" CA ALA C 264 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU D 263 " pdb=" C GLU D 263 " pdb=" N ALA D 264 " pdb=" CA ALA D 264 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N ALA A 264 " pdb=" CA ALA A 264 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1632 0.047 - 0.094: 577 0.094 - 0.141: 203 0.141 - 0.188: 24 0.188 - 0.235: 12 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CA ASP F 83 " pdb=" N ASP F 83 " pdb=" C ASP F 83 " pdb=" CB ASP F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASP A 83 " pdb=" N ASP A 83 " pdb=" C ASP A 83 " pdb=" CB ASP A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP E 83 " pdb=" N ASP E 83 " pdb=" C ASP E 83 " pdb=" CB ASP E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2445 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 120 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C VAL C 120 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL C 120 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 121 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 328 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO B 329 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 328 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO E 329 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 329 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 329 " -0.034 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5324 2.88 - 3.38: 13381 3.38 - 3.89: 24235 3.89 - 4.39: 25658 4.39 - 4.90: 45484 Nonbonded interactions: 114082 Sorted by model distance: nonbonded pdb=" NH1 ARG E 220 " pdb=" OH TYR E 271 " model vdw 2.373 3.120 nonbonded pdb=" NH1 ARG A 220 " pdb=" OH TYR A 271 " model vdw 2.373 3.120 nonbonded pdb=" NH1 ARG D 220 " pdb=" OH TYR D 271 " model vdw 2.373 3.120 nonbonded pdb=" NH1 ARG F 220 " pdb=" OH TYR F 271 " model vdw 2.373 3.120 nonbonded pdb=" NH1 ARG B 220 " pdb=" OH TYR B 271 " model vdw 2.374 3.120 ... (remaining 114077 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.006 0.080 15498 Z= 0.277 Angle : 0.878 11.352 21000 Z= 0.471 Chirality : 0.055 0.235 2448 Planarity : 0.006 0.062 2736 Dihedral : 10.190 75.363 5808 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.76 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.15), residues: 1998 helix: -4.19 (0.25), residues: 72 sheet: -1.86 (0.18), residues: 624 loop : -2.26 (0.13), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 182 TYR 0.015 0.002 TYR C 131 PHE 0.037 0.003 PHE C 253 TRP 0.012 0.002 TRP C 222 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00599 (15498) covalent geometry : angle 0.87770 (21000) hydrogen bonds : bond 0.26429 ( 420) hydrogen bonds : angle 10.33061 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8768 (mm-40) REVERT: A 142 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8518 (tp-100) REVERT: A 151 GLN cc_start: 0.8981 (tt0) cc_final: 0.8480 (tm-30) REVERT: B 98 MET cc_start: 0.9092 (tpp) cc_final: 0.8816 (tpt) REVERT: B 132 ILE cc_start: 0.9316 (pt) cc_final: 0.8887 (mp) REVERT: B 151 GLN cc_start: 0.8988 (tt0) cc_final: 0.8700 (tm-30) REVERT: B 273 ASP cc_start: 0.8371 (t0) cc_final: 0.7923 (t0) REVERT: B 362 LYS cc_start: 0.9289 (mmtp) cc_final: 0.9068 (tppt) REVERT: C 77 GLN cc_start: 0.8707 (mm110) cc_final: 0.8043 (mm110) REVERT: C 98 MET cc_start: 0.9043 (tpp) cc_final: 0.8651 (tpt) REVERT: C 132 ILE cc_start: 0.9380 (pt) cc_final: 0.9148 (mp) REVERT: C 134 MET cc_start: 0.8410 (ptm) cc_final: 0.8108 (ptt) REVERT: C 151 GLN cc_start: 0.9097 (tt0) cc_final: 0.8795 (tm-30) REVERT: C 161 LEU cc_start: 0.9192 (tp) cc_final: 0.8745 (tt) REVERT: C 273 ASP cc_start: 0.8110 (t0) cc_final: 0.7794 (t0) REVERT: C 359 LEU cc_start: 0.9184 (mm) cc_final: 0.8969 (mt) REVERT: C 362 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8896 (tppt) REVERT: D 142 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8488 (tp-100) REVERT: D 151 GLN cc_start: 0.9073 (tt0) cc_final: 0.8807 (tm-30) REVERT: D 161 LEU cc_start: 0.9163 (tp) cc_final: 0.8961 (tp) REVERT: D 273 ASP cc_start: 0.8202 (t0) cc_final: 0.7951 (t0) REVERT: D 376 GLU cc_start: 0.8775 (pt0) cc_final: 0.8535 (pp20) REVERT: E 69 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8710 (mm110) REVERT: E 72 GLU cc_start: 0.8837 (tt0) cc_final: 0.8630 (tm-30) REVERT: E 77 GLN cc_start: 0.8721 (mm110) cc_final: 0.8146 (mm110) REVERT: E 91 LYS cc_start: 0.9535 (mttt) cc_final: 0.9123 (mtmm) REVERT: E 98 MET cc_start: 0.9231 (tpp) cc_final: 0.8989 (tpt) REVERT: E 138 LYS cc_start: 0.9047 (mttt) cc_final: 0.8579 (mmmt) REVERT: E 151 GLN cc_start: 0.9094 (tt0) cc_final: 0.8676 (tm-30) REVERT: E 273 ASP cc_start: 0.8417 (t0) cc_final: 0.8045 (t0) REVERT: E 362 LYS cc_start: 0.9272 (mmtp) cc_final: 0.9000 (tppt) REVERT: F 77 GLN cc_start: 0.8720 (mm110) cc_final: 0.8178 (mm110) REVERT: F 151 GLN cc_start: 0.9179 (tt0) cc_final: 0.8890 (tm-30) REVERT: F 273 ASP cc_start: 0.8264 (t0) cc_final: 0.7982 (t0) REVERT: F 362 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8852 (tppt) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1404 time to fit residues: 89.9728 Evaluate side-chains 240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 164 HIS A 316 ASN B 47 ASN B 316 ASN B 345 ASN C 47 ASN C 345 ASN C 354 ASN D 47 ASN D 164 HIS D 345 ASN E 47 ASN E 345 ASN F 47 ASN F 69 GLN F 164 HIS F 316 ASN F 345 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085617 restraints weight = 33445.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088725 restraints weight = 19136.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090786 restraints weight = 13189.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092189 restraints weight = 10251.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.093119 restraints weight = 8626.249| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15498 Z= 0.132 Angle : 0.658 7.948 21000 Z= 0.345 Chirality : 0.047 0.178 2448 Planarity : 0.005 0.045 2736 Dihedral : 5.009 17.047 2136 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.19 % Allowed : 9.37 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.16), residues: 1998 helix: -2.55 (0.39), residues: 108 sheet: -1.45 (0.19), residues: 636 loop : -1.96 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 209 TYR 0.011 0.002 TYR A 154 PHE 0.013 0.001 PHE F 377 TRP 0.008 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00290 (15498) covalent geometry : angle 0.65779 (21000) hydrogen bonds : bond 0.04695 ( 420) hydrogen bonds : angle 8.09586 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 288 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8827 (mm-40) REVERT: A 98 MET cc_start: 0.8619 (mmm) cc_final: 0.7846 (tpt) REVERT: A 151 GLN cc_start: 0.8805 (tt0) cc_final: 0.8592 (tm-30) REVERT: A 162 MET cc_start: 0.7747 (tpt) cc_final: 0.7515 (tpt) REVERT: A 355 LEU cc_start: 0.9042 (mt) cc_final: 0.8553 (pp) REVERT: A 374 ARG cc_start: 0.8307 (ptm160) cc_final: 0.7693 (ptm-80) REVERT: B 85 LEU cc_start: 0.8665 (tp) cc_final: 0.8328 (mt) REVERT: B 151 GLN cc_start: 0.8843 (tt0) cc_final: 0.8587 (tm-30) REVERT: B 224 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6650 (m) REVERT: B 273 ASP cc_start: 0.8187 (t0) cc_final: 0.7848 (t0) REVERT: B 362 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8973 (tppt) REVERT: C 77 GLN cc_start: 0.8604 (mm110) cc_final: 0.8018 (mm110) REVERT: C 98 MET cc_start: 0.8889 (tpp) cc_final: 0.8285 (tpt) REVERT: C 132 ILE cc_start: 0.9378 (pt) cc_final: 0.9120 (mp) REVERT: C 161 LEU cc_start: 0.8980 (tp) cc_final: 0.8613 (tt) REVERT: C 162 MET cc_start: 0.8395 (tpp) cc_final: 0.8092 (tmm) REVERT: C 224 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6433 (m) REVERT: C 273 ASP cc_start: 0.8144 (t0) cc_final: 0.7841 (t0) REVERT: C 302 TYR cc_start: 0.9208 (t80) cc_final: 0.8887 (t80) REVERT: C 303 GLN cc_start: 0.9168 (mp10) cc_final: 0.8884 (mp10) REVERT: C 362 LYS cc_start: 0.9223 (mmtp) cc_final: 0.8901 (tppt) REVERT: C 376 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: D 85 LEU cc_start: 0.8871 (tp) cc_final: 0.8524 (mt) REVERT: D 98 MET cc_start: 0.8579 (mmm) cc_final: 0.8122 (tpt) REVERT: D 197 ASN cc_start: 0.8390 (t0) cc_final: 0.8156 (t0) REVERT: D 309 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8213 (tp40) REVERT: E 54 MET cc_start: 0.8162 (mmp) cc_final: 0.7879 (tpp) REVERT: E 77 GLN cc_start: 0.8672 (mm110) cc_final: 0.8277 (mm110) REVERT: E 85 LEU cc_start: 0.8798 (tp) cc_final: 0.8525 (mt) REVERT: E 91 LYS cc_start: 0.9543 (mttt) cc_final: 0.9182 (mtmm) REVERT: E 105 GLU cc_start: 0.8852 (tp30) cc_final: 0.8270 (mm-30) REVERT: E 166 GLN cc_start: 0.8696 (mt0) cc_final: 0.8192 (mt0) REVERT: E 273 ASP cc_start: 0.8149 (t0) cc_final: 0.7949 (t0) REVERT: E 303 GLN cc_start: 0.9168 (mp10) cc_final: 0.8968 (mp10) REVERT: F 63 ARG cc_start: 0.7805 (ppt170) cc_final: 0.7488 (ppt170) REVERT: F 77 GLN cc_start: 0.8738 (mm110) cc_final: 0.8489 (mm110) REVERT: F 98 MET cc_start: 0.8737 (mmm) cc_final: 0.8210 (tpt) REVERT: F 142 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8261 (tp-100) REVERT: F 224 VAL cc_start: 0.6859 (OUTLIER) cc_final: 0.6493 (m) REVERT: F 273 ASP cc_start: 0.8057 (t0) cc_final: 0.7804 (t0) REVERT: F 309 GLN cc_start: 0.8637 (tp40) cc_final: 0.8396 (tp40) REVERT: F 316 ASN cc_start: 0.9111 (m110) cc_final: 0.8807 (m110) REVERT: F 320 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8696 (mmmm) REVERT: F 356 SER cc_start: 0.9418 (m) cc_final: 0.9204 (p) REVERT: F 362 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8883 (tppt) outliers start: 20 outliers final: 5 residues processed: 304 average time/residue: 0.1257 time to fit residues: 55.5513 Evaluate side-chains 224 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN E 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077514 restraints weight = 35372.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080301 restraints weight = 20486.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082164 restraints weight = 14333.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.083383 restraints weight = 11252.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084193 restraints weight = 9586.772| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 15498 Z= 0.466 Angle : 0.880 10.057 21000 Z= 0.453 Chirality : 0.053 0.165 2448 Planarity : 0.006 0.040 2736 Dihedral : 5.974 20.823 2136 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.79 % Allowed : 10.74 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 1998 helix: -1.48 (0.44), residues: 114 sheet: -1.20 (0.19), residues: 600 loop : -1.78 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 374 TYR 0.022 0.002 TYR B 154 PHE 0.019 0.003 PHE C 221 TRP 0.012 0.003 TRP D 222 HIS 0.008 0.002 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.01021 (15498) covalent geometry : angle 0.88026 (21000) hydrogen bonds : bond 0.04977 ( 420) hydrogen bonds : angle 8.01568 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8470 (tp-100) REVERT: A 355 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8644 (pp) REVERT: B 63 ARG cc_start: 0.7953 (ppt170) cc_final: 0.7670 (ppt170) REVERT: B 151 GLN cc_start: 0.9043 (tt0) cc_final: 0.8728 (tm-30) REVERT: B 224 VAL cc_start: 0.7425 (OUTLIER) cc_final: 0.7167 (m) REVERT: B 273 ASP cc_start: 0.8553 (t0) cc_final: 0.8198 (t0) REVERT: C 77 GLN cc_start: 0.8755 (mm110) cc_final: 0.8220 (mm110) REVERT: C 98 MET cc_start: 0.8868 (tpp) cc_final: 0.8462 (tpt) REVERT: C 135 MET cc_start: 0.8890 (mmm) cc_final: 0.8553 (ttp) REVERT: C 224 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7224 (m) REVERT: C 303 GLN cc_start: 0.9118 (mp10) cc_final: 0.8827 (mp10) REVERT: D 54 MET cc_start: 0.8428 (tpp) cc_final: 0.8075 (tpp) REVERT: D 98 MET cc_start: 0.8533 (mmm) cc_final: 0.8201 (tpt) REVERT: D 142 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8351 (tp-100) REVERT: D 303 GLN cc_start: 0.9086 (mp10) cc_final: 0.8789 (mp10) REVERT: E 54 MET cc_start: 0.7948 (mmp) cc_final: 0.7549 (mmp) REVERT: E 77 GLN cc_start: 0.8851 (mm110) cc_final: 0.8337 (mm110) REVERT: E 224 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7255 (m) REVERT: E 273 ASP cc_start: 0.8524 (t0) cc_final: 0.8204 (t0) REVERT: E 303 GLN cc_start: 0.9048 (mp10) cc_final: 0.8806 (mp10) REVERT: F 54 MET cc_start: 0.8593 (mmp) cc_final: 0.8361 (tpp) REVERT: F 77 GLN cc_start: 0.8731 (mm110) cc_final: 0.8244 (mm110) REVERT: F 98 MET cc_start: 0.8646 (mmm) cc_final: 0.8382 (tpt) REVERT: F 142 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8497 (tp-100) REVERT: F 224 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7132 (m) REVERT: F 309 GLN cc_start: 0.8786 (tp40) cc_final: 0.8467 (tp40) REVERT: F 316 ASN cc_start: 0.9142 (m110) cc_final: 0.8863 (m-40) REVERT: F 356 SER cc_start: 0.9460 (m) cc_final: 0.9242 (p) outliers start: 47 outliers final: 23 residues processed: 263 average time/residue: 0.1179 time to fit residues: 45.8174 Evaluate side-chains 214 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.0010 chunk 113 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 HIS ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081723 restraints weight = 33727.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084757 restraints weight = 19054.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086762 restraints weight = 13092.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088068 restraints weight = 10191.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089005 restraints weight = 8612.067| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15498 Z= 0.122 Angle : 0.621 8.398 21000 Z= 0.326 Chirality : 0.047 0.162 2448 Planarity : 0.004 0.041 2736 Dihedral : 5.033 17.320 2136 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.66 % Allowed : 13.05 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 1998 helix: -0.92 (0.51), residues: 108 sheet: -0.94 (0.19), residues: 612 loop : -1.75 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 336 TYR 0.012 0.001 TYR B 154 PHE 0.014 0.001 PHE C 253 TRP 0.006 0.001 TRP C 222 HIS 0.002 0.000 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00262 (15498) covalent geometry : angle 0.62148 (21000) hydrogen bonds : bond 0.03769 ( 420) hydrogen bonds : angle 7.51741 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8635 (mmm) cc_final: 0.8009 (tpt) REVERT: B 224 VAL cc_start: 0.7148 (OUTLIER) cc_final: 0.6839 (m) REVERT: B 273 ASP cc_start: 0.8364 (t0) cc_final: 0.8039 (t0) REVERT: B 302 TYR cc_start: 0.9323 (t80) cc_final: 0.8890 (t80) REVERT: B 303 GLN cc_start: 0.9092 (mp10) cc_final: 0.8790 (mp10) REVERT: B 309 GLN cc_start: 0.8723 (tp40) cc_final: 0.8468 (tp40) REVERT: B 336 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8448 (ttm-80) REVERT: C 54 MET cc_start: 0.8382 (mmp) cc_final: 0.8058 (mmp) REVERT: C 77 GLN cc_start: 0.8653 (mm110) cc_final: 0.8212 (mm110) REVERT: C 98 MET cc_start: 0.8860 (tpp) cc_final: 0.8199 (tpt) REVERT: C 105 GLU cc_start: 0.8930 (tp30) cc_final: 0.8582 (mm-30) REVERT: C 224 VAL cc_start: 0.7022 (OUTLIER) cc_final: 0.6753 (m) REVERT: C 303 GLN cc_start: 0.9115 (mp10) cc_final: 0.8794 (mp10) REVERT: D 54 MET cc_start: 0.8278 (tpp) cc_final: 0.7992 (tpp) REVERT: D 98 MET cc_start: 0.8646 (mmm) cc_final: 0.8270 (tpt) REVERT: D 151 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 303 GLN cc_start: 0.9132 (mp10) cc_final: 0.8882 (mp10) REVERT: D 309 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8272 (tp40) REVERT: E 54 MET cc_start: 0.8019 (mmp) cc_final: 0.7668 (mmp) REVERT: E 63 ARG cc_start: 0.7895 (ppt170) cc_final: 0.7530 (ppt170) REVERT: E 77 GLN cc_start: 0.8793 (mm110) cc_final: 0.8572 (mp10) REVERT: E 134 MET cc_start: 0.8319 (ppp) cc_final: 0.7475 (ppp) REVERT: E 224 VAL cc_start: 0.7213 (OUTLIER) cc_final: 0.6897 (m) REVERT: E 273 ASP cc_start: 0.8348 (t0) cc_final: 0.8081 (t0) REVERT: E 303 GLN cc_start: 0.9064 (mp10) cc_final: 0.8771 (mp10) REVERT: F 77 GLN cc_start: 0.8761 (mm110) cc_final: 0.8490 (mm110) REVERT: F 98 MET cc_start: 0.8602 (mmm) cc_final: 0.8308 (tpt) REVERT: F 142 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8618 (tp-100) REVERT: F 151 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8412 (tm-30) REVERT: F 224 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6647 (m) REVERT: F 309 GLN cc_start: 0.8733 (tp40) cc_final: 0.8430 (tp40) REVERT: F 316 ASN cc_start: 0.9057 (m110) cc_final: 0.8849 (m110) outliers start: 28 outliers final: 9 residues processed: 252 average time/residue: 0.1231 time to fit residues: 45.4795 Evaluate side-chains 211 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 53 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.080931 restraints weight = 34151.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083866 restraints weight = 19395.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085845 restraints weight = 13361.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087171 restraints weight = 10411.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088092 restraints weight = 8793.359| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15498 Z= 0.160 Angle : 0.620 10.552 21000 Z= 0.324 Chirality : 0.047 0.162 2448 Planarity : 0.004 0.055 2736 Dihedral : 4.857 21.346 2136 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.08 % Allowed : 13.52 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.17), residues: 1998 helix: -0.69 (0.53), residues: 108 sheet: -0.74 (0.20), residues: 570 loop : -1.64 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 103 TYR 0.020 0.001 TYR F 302 PHE 0.018 0.001 PHE B 377 TRP 0.007 0.001 TRP A 222 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00353 (15498) covalent geometry : angle 0.62048 (21000) hydrogen bonds : bond 0.03663 ( 420) hydrogen bonds : angle 7.33067 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8507 (mmm) cc_final: 0.7969 (tpt) REVERT: A 151 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 359 LEU cc_start: 0.9402 (mm) cc_final: 0.9120 (mp) REVERT: B 224 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6953 (m) REVERT: B 273 ASP cc_start: 0.8399 (t0) cc_final: 0.8163 (t0) REVERT: B 302 TYR cc_start: 0.9307 (t80) cc_final: 0.8912 (t80) REVERT: B 303 GLN cc_start: 0.9056 (mp10) cc_final: 0.8793 (mp10) REVERT: B 309 GLN cc_start: 0.8654 (tp40) cc_final: 0.8392 (tp40) REVERT: B 374 ARG cc_start: 0.7845 (ptt180) cc_final: 0.7133 (ptt180) REVERT: C 54 MET cc_start: 0.8428 (mmp) cc_final: 0.7929 (mmm) REVERT: C 85 LEU cc_start: 0.8881 (tp) cc_final: 0.8653 (tp) REVERT: C 98 MET cc_start: 0.8802 (tpp) cc_final: 0.8175 (tpt) REVERT: C 224 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.6965 (m) REVERT: C 303 GLN cc_start: 0.9088 (mp10) cc_final: 0.8735 (mp10) REVERT: D 54 MET cc_start: 0.8338 (tpp) cc_final: 0.8075 (tpp) REVERT: D 98 MET cc_start: 0.8620 (mmm) cc_final: 0.8260 (tpt) REVERT: D 151 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8123 (tm-30) REVERT: D 303 GLN cc_start: 0.9064 (mp10) cc_final: 0.8716 (mp10) REVERT: D 309 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8461 (tp40) REVERT: D 359 LEU cc_start: 0.9397 (mm) cc_final: 0.9115 (mp) REVERT: E 54 MET cc_start: 0.8021 (mmp) cc_final: 0.7645 (mmp) REVERT: E 63 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7540 (ppt170) REVERT: E 134 MET cc_start: 0.8299 (ppp) cc_final: 0.7765 (ppp) REVERT: E 151 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8325 (tm-30) REVERT: E 224 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.7030 (m) REVERT: E 273 ASP cc_start: 0.8355 (t0) cc_final: 0.8103 (t0) REVERT: E 303 GLN cc_start: 0.9011 (mp10) cc_final: 0.8667 (mp10) REVERT: F 77 GLN cc_start: 0.8725 (mm110) cc_final: 0.8477 (mm110) REVERT: F 98 MET cc_start: 0.8572 (mmm) cc_final: 0.8261 (tpt) REVERT: F 224 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6838 (m) REVERT: F 309 GLN cc_start: 0.8750 (tp40) cc_final: 0.8425 (tp40) outliers start: 35 outliers final: 20 residues processed: 234 average time/residue: 0.1172 time to fit residues: 41.1814 Evaluate side-chains 220 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 376 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078506 restraints weight = 34290.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081352 restraints weight = 19713.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083221 restraints weight = 13743.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.084525 restraints weight = 10793.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085339 restraints weight = 9167.553| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15498 Z= 0.270 Angle : 0.690 11.689 21000 Z= 0.359 Chirality : 0.049 0.205 2448 Planarity : 0.004 0.041 2736 Dihedral : 5.200 19.601 2136 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.37 % Allowed : 14.53 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 1998 helix: -0.65 (0.66), residues: 72 sheet: -0.72 (0.21), residues: 570 loop : -1.55 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 209 TYR 0.015 0.002 TYR F 302 PHE 0.010 0.002 PHE E 364 TRP 0.010 0.002 TRP C 222 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00595 (15498) covalent geometry : angle 0.69005 (21000) hydrogen bonds : bond 0.03965 ( 420) hydrogen bonds : angle 7.42109 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8562 (mmm) cc_final: 0.8127 (tpt) REVERT: A 151 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 224 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7061 (m) REVERT: B 273 ASP cc_start: 0.8508 (t0) cc_final: 0.8184 (t0) REVERT: B 303 GLN cc_start: 0.9079 (mp10) cc_final: 0.8797 (mp10) REVERT: B 309 GLN cc_start: 0.8741 (tp40) cc_final: 0.8425 (tp40) REVERT: C 63 ARG cc_start: 0.7993 (ppt170) cc_final: 0.7582 (ppt170) REVERT: C 98 MET cc_start: 0.8824 (tpp) cc_final: 0.8253 (tpt) REVERT: C 224 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7262 (m) REVERT: C 303 GLN cc_start: 0.9044 (mp10) cc_final: 0.8676 (mp10) REVERT: D 54 MET cc_start: 0.8307 (tpp) cc_final: 0.8022 (tpp) REVERT: D 98 MET cc_start: 0.8505 (mmm) cc_final: 0.8204 (tpt) REVERT: D 151 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 303 GLN cc_start: 0.9038 (mp10) cc_final: 0.8623 (mp10) REVERT: D 309 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8357 (tp40) REVERT: D 359 LEU cc_start: 0.9419 (mm) cc_final: 0.9170 (mp) REVERT: E 63 ARG cc_start: 0.8023 (ppt170) cc_final: 0.7494 (ppt170) REVERT: E 69 GLN cc_start: 0.8783 (mp10) cc_final: 0.8553 (mp10) REVERT: E 134 MET cc_start: 0.8513 (ppp) cc_final: 0.7821 (ppp) REVERT: E 224 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7184 (m) REVERT: E 273 ASP cc_start: 0.8454 (t0) cc_final: 0.8170 (t0) REVERT: E 303 GLN cc_start: 0.8963 (mp10) cc_final: 0.8572 (mp10) REVERT: F 77 GLN cc_start: 0.8742 (mm110) cc_final: 0.8394 (mm110) REVERT: F 224 VAL cc_start: 0.7425 (OUTLIER) cc_final: 0.7208 (m) REVERT: F 309 GLN cc_start: 0.8748 (tp40) cc_final: 0.8361 (tp40) REVERT: F 324 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7800 (pt0) outliers start: 40 outliers final: 23 residues processed: 218 average time/residue: 0.1163 time to fit residues: 37.8040 Evaluate side-chains 205 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 376 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 126 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 87 optimal weight: 0.0020 chunk 144 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.081311 restraints weight = 33567.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084239 restraints weight = 19090.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086222 restraints weight = 13193.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087551 restraints weight = 10301.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088449 restraints weight = 8718.922| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15498 Z= 0.126 Angle : 0.617 12.693 21000 Z= 0.321 Chirality : 0.047 0.194 2448 Planarity : 0.004 0.054 2736 Dihedral : 4.774 19.295 2136 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.84 % Allowed : 15.36 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 1998 helix: -0.41 (0.68), residues: 72 sheet: -0.71 (0.20), residues: 624 loop : -1.51 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 209 TYR 0.035 0.001 TYR A 68 PHE 0.013 0.001 PHE C 253 TRP 0.007 0.001 TRP C 222 HIS 0.002 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00276 (15498) covalent geometry : angle 0.61688 (21000) hydrogen bonds : bond 0.03487 ( 420) hydrogen bonds : angle 7.15530 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8541 (mmm) cc_final: 0.8010 (tpt) REVERT: A 151 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B 151 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 224 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6894 (m) REVERT: B 273 ASP cc_start: 0.8388 (t0) cc_final: 0.8102 (t0) REVERT: B 301 MET cc_start: 0.8791 (mmp) cc_final: 0.8441 (mmm) REVERT: B 302 TYR cc_start: 0.9329 (t80) cc_final: 0.8720 (t80) REVERT: B 303 GLN cc_start: 0.9054 (mp10) cc_final: 0.8746 (mp10) REVERT: B 309 GLN cc_start: 0.8534 (tp40) cc_final: 0.8319 (tp40) REVERT: C 54 MET cc_start: 0.8517 (mmp) cc_final: 0.7993 (mmm) REVERT: C 63 ARG cc_start: 0.8079 (ppt170) cc_final: 0.7599 (ppt170) REVERT: C 98 MET cc_start: 0.8809 (tpp) cc_final: 0.8201 (tpt) REVERT: C 224 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.6932 (m) REVERT: C 303 GLN cc_start: 0.9068 (mp10) cc_final: 0.8715 (mp10) REVERT: C 324 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: D 54 MET cc_start: 0.8320 (tpp) cc_final: 0.7994 (mmm) REVERT: D 63 ARG cc_start: 0.7878 (ppt170) cc_final: 0.7600 (ppt170) REVERT: D 77 GLN cc_start: 0.8423 (mp10) cc_final: 0.8186 (mp10) REVERT: D 98 MET cc_start: 0.8702 (mmm) cc_final: 0.8253 (tpt) REVERT: D 151 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8180 (tm-30) REVERT: D 303 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8691 (mp10) REVERT: D 309 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8413 (tp40) REVERT: E 54 MET cc_start: 0.7970 (mmp) cc_final: 0.7642 (mmp) REVERT: E 63 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7604 (ppt170) REVERT: E 134 MET cc_start: 0.8347 (ppp) cc_final: 0.7808 (ppp) REVERT: E 224 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.7011 (m) REVERT: E 273 ASP cc_start: 0.8393 (t0) cc_final: 0.8113 (t0) REVERT: E 302 TYR cc_start: 0.9328 (t80) cc_final: 0.8280 (t80) REVERT: E 303 GLN cc_start: 0.8966 (mp10) cc_final: 0.8473 (mp10) REVERT: F 132 ILE cc_start: 0.9281 (pt) cc_final: 0.9026 (mt) REVERT: F 151 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 224 VAL cc_start: 0.7172 (OUTLIER) cc_final: 0.6909 (m) REVERT: F 309 GLN cc_start: 0.8654 (tp40) cc_final: 0.8374 (tp40) REVERT: F 355 LEU cc_start: 0.9031 (mt) cc_final: 0.8684 (pp) REVERT: F 362 LYS cc_start: 0.9057 (mmtm) cc_final: 0.8831 (tppt) outliers start: 31 outliers final: 18 residues processed: 227 average time/residue: 0.1206 time to fit residues: 40.9478 Evaluate side-chains 215 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 95 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.0050 chunk 66 optimal weight: 6.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.082910 restraints weight = 33759.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.085898 restraints weight = 19002.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087964 restraints weight = 13080.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089341 restraints weight = 10149.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090258 restraints weight = 8558.841| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15498 Z= 0.109 Angle : 0.618 12.824 21000 Z= 0.319 Chirality : 0.047 0.189 2448 Planarity : 0.004 0.041 2736 Dihedral : 4.504 24.074 2136 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.25 % Allowed : 15.42 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1998 helix: -0.62 (0.68), residues: 72 sheet: -0.61 (0.20), residues: 612 loop : -1.44 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.020 0.001 TYR E 68 PHE 0.012 0.001 PHE C 253 TRP 0.006 0.001 TRP C 222 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00239 (15498) covalent geometry : angle 0.61778 (21000) hydrogen bonds : bond 0.03240 ( 420) hydrogen bonds : angle 6.97647 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7798 (ppt170) cc_final: 0.7545 (ppt170) REVERT: A 98 MET cc_start: 0.8462 (mmm) cc_final: 0.8091 (tpt) REVERT: A 302 TYR cc_start: 0.9122 (t80) cc_final: 0.8866 (t80) REVERT: A 355 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8713 (pp) REVERT: B 151 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 166 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8792 (mm-40) REVERT: B 224 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6883 (m) REVERT: B 301 MET cc_start: 0.8597 (mmp) cc_final: 0.8313 (mmm) REVERT: B 302 TYR cc_start: 0.9326 (t80) cc_final: 0.8727 (t80) REVERT: B 303 GLN cc_start: 0.9042 (mp10) cc_final: 0.8758 (mp10) REVERT: C 54 MET cc_start: 0.8435 (mmp) cc_final: 0.7917 (mmm) REVERT: C 63 ARG cc_start: 0.8063 (ppt170) cc_final: 0.7620 (ppt170) REVERT: C 85 LEU cc_start: 0.8823 (tp) cc_final: 0.8583 (tp) REVERT: C 98 MET cc_start: 0.8835 (tpp) cc_final: 0.8200 (tpt) REVERT: C 138 LYS cc_start: 0.9060 (mttt) cc_final: 0.8826 (mmmt) REVERT: C 224 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6886 (m) REVERT: C 303 GLN cc_start: 0.9073 (mp10) cc_final: 0.8704 (mp10) REVERT: C 324 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: D 54 MET cc_start: 0.8343 (tpp) cc_final: 0.7975 (mmm) REVERT: D 63 ARG cc_start: 0.7844 (ppt170) cc_final: 0.7572 (ppt170) REVERT: D 98 MET cc_start: 0.8553 (mmm) cc_final: 0.8342 (tpt) REVERT: D 151 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 303 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8722 (mp10) REVERT: D 309 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8450 (tp40) REVERT: D 359 LEU cc_start: 0.9351 (mm) cc_final: 0.9094 (mp) REVERT: E 63 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7627 (ppt170) REVERT: E 134 MET cc_start: 0.8225 (ppp) cc_final: 0.7695 (ppp) REVERT: E 224 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.6972 (m) REVERT: E 303 GLN cc_start: 0.8980 (mp10) cc_final: 0.8673 (mp10) REVERT: F 224 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6732 (m) REVERT: F 309 GLN cc_start: 0.8636 (tp40) cc_final: 0.8379 (tp40) REVERT: F 324 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: F 355 LEU cc_start: 0.9036 (mt) cc_final: 0.8767 (pp) REVERT: F 362 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8806 (tppt) outliers start: 38 outliers final: 19 residues processed: 238 average time/residue: 0.1169 time to fit residues: 41.9327 Evaluate side-chains 223 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 331 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.081047 restraints weight = 33638.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.083960 restraints weight = 19192.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085912 restraints weight = 13312.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087243 restraints weight = 10440.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088108 restraints weight = 8873.320| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15498 Z= 0.159 Angle : 0.659 12.807 21000 Z= 0.340 Chirality : 0.048 0.203 2448 Planarity : 0.004 0.041 2736 Dihedral : 4.650 28.605 2136 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.31 % Allowed : 15.84 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1998 helix: -0.83 (0.67), residues: 72 sheet: -0.59 (0.20), residues: 624 loop : -1.44 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 209 TYR 0.021 0.001 TYR E 68 PHE 0.011 0.001 PHE C 253 TRP 0.008 0.001 TRP A 222 HIS 0.002 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00351 (15498) covalent geometry : angle 0.65873 (21000) hydrogen bonds : bond 0.03381 ( 420) hydrogen bonds : angle 6.97491 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7781 (ppt170) cc_final: 0.7555 (ppt170) REVERT: A 98 MET cc_start: 0.8532 (mmm) cc_final: 0.8244 (tpt) REVERT: A 355 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8683 (pp) REVERT: B 151 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 224 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.7029 (m) REVERT: B 301 MET cc_start: 0.8726 (mmp) cc_final: 0.8306 (mmm) REVERT: C 63 ARG cc_start: 0.8090 (ppt170) cc_final: 0.7618 (ppt170) REVERT: C 224 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.7169 (m) REVERT: C 303 GLN cc_start: 0.9049 (mp10) cc_final: 0.8671 (mp10) REVERT: C 324 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: C 355 LEU cc_start: 0.9178 (mt) cc_final: 0.8933 (pp) REVERT: D 54 MET cc_start: 0.8348 (tpp) cc_final: 0.8057 (tpp) REVERT: D 63 ARG cc_start: 0.7886 (ppt170) cc_final: 0.7625 (ppt170) REVERT: D 98 MET cc_start: 0.8712 (mmm) cc_final: 0.8421 (tpt) REVERT: D 151 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8195 (tm-30) REVERT: D 303 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8692 (mp10) REVERT: D 309 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8438 (tp40) REVERT: D 359 LEU cc_start: 0.9357 (mm) cc_final: 0.9135 (mp) REVERT: E 54 MET cc_start: 0.8078 (mmp) cc_final: 0.7726 (mmp) REVERT: E 63 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7649 (ppt170) REVERT: E 134 MET cc_start: 0.8209 (ppp) cc_final: 0.7726 (ppp) REVERT: E 224 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7176 (m) REVERT: E 303 GLN cc_start: 0.8955 (mp10) cc_final: 0.8628 (mp10) REVERT: F 224 VAL cc_start: 0.7250 (OUTLIER) cc_final: 0.6997 (m) REVERT: F 309 GLN cc_start: 0.8679 (tp40) cc_final: 0.8349 (tp40) REVERT: F 324 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: F 355 LEU cc_start: 0.9065 (mt) cc_final: 0.8730 (pp) REVERT: F 362 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8805 (tppt) outliers start: 39 outliers final: 22 residues processed: 222 average time/residue: 0.1163 time to fit residues: 38.5350 Evaluate side-chains 221 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 350 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 115 optimal weight: 0.0370 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081357 restraints weight = 33880.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084277 restraints weight = 19204.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086263 restraints weight = 13304.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087585 restraints weight = 10409.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088365 restraints weight = 8842.967| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15498 Z= 0.148 Angle : 0.674 12.746 21000 Z= 0.348 Chirality : 0.048 0.199 2448 Planarity : 0.004 0.042 2736 Dihedral : 4.654 25.195 2136 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.72 % Allowed : 16.84 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1998 helix: -0.89 (0.68), residues: 72 sheet: -0.59 (0.20), residues: 624 loop : -1.44 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.025 0.001 TYR E 68 PHE 0.011 0.001 PHE C 253 TRP 0.007 0.001 TRP E 222 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00329 (15498) covalent geometry : angle 0.67389 (21000) hydrogen bonds : bond 0.03346 ( 420) hydrogen bonds : angle 6.92255 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7764 (ppt170) cc_final: 0.7545 (ppt170) REVERT: A 98 MET cc_start: 0.8542 (mmm) cc_final: 0.8156 (tpt) REVERT: A 355 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8666 (pp) REVERT: B 54 MET cc_start: 0.7781 (tpp) cc_final: 0.7577 (tpp) REVERT: B 151 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 224 VAL cc_start: 0.7244 (OUTLIER) cc_final: 0.6995 (m) REVERT: B 301 MET cc_start: 0.8638 (mmp) cc_final: 0.8222 (mmm) REVERT: B 303 GLN cc_start: 0.9029 (mp10) cc_final: 0.8827 (mp10) REVERT: C 63 ARG cc_start: 0.8085 (ppt170) cc_final: 0.7353 (ppt170) REVERT: C 224 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7183 (m) REVERT: C 303 GLN cc_start: 0.9045 (mp10) cc_final: 0.8670 (mp10) REVERT: C 324 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: C 355 LEU cc_start: 0.9169 (mt) cc_final: 0.8930 (pp) REVERT: D 54 MET cc_start: 0.8346 (tpp) cc_final: 0.8027 (mmm) REVERT: D 63 ARG cc_start: 0.7856 (ppt170) cc_final: 0.7595 (ppt170) REVERT: D 98 MET cc_start: 0.8686 (mmm) cc_final: 0.8291 (tpt) REVERT: D 151 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 303 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: D 309 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8454 (tp40) REVERT: D 355 LEU cc_start: 0.9038 (mt) cc_final: 0.8672 (pp) REVERT: D 359 LEU cc_start: 0.9367 (mm) cc_final: 0.9132 (mp) REVERT: E 54 MET cc_start: 0.8107 (mmp) cc_final: 0.7746 (mmp) REVERT: E 63 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7727 (ppt170) REVERT: E 134 MET cc_start: 0.8145 (ppp) cc_final: 0.7664 (ppp) REVERT: E 224 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7158 (m) REVERT: E 303 GLN cc_start: 0.8949 (mp10) cc_final: 0.8641 (mp10) REVERT: F 224 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6969 (m) REVERT: F 309 GLN cc_start: 0.8682 (tp40) cc_final: 0.8341 (tp40) REVERT: F 324 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: F 355 LEU cc_start: 0.9069 (mt) cc_final: 0.8817 (pp) REVERT: F 362 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8815 (tppt) outliers start: 29 outliers final: 19 residues processed: 217 average time/residue: 0.1195 time to fit residues: 38.9299 Evaluate side-chains 218 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 350 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.079358 restraints weight = 34049.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.082195 restraints weight = 19506.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084149 restraints weight = 13599.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085416 restraints weight = 10677.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086276 restraints weight = 9076.211| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15498 Z= 0.218 Angle : 0.711 13.275 21000 Z= 0.368 Chirality : 0.049 0.208 2448 Planarity : 0.004 0.041 2736 Dihedral : 4.934 28.500 2136 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.90 % Allowed : 16.79 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1998 helix: -0.84 (0.68), residues: 72 sheet: -0.58 (0.21), residues: 570 loop : -1.42 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 103 TYR 0.021 0.002 TYR E 68 PHE 0.011 0.001 PHE C 253 TRP 0.010 0.002 TRP A 222 HIS 0.004 0.001 HIS F 276 Details of bonding type rmsd covalent geometry : bond 0.00483 (15498) covalent geometry : angle 0.71114 (21000) hydrogen bonds : bond 0.03618 ( 420) hydrogen bonds : angle 7.04822 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.17 seconds wall clock time: 41 minutes 4.74 seconds (2464.74 seconds total)