Starting phenix.real_space_refine on Sat Jul 4 01:52:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2x_38021/07_2026/8x2x_38021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2x_38021/07_2026/8x2x_38021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2x_38021/07_2026/8x2x_38021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2x_38021/07_2026/8x2x_38021.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2x_38021/07_2026/8x2x_38021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2x_38021/07_2026/8x2x_38021.cif" } resolution = 3.8 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= -0.019 sd= 0.471 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1064 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 23 5.16 5 C 9816 2.51 5 N 3042 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16939 Number of models: 1 Model: "" Number of chains: 14 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 205 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "N" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "K" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2309 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 261} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1919 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 3.25, per 1000 atoms: 0.19 Number of scatterers: 16939 At special positions: 0 Unit cell: (136.24, 135.2, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 290 15.00 O 3768 8.00 N 3042 7.00 C 9816 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: 1.05 Conformation dependent library (CDL) restraints added in 517.5 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 55.7% alpha, 3.2% beta 142 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'L' and resid 28 through 41 removed outlier: 4.047A pdb=" N LEU L 32 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU L 35 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR L 37 " --> pdb=" O GLN L 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 removed outlier: 3.553A pdb=" N LEU N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR N 10 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 23 through 32 removed outlier: 3.892A pdb=" N ASN N 31 " --> pdb=" O GLU N 27 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP N 32 " --> pdb=" O ILE N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 89 removed outlier: 3.614A pdb=" N GLU N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 112 removed outlier: 3.580A pdb=" N GLU N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS N 106 " --> pdb=" O ASN N 102 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE N 108 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU N 112 " --> pdb=" O ILE N 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 245 through 257 removed outlier: 3.805A pdb=" N ARG K 249 " --> pdb=" O ARG K 245 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS K 256 " --> pdb=" O CYS K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 312 removed outlier: 4.201A pdb=" N GLN K 312 " --> pdb=" O PRO K 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 309 through 312' Processing helix chain 'K' and resid 314 through 317 removed outlier: 3.716A pdb=" N GLY K 317 " --> pdb=" O MET K 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 314 through 317' Processing helix chain 'K' and resid 318 through 332 removed outlier: 3.724A pdb=" N TYR K 325 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU K 326 " --> pdb=" O GLU K 322 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU K 327 " --> pdb=" O PHE K 323 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER K 328 " --> pdb=" O SER K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 358 removed outlier: 3.503A pdb=" N LEU K 347 " --> pdb=" O ASP K 343 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER K 348 " --> pdb=" O LEU K 344 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA K 351 " --> pdb=" O LEU K 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR K 352 " --> pdb=" O SER K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 363 Processing helix chain 'K' and resid 380 through 392 removed outlier: 4.522A pdb=" N HIS K 386 " --> pdb=" O THR K 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR K 390 " --> pdb=" O HIS K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 419 removed outlier: 4.366A pdb=" N ASN K 414 " --> pdb=" O LEU K 410 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU K 416 " --> pdb=" O ARG K 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 159 Processing helix chain 'M' and resid 165 through 173 removed outlier: 3.606A pdb=" N THR M 170 " --> pdb=" O GLU M 166 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 200 removed outlier: 4.125A pdb=" N CYS M 193 " --> pdb=" O PHE M 189 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 220 removed outlier: 3.505A pdb=" N GLU M 219 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 243 removed outlier: 4.439A pdb=" N GLU M 241 " --> pdb=" O GLN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 269 removed outlier: 3.673A pdb=" N ILE M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU M 269 " --> pdb=" O ILE M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 264 through 269' Processing helix chain 'M' and resid 271 through 274 Processing helix chain 'M' and resid 275 through 282 removed outlier: 3.542A pdb=" N TRP M 279 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 332 removed outlier: 4.163A pdb=" N GLN M 332 " --> pdb=" O LEU M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 337 removed outlier: 4.228A pdb=" N ALA M 336 " --> pdb=" O ARG M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 354 removed outlier: 3.516A pdb=" N LYS M 342 " --> pdb=" O HIS M 338 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA M 344 " --> pdb=" O GLU M 340 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS M 345 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU M 347 " --> pdb=" O ASN M 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU M 349 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU M 350 " --> pdb=" O ASP M 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.885A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.033A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.747A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.675A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.580A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.370A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.230A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.703A pdb=" N ALA C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.771A pdb=" N ILE C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 removed outlier: 3.787A pdb=" N ALA C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 63 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 4.330A pdb=" N LEU C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 removed outlier: 4.191A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 60 through 87 Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.763A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.509A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.659A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 33 through 41 removed outlier: 5.236A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.314A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.699A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.645A pdb=" N ILE G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 72 removed outlier: 3.987A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 89 removed outlier: 3.550A pdb=" N GLN G 86 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.534A pdb=" N ASP G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.643A pdb=" N LEU H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 3.544A pdb=" N SER H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'K' and resid 226 through 230 removed outlier: 3.551A pdb=" N ASN K 226 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE K 236 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG K 230 " --> pdb=" O VAL K 234 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL K 234 " --> pdb=" O ARG K 230 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER K 235 " --> pdb=" O THR K 277 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS K 275 " --> pdb=" O PHE K 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.198A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.925A pdb=" N THR C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.517A pdb=" N ARG C 79 " --> pdb=" O GLY D 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.130A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.195A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.122A pdb=" N THR G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 452 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 688 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3363 1.33 - 1.45: 5474 1.45 - 1.57: 8397 1.57 - 1.69: 580 1.69 - 1.81: 36 Bond restraints: 17850 Sorted by residual: bond pdb=" C1' DT I 37 " pdb=" N1 DT I 37 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C3' DA I 35 " pdb=" O3' DA I 35 " ideal model delta sigma weight residual 1.435 1.495 -0.060 1.30e-02 5.92e+03 2.11e+01 bond pdb=" C3' DG I 81 " pdb=" O3' DG I 81 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.60e+01 bond pdb=" C3' DG J 204 " pdb=" O3' DG J 204 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" C1' DT I 119 " pdb=" N1 DT I 119 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 ... (remaining 17845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 24859 3.39 - 6.79: 435 6.79 - 10.18: 37 10.18 - 13.57: 4 13.57 - 16.96: 5 Bond angle restraints: 25340 Sorted by residual: angle pdb=" O4' DT I 128 " pdb=" C1' DT I 128 " pdb=" N1 DT I 128 " ideal model delta sigma weight residual 108.00 113.43 -5.43 7.00e-01 2.04e+00 6.02e+01 angle pdb=" C ILE K 177 " pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 120.94 109.53 11.41 1.90e+00 2.77e-01 3.60e+01 angle pdb=" O4' DA J 188 " pdb=" C1' DA J 188 " pdb=" N9 DA J 188 " ideal model delta sigma weight residual 108.00 112.19 -4.19 7.00e-01 2.04e+00 3.58e+01 angle pdb=" O4' DA J 256 " pdb=" C1' DA J 256 " pdb=" N9 DA J 256 " ideal model delta sigma weight residual 108.00 112.11 -4.11 7.00e-01 2.04e+00 3.45e+01 angle pdb=" O4' DT I 106 " pdb=" C4' DT I 106 " pdb=" C3' DT I 106 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.40e+01 ... (remaining 25335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.66: 8007 27.66 - 55.31: 1845 55.31 - 82.97: 250 82.97 - 110.62: 2 110.62 - 138.28: 2 Dihedral angle restraints: 10106 sinusoidal: 6135 harmonic: 3971 Sorted by residual: dihedral pdb=" CA GLU K 372 " pdb=" C GLU K 372 " pdb=" N ILE K 373 " pdb=" CA ILE K 373 " ideal model delta harmonic sigma weight residual 180.00 141.21 38.79 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA PRO M 71 " pdb=" C PRO M 71 " pdb=" N ASN M 72 " pdb=" CA ASN M 72 " ideal model delta harmonic sigma weight residual -180.00 -141.36 -38.64 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA TYR K 181 " pdb=" C TYR K 181 " pdb=" N PHE K 182 " pdb=" CA PHE K 182 " ideal model delta harmonic sigma weight residual -180.00 -141.61 -38.39 0 5.00e+00 4.00e-02 5.90e+01 ... (remaining 10103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2244 0.082 - 0.163: 557 0.163 - 0.245: 46 0.245 - 0.326: 7 0.326 - 0.408: 4 Chirality restraints: 2858 Sorted by residual: chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL K 287 " pdb=" CA VAL K 287 " pdb=" CG1 VAL K 287 " pdb=" CG2 VAL K 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL M 62 " pdb=" CA VAL M 62 " pdb=" CG1 VAL M 62 " pdb=" CG2 VAL M 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2855 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 404 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C PHE K 404 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE K 404 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU K 405 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 52 " -0.042 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR G 52 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR G 52 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR G 52 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR G 52 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR G 52 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 52 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 52 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " 0.039 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR F 98 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " 0.014 2.00e-02 2.50e+03 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3878 2.79 - 3.32: 15435 3.32 - 3.84: 33518 3.84 - 4.37: 37243 4.37 - 4.90: 52946 Nonbonded interactions: 143020 Sorted by model distance: nonbonded pdb=" OG1 THR M 185 " pdb=" OD1 ASP M 187 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR G 34 " pdb=" OE1 GLU H 38 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR M 144 " pdb=" O SER M 146 " model vdw 2.285 3.040 nonbonded pdb=" O ASP M 210 " pdb=" OG SER M 213 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR K 204 " pdb=" O GLN M 294 " model vdw 2.295 3.040 ... (remaining 143015 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.230 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.008 0.075 17850 Z= 0.650 Angle : 1.213 16.965 25340 Z= 0.857 Chirality : 0.069 0.408 2858 Planarity : 0.008 0.071 2190 Dihedral : 25.562 138.278 7530 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.34 % Allowed : 9.62 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.77 % 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: -4.90 (0.18), residues: 1319 helix: -3.44 (0.13), residues: 697 sheet: -2.63 (1.01), residues: 29 loop : -2.92 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 95 TYR 0.048 0.004 TYR F 98 PHE 0.036 0.004 PHE K 237 TRP 0.036 0.005 TRP M 361 HIS 0.022 0.003 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.65 (17850) covalent geometry : angle 1.21274 / 0.86 (25340) hydrogen bonds : bond 0.17021 / 10.54 ( 796) hydrogen bonds : angle 6.48210 / 4.34 ( 2011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 541 time to evaluate : 0.322 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6927 (tp30) REVERT: N 17 LEU cc_start: 0.8161 (tt) cc_final: 0.7828 (tt) REVERT: N 91 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7460 (t0) REVERT: K 223 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7471 (Cg_endo) REVERT: K 240 ASP cc_start: 0.6206 (p0) cc_final: 0.5916 (p0) REVERT: K 287 VAL cc_start: 0.8641 (p) cc_final: 0.8432 (m) REVERT: K 318 LYS cc_start: 0.8052 (tppt) cc_final: 0.7689 (mmmt) REVERT: K 322 GLU cc_start: 0.6530 (mp0) cc_final: 0.6172 (mp0) REVERT: K 377 THR cc_start: 0.7703 (p) cc_final: 0.6832 (t) REVERT: K 379 MET cc_start: 0.6327 (mpp) cc_final: 0.5987 (mpp) REVERT: M 70 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4556 (tt) REVERT: M 147 TYR cc_start: 0.6264 (m-10) cc_final: 0.6001 (m-10) REVERT: M 161 ASN cc_start: 0.6925 (p0) cc_final: 0.6405 (p0) REVERT: M 200 ILE cc_start: 0.8471 (pp) cc_final: 0.8061 (mm) REVERT: M 241 GLU cc_start: 0.8312 (mp0) cc_final: 0.8049 (mp0) REVERT: A 77 ASP cc_start: 0.7545 (p0) cc_final: 0.6894 (p0) REVERT: A 81 ASP cc_start: 0.7194 (t0) cc_final: 0.6896 (t70) REVERT: A 89 ILE cc_start: 0.8559 (mm) cc_final: 0.8249 (tp) REVERT: A 123 ASP cc_start: 0.7744 (m-30) cc_final: 0.7155 (m-30) REVERT: A 124 ILE cc_start: 0.7770 (mt) cc_final: 0.7514 (mm) REVERT: B 49 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.5044 (pp) REVERT: C 48 LYS cc_start: 0.8285 (pptt) cc_final: 0.7484 (pptt) REVERT: C 93 ASP cc_start: 0.7275 (p0) cc_final: 0.6588 (p0) REVERT: D 38 GLU cc_start: 0.7198 (tp30) cc_final: 0.6932 (tp30) REVERT: D 46 LYS cc_start: 0.8330 (pttm) cc_final: 0.8106 (ptpp) REVERT: D 116 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6400 (tm-30) REVERT: E 61 LEU cc_start: 0.7720 (mm) cc_final: 0.7089 (mt) REVERT: G 60 LEU cc_start: 0.8088 (tp) cc_final: 0.7746 (tt) REVERT: H 46 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7812 (ttpp) REVERT: H 47 VAL cc_start: 0.7606 (t) cc_final: 0.7394 (t) REVERT: H 82 LYS cc_start: 0.7879 (pttm) cc_final: 0.7666 (ptmm) REVERT: H 88 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7936 (mmpt) REVERT: H 97 ILE cc_start: 0.8388 (tp) cc_final: 0.8171 (tp) outliers start: 16 outliers final: 5 residues processed: 552 average time/residue: 0.1697 time to fit residues: 126.8892 Evaluate side-chains 444 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 436 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain F residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 91 ASN ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN K 301 ASN ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN K 401 HIS ** M 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 233 ASN M 245 HIS ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 111 HIS E 55 GLN E 93 GLN F 25 ASN G 16 GLN H 87 ASN H 98 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.101811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086642 restraints weight = 53655.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.088725 restraints weight = 26757.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090090 restraints weight = 16531.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.091001 restraints weight = 12063.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091558 restraints weight = 9831.668| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17850 Z= 0.232 Angle : 0.949 10.523 25340 Z= 0.524 Chirality : 0.055 0.382 2858 Planarity : 0.008 0.078 2190 Dihedral : 29.896 128.006 4780 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.93 % Allowed : 20.82 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.23 % 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: -3.89 (0.20), residues: 1319 helix: -2.32 (0.16), residues: 723 sheet: -1.90 (1.29), residues: 19 loop : -2.87 (0.23), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 40 TYR 0.054 0.004 TYR G 52 PHE 0.020 0.003 PHE K 182 TRP 0.022 0.003 TRP M 361 HIS 0.019 0.003 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (17850) covalent geometry : angle 0.94850 / 0.52 (25340) hydrogen bonds : bond 0.06688 / 4.23 ( 796) hydrogen bonds : angle 4.66954 / 3.19 ( 2011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 482 time to evaluate : 0.481 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: L 35 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7509 (tp30) REVERT: N 91 ASN cc_start: 0.8076 (t0) cc_final: 0.7836 (t0) REVERT: K 235 SER cc_start: 0.6122 (p) cc_final: 0.5762 (m) REVERT: K 245 ARG cc_start: 0.7006 (tpt170) cc_final: 0.6743 (tpm170) REVERT: K 318 LYS cc_start: 0.8106 (tppt) cc_final: 0.7579 (mmtm) REVERT: K 322 GLU cc_start: 0.6598 (mp0) cc_final: 0.6121 (mp0) REVERT: K 353 TRP cc_start: 0.8199 (m-10) cc_final: 0.7848 (m-10) REVERT: K 357 LEU cc_start: 0.7638 (mt) cc_final: 0.7344 (mt) REVERT: K 383 ASP cc_start: 0.7713 (t0) cc_final: 0.7290 (t0) REVERT: M 70 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4320 (tt) REVERT: M 74 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7201 (pp) REVERT: M 135 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7492 (ptpp) REVERT: M 161 ASN cc_start: 0.6966 (p0) cc_final: 0.6406 (p0) REVERT: M 189 PHE cc_start: 0.7761 (m-10) cc_final: 0.7464 (m-10) REVERT: M 200 ILE cc_start: 0.8448 (pp) cc_final: 0.8142 (mm) REVERT: M 224 LEU cc_start: 0.8223 (pt) cc_final: 0.7602 (mp) REVERT: M 249 PHE cc_start: 0.7866 (t80) cc_final: 0.7464 (t80) REVERT: M 267 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6365 (mt) REVERT: A 77 ASP cc_start: 0.7564 (p0) cc_final: 0.7333 (p0) REVERT: B 39 ARG cc_start: 0.7208 (tpp80) cc_final: 0.6834 (tpp80) REVERT: B 49 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5339 (pp) REVERT: B 88 TYR cc_start: 0.7580 (m-80) cc_final: 0.7137 (m-80) REVERT: C 25 GLN cc_start: 0.6777 (mm-40) cc_final: 0.6426 (mm110) REVERT: C 28 VAL cc_start: 0.8604 (t) cc_final: 0.8321 (m) REVERT: C 48 LYS cc_start: 0.7619 (pptt) cc_final: 0.7049 (pptt) REVERT: C 63 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7148 (tm-30) REVERT: C 66 GLU cc_start: 0.7607 (pp20) cc_final: 0.6959 (pp20) REVERT: C 84 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.6177 (t-90) REVERT: C 87 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6024 (pp) REVERT: D 46 LYS cc_start: 0.8191 (pttm) cc_final: 0.7566 (pttp) REVERT: D 101 VAL cc_start: 0.8782 (t) cc_final: 0.8459 (p) REVERT: D 116 GLU cc_start: 0.7433 (tm-30) cc_final: 0.5869 (tm-30) REVERT: E 57 SER cc_start: 0.8553 (t) cc_final: 0.8192 (p) REVERT: E 64 LYS cc_start: 0.8308 (ptmm) cc_final: 0.7977 (ttpp) REVERT: E 67 PHE cc_start: 0.7747 (t80) cc_final: 0.7524 (t80) REVERT: E 76 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: G 81 THR cc_start: 0.7781 (p) cc_final: 0.7472 (p) REVERT: H 97 ILE cc_start: 0.8620 (tp) cc_final: 0.8348 (tp) REVERT: H 123 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8130 (tppp) outliers start: 59 outliers final: 26 residues processed: 507 average time/residue: 0.1421 time to fit residues: 99.5440 Evaluate side-chains 485 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 451 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 332 GLN M 363 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.101445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086123 restraints weight = 54865.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088228 restraints weight = 27649.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089603 restraints weight = 17183.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090474 restraints weight = 12534.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091043 restraints weight = 10277.864| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17850 Z= 0.223 Angle : 0.899 11.681 25340 Z= 0.497 Chirality : 0.053 0.355 2858 Planarity : 0.007 0.075 2190 Dihedral : 29.721 125.619 4772 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.69 % Allowed : 24.41 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.15 % 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: -3.37 (0.21), residues: 1319 helix: -1.81 (0.17), residues: 733 sheet: -1.87 (1.11), residues: 21 loop : -2.76 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 335 TYR 0.044 0.003 TYR G 52 PHE 0.030 0.003 PHE M 196 TRP 0.018 0.002 TRP M 361 HIS 0.017 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (17850) covalent geometry : angle 0.89873 / 0.50 (25340) hydrogen bonds : bond 0.06533 / 4.12 ( 796) hydrogen bonds : angle 4.49526 / 3.06 ( 2011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 483 time to evaluate : 0.531 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: N 12 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: N 17 LEU cc_start: 0.7989 (tt) cc_final: 0.7736 (mt) REVERT: N 91 ASN cc_start: 0.8263 (t0) cc_final: 0.7992 (t0) REVERT: K 212 GLU cc_start: 0.8140 (pp20) cc_final: 0.7802 (pt0) REVERT: K 236 PHE cc_start: 0.6397 (m-80) cc_final: 0.6185 (m-80) REVERT: K 289 TYR cc_start: 0.7389 (p90) cc_final: 0.6856 (p90) REVERT: K 293 GLU cc_start: 0.7016 (mp0) cc_final: 0.6778 (mp0) REVERT: K 353 TRP cc_start: 0.8407 (m-10) cc_final: 0.7896 (m-10) REVERT: K 357 LEU cc_start: 0.7873 (mt) cc_final: 0.7562 (mt) REVERT: K 376 MET cc_start: 0.8285 (tpp) cc_final: 0.7757 (tpp) REVERT: K 383 ASP cc_start: 0.7929 (t0) cc_final: 0.6930 (t0) REVERT: K 409 ILE cc_start: 0.7538 (mt) cc_final: 0.7286 (mp) REVERT: M 70 LEU cc_start: 0.5063 (OUTLIER) cc_final: 0.4160 (tt) REVERT: M 74 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7341 (pp) REVERT: M 161 ASN cc_start: 0.7068 (p0) cc_final: 0.6651 (p0) REVERT: M 167 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6989 (ttp80) REVERT: M 189 PHE cc_start: 0.8079 (m-10) cc_final: 0.7849 (m-80) REVERT: M 200 ILE cc_start: 0.8304 (pp) cc_final: 0.7965 (mm) REVERT: M 215 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6843 (tt) REVERT: M 249 PHE cc_start: 0.8033 (t80) cc_final: 0.7600 (t80) REVERT: M 267 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6311 (mt) REVERT: A 77 ASP cc_start: 0.7955 (p0) cc_final: 0.7748 (p0) REVERT: A 83 ARG cc_start: 0.7670 (mmp80) cc_final: 0.7005 (mmp80) REVERT: B 35 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7464 (ttt90) REVERT: B 39 ARG cc_start: 0.7329 (tpp80) cc_final: 0.7088 (tpp80) REVERT: B 98 TYR cc_start: 0.7891 (m-10) cc_final: 0.7624 (m-10) REVERT: C 28 VAL cc_start: 0.8849 (t) cc_final: 0.8533 (p) REVERT: C 52 TYR cc_start: 0.7017 (t80) cc_final: 0.6682 (t80) REVERT: C 66 GLU cc_start: 0.7224 (pp20) cc_final: 0.6332 (pp20) REVERT: C 87 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6666 (pp) REVERT: D 73 PHE cc_start: 0.8745 (t80) cc_final: 0.8379 (t80) REVERT: D 86 TYR cc_start: 0.7194 (p90) cc_final: 0.6984 (p90) REVERT: D 101 VAL cc_start: 0.8854 (t) cc_final: 0.8548 (p) REVERT: D 116 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6174 (tm-30) REVERT: E 57 SER cc_start: 0.8716 (t) cc_final: 0.8473 (p) REVERT: E 94 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7940 (mm-30) REVERT: F 53 GLU cc_start: 0.7311 (mp0) cc_final: 0.7098 (mp0) REVERT: F 67 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6562 (mtm-85) REVERT: G 81 THR cc_start: 0.7835 (p) cc_final: 0.7585 (p) REVERT: H 86 TYR cc_start: 0.7101 (p90) cc_final: 0.6601 (p90) REVERT: H 88 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7902 (mmpt) REVERT: H 97 ILE cc_start: 0.8802 (tp) cc_final: 0.8507 (tp) REVERT: H 123 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8258 (tppp) outliers start: 68 outliers final: 37 residues processed: 517 average time/residue: 0.1543 time to fit residues: 109.8047 Evaluate side-chains 506 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 463 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 299 ARG Chi-restraints excluded: chain M residue 332 GLN Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 100 HIS ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN F 25 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086575 restraints weight = 54850.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088722 restraints weight = 27407.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090075 restraints weight = 16949.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090939 restraints weight = 12332.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091503 restraints weight = 10088.539| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17850 Z= 0.186 Angle : 0.863 12.047 25340 Z= 0.474 Chirality : 0.051 0.427 2858 Planarity : 0.006 0.075 2190 Dihedral : 29.619 122.298 4770 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 6.35 % Allowed : 26.00 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.23 % 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: -3.14 (0.21), residues: 1319 helix: -1.64 (0.17), residues: 734 sheet: -1.70 (1.20), residues: 19 loop : -2.64 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 213 TYR 0.038 0.003 TYR F 72 PHE 0.042 0.002 PHE K 323 TRP 0.013 0.001 TRP M 361 HIS 0.008 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (17850) covalent geometry : angle 0.86291 / 0.47 (25340) hydrogen bonds : bond 0.05898 / 3.73 ( 796) hydrogen bonds : angle 4.38009 / 2.98 ( 2011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 476 time to evaluate : 0.464 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: L 35 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7469 (tp30) REVERT: N 12 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: N 13 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (p0) REVERT: N 17 LEU cc_start: 0.8017 (tt) cc_final: 0.7753 (mt) REVERT: N 91 ASN cc_start: 0.8339 (t0) cc_final: 0.8075 (t0) REVERT: N 100 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.5947 (m-70) REVERT: K 230 ARG cc_start: 0.6587 (tpm170) cc_final: 0.6304 (tpm170) REVERT: K 276 MET cc_start: 0.7297 (tmm) cc_final: 0.7044 (tmm) REVERT: K 353 TRP cc_start: 0.8440 (m-10) cc_final: 0.7999 (m-10) REVERT: K 357 LEU cc_start: 0.7884 (mt) cc_final: 0.7582 (mt) REVERT: K 376 MET cc_start: 0.8129 (tpp) cc_final: 0.7816 (tpp) REVERT: K 379 MET cc_start: 0.7328 (mpp) cc_final: 0.6980 (mpp) REVERT: K 383 ASP cc_start: 0.7918 (t0) cc_final: 0.6797 (t0) REVERT: M 70 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4030 (tt) REVERT: M 130 TRP cc_start: 0.5622 (t60) cc_final: 0.5422 (t60) REVERT: M 161 ASN cc_start: 0.7075 (p0) cc_final: 0.6735 (p0) REVERT: M 224 LEU cc_start: 0.8331 (pt) cc_final: 0.7742 (mp) REVERT: M 249 PHE cc_start: 0.7996 (t80) cc_final: 0.7441 (t80) REVERT: M 250 ILE cc_start: 0.7343 (mm) cc_final: 0.6984 (mp) REVERT: M 267 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6465 (mt) REVERT: A 77 ASP cc_start: 0.8233 (p0) cc_final: 0.7920 (p0) REVERT: A 83 ARG cc_start: 0.7571 (mmp80) cc_final: 0.6831 (mmp80) REVERT: B 35 ARG cc_start: 0.7777 (ttt90) cc_final: 0.7436 (tpt170) REVERT: B 39 ARG cc_start: 0.7474 (tpp80) cc_final: 0.7173 (tpp-160) REVERT: C 28 VAL cc_start: 0.8866 (t) cc_final: 0.8547 (p) REVERT: C 52 TYR cc_start: 0.6935 (t80) cc_final: 0.6502 (t80) REVERT: C 87 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6573 (pp) REVERT: C 92 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8303 (t0) REVERT: C 95 LEU cc_start: 0.8182 (tp) cc_final: 0.7970 (tp) REVERT: D 101 VAL cc_start: 0.8945 (t) cc_final: 0.8712 (p) REVERT: D 111 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7793 (ptpp) REVERT: D 116 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7076 (tm-30) REVERT: E 57 SER cc_start: 0.8748 (t) cc_final: 0.8324 (p) REVERT: F 59 LYS cc_start: 0.8372 (pttt) cc_final: 0.8159 (tmtt) REVERT: F 63 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6284 (mp0) REVERT: F 67 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6544 (mtm-85) REVERT: F 91 LYS cc_start: 0.8668 (tptp) cc_final: 0.8385 (tptp) REVERT: G 30 ARG cc_start: 0.7188 (ttm-80) cc_final: 0.6664 (ttp80) REVERT: H 88 LYS cc_start: 0.8249 (mmpt) cc_final: 0.7880 (mmpt) REVERT: H 97 ILE cc_start: 0.8935 (tp) cc_final: 0.8675 (tp) REVERT: H 123 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8285 (tppp) outliers start: 76 outliers final: 39 residues processed: 514 average time/residue: 0.1587 time to fit residues: 112.4633 Evaluate side-chains 505 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 459 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 100 HIS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 0.0040 chunk 107 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 107 ASN ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.102827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087438 restraints weight = 54070.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089556 restraints weight = 26781.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.090940 restraints weight = 16446.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091810 restraints weight = 11892.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092374 restraints weight = 9687.622| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17850 Z= 0.173 Angle : 0.862 13.821 25340 Z= 0.471 Chirality : 0.050 0.433 2858 Planarity : 0.006 0.077 2190 Dihedral : 29.513 118.894 4770 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.94 % Allowed : 27.42 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.15 % 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: -2.95 (0.21), residues: 1319 helix: -1.47 (0.18), residues: 714 sheet: -1.64 (1.18), residues: 19 loop : -2.55 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 167 TYR 0.048 0.003 TYR G 52 PHE 0.043 0.003 PHE M 189 TRP 0.019 0.002 TRP K 247 HIS 0.008 0.001 HIS M 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (17850) covalent geometry : angle 0.86229 / 0.47 (25340) hydrogen bonds : bond 0.05681 / 3.59 ( 796) hydrogen bonds : angle 4.32576 / 2.94 ( 2011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 488 time to evaluate : 0.498 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: L 35 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7538 (tp30) REVERT: N 12 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: N 17 LEU cc_start: 0.8042 (tt) cc_final: 0.7681 (mt) REVERT: N 91 ASN cc_start: 0.8390 (t0) cc_final: 0.8152 (t0) REVERT: K 176 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: K 276 MET cc_start: 0.7333 (tmm) cc_final: 0.7114 (tmm) REVERT: K 289 TYR cc_start: 0.7493 (p90) cc_final: 0.7103 (p90) REVERT: K 353 TRP cc_start: 0.8447 (m-10) cc_final: 0.8071 (m-10) REVERT: K 357 LEU cc_start: 0.7884 (mt) cc_final: 0.7568 (mt) REVERT: K 376 MET cc_start: 0.8243 (tpp) cc_final: 0.7807 (tpp) REVERT: K 379 MET cc_start: 0.7252 (mpp) cc_final: 0.6848 (mpp) REVERT: K 383 ASP cc_start: 0.8011 (t0) cc_final: 0.6805 (t0) REVERT: K 432 LYS cc_start: 0.8372 (tmtt) cc_final: 0.8156 (tmtt) REVERT: M 69 TYR cc_start: 0.5136 (t80) cc_final: 0.4699 (t80) REVERT: M 70 LEU cc_start: 0.5013 (OUTLIER) cc_final: 0.4139 (tt) REVERT: M 74 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7622 (mt) REVERT: M 161 ASN cc_start: 0.6974 (p0) cc_final: 0.6685 (p0) REVERT: M 189 PHE cc_start: 0.8048 (m-80) cc_final: 0.7840 (m-80) REVERT: M 215 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6919 (tt) REVERT: M 249 PHE cc_start: 0.8008 (t80) cc_final: 0.7496 (t80) REVERT: M 250 ILE cc_start: 0.7275 (mm) cc_final: 0.6980 (mp) REVERT: M 267 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6452 (mt) REVERT: M 342 LYS cc_start: 0.8456 (pttm) cc_final: 0.8173 (pttm) REVERT: A 83 ARG cc_start: 0.7605 (mmp80) cc_final: 0.6873 (mmp80) REVERT: B 35 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7590 (ttt90) REVERT: B 39 ARG cc_start: 0.7533 (tpp80) cc_final: 0.7242 (tpp-160) REVERT: B 68 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6989 (p0) REVERT: C 28 VAL cc_start: 0.8903 (t) cc_final: 0.8549 (p) REVERT: C 66 GLU cc_start: 0.7230 (pp20) cc_final: 0.7016 (pp20) REVERT: C 87 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6487 (pp) REVERT: C 92 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8270 (t0) REVERT: D 101 VAL cc_start: 0.8911 (t) cc_final: 0.8709 (p) REVERT: D 111 LYS cc_start: 0.8235 (ptpp) cc_final: 0.7841 (ptpp) REVERT: E 57 SER cc_start: 0.8694 (t) cc_final: 0.8363 (p) REVERT: E 62 ILE cc_start: 0.8082 (mm) cc_final: 0.7873 (mm) REVERT: F 67 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6767 (mtm110) REVERT: F 91 LYS cc_start: 0.8663 (tptp) cc_final: 0.8398 (tptp) REVERT: G 81 THR cc_start: 0.7853 (p) cc_final: 0.7553 (p) REVERT: G 90 ARG cc_start: 0.8003 (ptt180) cc_final: 0.7634 (ttt180) REVERT: H 76 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7151 (tt) REVERT: H 86 TYR cc_start: 0.7204 (p90) cc_final: 0.6915 (p90) REVERT: H 88 LYS cc_start: 0.8302 (mmpt) cc_final: 0.7907 (mmpt) REVERT: H 97 ILE cc_start: 0.8971 (tp) cc_final: 0.8738 (tp) REVERT: H 123 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8294 (tppp) REVERT: H 124 TYR cc_start: 0.8878 (t80) cc_final: 0.8647 (t80) outliers start: 71 outliers final: 46 residues processed: 524 average time/residue: 0.1530 time to fit residues: 111.2218 Evaluate side-chains 524 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 468 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 176 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 214 TYR Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 130 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 108 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 139 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 168 ASN ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN K 301 ASN M 201 HIS C 84 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.103274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.087789 restraints weight = 54378.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089912 restraints weight = 27251.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091255 restraints weight = 16872.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092099 restraints weight = 12319.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092648 restraints weight = 10115.526| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17850 Z= 0.174 Angle : 0.866 14.854 25340 Z= 0.470 Chirality : 0.051 0.451 2858 Planarity : 0.006 0.057 2190 Dihedral : 29.417 114.130 4770 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.86 % Allowed : 29.26 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.15 % 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: -2.89 (0.21), residues: 1319 helix: -1.40 (0.17), residues: 723 sheet: -1.47 (1.11), residues: 20 loop : -2.55 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 167 TYR 0.054 0.003 TYR G 52 PHE 0.042 0.003 PHE M 189 TRP 0.010 0.001 TRP M 361 HIS 0.005 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (17850) covalent geometry : angle 0.86564 / 0.47 (25340) hydrogen bonds : bond 0.05577 / 3.52 ( 796) hydrogen bonds : angle 4.23521 / 2.88 ( 2011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 489 time to evaluate : 0.328 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: L 35 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7521 (tp30) REVERT: N 12 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: N 17 LEU cc_start: 0.8056 (tt) cc_final: 0.7706 (mt) REVERT: N 23 TYR cc_start: 0.8325 (t80) cc_final: 0.8118 (t80) REVERT: N 91 ASN cc_start: 0.8411 (t0) cc_final: 0.8187 (t0) REVERT: K 226 ASN cc_start: 0.6858 (m-40) cc_final: 0.6347 (m-40) REVERT: K 272 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7591 (tp) REVERT: K 289 TYR cc_start: 0.7578 (p90) cc_final: 0.7237 (p90) REVERT: K 352 TYR cc_start: 0.6779 (t80) cc_final: 0.6565 (t80) REVERT: K 353 TRP cc_start: 0.8480 (m-10) cc_final: 0.8068 (m-10) REVERT: K 357 LEU cc_start: 0.7939 (mt) cc_final: 0.7657 (mt) REVERT: K 370 ILE cc_start: 0.7687 (tt) cc_final: 0.7309 (pt) REVERT: K 376 MET cc_start: 0.8220 (tpp) cc_final: 0.7707 (tpp) REVERT: K 379 MET cc_start: 0.7216 (mpp) cc_final: 0.6959 (mpp) REVERT: K 383 ASP cc_start: 0.8002 (t0) cc_final: 0.6509 (t0) REVERT: M 70 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4007 (tt) REVERT: M 74 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7780 (mt) REVERT: M 161 ASN cc_start: 0.6959 (p0) cc_final: 0.6695 (p0) REVERT: M 168 ASP cc_start: 0.7807 (t0) cc_final: 0.7547 (t0) REVERT: M 169 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5396 (tm-30) REVERT: M 189 PHE cc_start: 0.8116 (m-80) cc_final: 0.7337 (m-80) REVERT: M 193 CYS cc_start: 0.7254 (m) cc_final: 0.7027 (p) REVERT: M 215 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6826 (tt) REVERT: M 224 LEU cc_start: 0.8412 (pt) cc_final: 0.7779 (mp) REVERT: M 249 PHE cc_start: 0.8031 (t80) cc_final: 0.7621 (t80) REVERT: A 83 ARG cc_start: 0.7605 (mmp80) cc_final: 0.6907 (mmp80) REVERT: B 35 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7599 (tpt170) REVERT: B 67 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7188 (ttp80) REVERT: B 79 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7831 (mtpt) REVERT: C 28 VAL cc_start: 0.8917 (t) cc_final: 0.8558 (p) REVERT: C 87 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6380 (pp) REVERT: C 92 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8062 (t0) REVERT: D 101 VAL cc_start: 0.8950 (t) cc_final: 0.8706 (p) REVERT: D 111 LYS cc_start: 0.8241 (ptpp) cc_final: 0.7899 (ptpp) REVERT: D 114 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8508 (p) REVERT: E 57 SER cc_start: 0.8745 (t) cc_final: 0.8225 (p) REVERT: E 62 ILE cc_start: 0.8066 (mm) cc_final: 0.7857 (mm) REVERT: F 67 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6786 (mtm110) REVERT: F 91 LYS cc_start: 0.8701 (tptp) cc_final: 0.8441 (tptp) REVERT: G 30 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6895 (ttp80) REVERT: G 81 THR cc_start: 0.7842 (p) cc_final: 0.7488 (p) REVERT: G 90 ARG cc_start: 0.7894 (ptt180) cc_final: 0.7663 (ttt180) REVERT: H 49 LYS cc_start: 0.8410 (pttp) cc_final: 0.8061 (pttp) REVERT: H 62 MET cc_start: 0.7995 (tpp) cc_final: 0.7478 (tpp) REVERT: H 86 TYR cc_start: 0.7137 (p90) cc_final: 0.6922 (p90) REVERT: H 88 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7846 (mmpt) REVERT: H 97 ILE cc_start: 0.9054 (tp) cc_final: 0.8813 (tp) REVERT: H 108 GLU cc_start: 0.7137 (mp0) cc_final: 0.6672 (pp20) REVERT: H 123 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8341 (tppp) outliers start: 82 outliers final: 51 residues processed: 529 average time/residue: 0.1475 time to fit residues: 107.8901 Evaluate side-chains 541 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 480 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 100 HIS Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 214 TYR Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 73 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS M 332 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.103078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087414 restraints weight = 55390.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089555 restraints weight = 27831.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090903 restraints weight = 17325.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091771 restraints weight = 12720.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.092327 restraints weight = 10475.431| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17850 Z= 0.186 Angle : 0.878 15.036 25340 Z= 0.477 Chirality : 0.051 0.478 2858 Planarity : 0.006 0.091 2190 Dihedral : 29.334 104.073 4770 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.65 % Rotamer: Outliers : 6.10 % Allowed : 30.69 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.82 (0.21), residues: 1319 helix: -1.39 (0.18), residues: 720 sheet: -1.74 (1.15), residues: 20 loop : -2.45 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 37 TYR 0.066 0.003 TYR G 52 PHE 0.037 0.003 PHE M 189 TRP 0.010 0.001 TRP M 361 HIS 0.008 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (17850) covalent geometry : angle 0.87821 / 0.48 (25340) hydrogen bonds : bond 0.05640 / 3.55 ( 796) hydrogen bonds : angle 4.31411 / 2.95 ( 2011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 494 time to evaluate : 0.539 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: L 35 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7555 (tp30) REVERT: N 12 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: N 17 LEU cc_start: 0.8091 (tt) cc_final: 0.7734 (mt) REVERT: K 226 ASN cc_start: 0.7074 (m-40) cc_final: 0.6670 (m-40) REVERT: K 266 TYR cc_start: 0.6561 (t80) cc_final: 0.5763 (t80) REVERT: K 272 LEU cc_start: 0.7937 (tp) cc_final: 0.7618 (tp) REVERT: K 289 TYR cc_start: 0.7644 (p90) cc_final: 0.7363 (p90) REVERT: K 352 TYR cc_start: 0.6889 (t80) cc_final: 0.6605 (t80) REVERT: K 353 TRP cc_start: 0.8489 (m-10) cc_final: 0.8102 (m-10) REVERT: K 357 LEU cc_start: 0.7983 (mt) cc_final: 0.7714 (mt) REVERT: K 370 ILE cc_start: 0.7768 (tt) cc_final: 0.7411 (pt) REVERT: K 383 ASP cc_start: 0.8023 (t0) cc_final: 0.6572 (t0) REVERT: M 70 LEU cc_start: 0.4879 (OUTLIER) cc_final: 0.4110 (tt) REVERT: M 74 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7709 (mt) REVERT: M 161 ASN cc_start: 0.6956 (p0) cc_final: 0.6694 (p0) REVERT: M 168 ASP cc_start: 0.7851 (t0) cc_final: 0.7647 (t0) REVERT: M 189 PHE cc_start: 0.8140 (m-80) cc_final: 0.7447 (m-80) REVERT: M 193 CYS cc_start: 0.7392 (m) cc_final: 0.7071 (p) REVERT: M 215 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6888 (tt) REVERT: M 224 LEU cc_start: 0.8403 (pt) cc_final: 0.7779 (mp) REVERT: M 249 PHE cc_start: 0.8057 (t80) cc_final: 0.7628 (t80) REVERT: A 83 ARG cc_start: 0.7592 (mmp80) cc_final: 0.6873 (mmp80) REVERT: A 93 GLN cc_start: 0.7915 (tp40) cc_final: 0.7658 (tp40) REVERT: B 35 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7636 (tpt170) REVERT: B 44 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8517 (mmmm) REVERT: B 79 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7895 (mtpt) REVERT: C 28 VAL cc_start: 0.8986 (t) cc_final: 0.8634 (p) REVERT: C 44 ARG cc_start: 0.4982 (ptm160) cc_final: 0.4623 (ptm160) REVERT: C 57 LEU cc_start: 0.7856 (tp) cc_final: 0.7646 (tp) REVERT: C 63 GLU cc_start: 0.8143 (tp30) cc_final: 0.7614 (tp30) REVERT: C 87 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6479 (pp) REVERT: C 92 ASP cc_start: 0.8364 (t0) cc_final: 0.8133 (t0) REVERT: D 101 VAL cc_start: 0.8957 (t) cc_final: 0.8699 (p) REVERT: D 111 LYS cc_start: 0.8226 (ptpp) cc_final: 0.7900 (ptpp) REVERT: E 57 SER cc_start: 0.8723 (t) cc_final: 0.8325 (p) REVERT: E 62 ILE cc_start: 0.8178 (mm) cc_final: 0.7923 (mm) REVERT: F 23 ARG cc_start: 0.7468 (mmp-170) cc_final: 0.6963 (mmp80) REVERT: F 63 GLU cc_start: 0.7108 (mp0) cc_final: 0.5818 (mp0) REVERT: F 67 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6773 (mtm110) REVERT: F 91 LYS cc_start: 0.8773 (tptp) cc_final: 0.8525 (tptp) REVERT: G 81 THR cc_start: 0.7875 (p) cc_final: 0.7570 (p) REVERT: H 62 MET cc_start: 0.8004 (tpp) cc_final: 0.7472 (tpp) REVERT: H 88 LYS cc_start: 0.8358 (mmpt) cc_final: 0.7887 (mmpt) REVERT: H 97 ILE cc_start: 0.9137 (tp) cc_final: 0.8867 (tp) REVERT: H 123 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8348 (tppp) outliers start: 73 outliers final: 54 residues processed: 523 average time/residue: 0.1523 time to fit residues: 110.0227 Evaluate side-chains 542 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 482 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 100 HIS Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 304 CYS Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 334 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 332 GLN Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 129 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.103092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087371 restraints weight = 55848.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089491 restraints weight = 28356.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090860 restraints weight = 17769.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091698 restraints weight = 13054.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092224 restraints weight = 10806.286| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17850 Z= 0.191 Angle : 0.905 14.720 25340 Z= 0.488 Chirality : 0.050 0.380 2858 Planarity : 0.006 0.069 2190 Dihedral : 29.281 91.024 4770 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.35 % Allowed : 32.11 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.81 (0.21), residues: 1319 helix: -1.35 (0.18), residues: 723 sheet: -1.53 (1.25), residues: 20 loop : -2.51 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 49 TYR 0.051 0.003 TYR G 52 PHE 0.035 0.003 PHE K 236 TRP 0.011 0.001 TRP K 247 HIS 0.007 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (17850) covalent geometry : angle 0.90508 / 0.49 (25340) hydrogen bonds : bond 0.05636 / 3.55 ( 796) hydrogen bonds : angle 4.31358 / 2.94 ( 2011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 493 time to evaluate : 0.431 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: L 35 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7551 (tp30) REVERT: N 17 LEU cc_start: 0.8190 (tt) cc_final: 0.7815 (mt) REVERT: N 91 ASN cc_start: 0.8124 (t0) cc_final: 0.7826 (t0) REVERT: K 176 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: K 251 LEU cc_start: 0.8602 (mm) cc_final: 0.8353 (mm) REVERT: K 272 LEU cc_start: 0.7994 (tp) cc_final: 0.7712 (tp) REVERT: K 349 TYR cc_start: 0.6881 (m-10) cc_final: 0.6669 (m-80) REVERT: K 352 TYR cc_start: 0.6934 (t80) cc_final: 0.6684 (t80) REVERT: K 353 TRP cc_start: 0.8429 (m-10) cc_final: 0.8147 (m-10) REVERT: K 357 LEU cc_start: 0.8091 (mt) cc_final: 0.7812 (mt) REVERT: K 370 ILE cc_start: 0.7786 (tt) cc_final: 0.7505 (pt) REVERT: K 383 ASP cc_start: 0.8029 (t0) cc_final: 0.7270 (t0) REVERT: K 391 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8220 (tp) REVERT: M 70 LEU cc_start: 0.4908 (OUTLIER) cc_final: 0.4151 (tt) REVERT: M 74 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8020 (pt) REVERT: M 161 ASN cc_start: 0.6961 (p0) cc_final: 0.6676 (p0) REVERT: M 175 GLN cc_start: 0.7270 (mm-40) cc_final: 0.7007 (mm-40) REVERT: M 189 PHE cc_start: 0.8062 (m-80) cc_final: 0.7611 (m-80) REVERT: M 193 CYS cc_start: 0.7432 (m) cc_final: 0.7166 (p) REVERT: M 215 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6916 (tt) REVERT: M 224 LEU cc_start: 0.8381 (pt) cc_final: 0.7744 (mp) REVERT: M 342 LYS cc_start: 0.8482 (pttm) cc_final: 0.8214 (pttm) REVERT: A 83 ARG cc_start: 0.7616 (mmp80) cc_final: 0.6892 (mmp80) REVERT: A 93 GLN cc_start: 0.7826 (tp40) cc_final: 0.7613 (tp40) REVERT: B 35 ARG cc_start: 0.7929 (ttt90) cc_final: 0.7706 (tpt170) REVERT: B 44 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8587 (mmmm) REVERT: B 79 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7911 (mtpt) REVERT: C 28 VAL cc_start: 0.9031 (t) cc_final: 0.8675 (p) REVERT: C 66 GLU cc_start: 0.7233 (pp20) cc_final: 0.6793 (pp20) REVERT: C 84 HIS cc_start: 0.7151 (t-90) cc_final: 0.6905 (t-170) REVERT: C 87 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6790 (pp) REVERT: C 92 ASP cc_start: 0.8293 (t0) cc_final: 0.8000 (t0) REVERT: D 101 VAL cc_start: 0.9032 (t) cc_final: 0.8793 (p) REVERT: E 57 SER cc_start: 0.8631 (t) cc_final: 0.8414 (p) REVERT: E 131 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6633 (ttm110) REVERT: F 39 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7711 (mmt90) REVERT: F 59 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7652 (ttmm) REVERT: F 67 ARG cc_start: 0.7208 (mtm-85) cc_final: 0.6778 (mtm110) REVERT: H 49 LYS cc_start: 0.8447 (pttp) cc_final: 0.8066 (pttp) REVERT: H 62 MET cc_start: 0.8112 (tpp) cc_final: 0.7674 (tpp) REVERT: H 88 LYS cc_start: 0.8406 (mmpt) cc_final: 0.7961 (mmpt) REVERT: H 123 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8323 (tppp) outliers start: 64 outliers final: 47 residues processed: 521 average time/residue: 0.1665 time to fit residues: 119.3712 Evaluate side-chains 538 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 483 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 100 HIS Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 176 GLU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 39 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 120 GLN ** 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 = 0.3800 r_free = 0.3800 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087498 restraints weight = 55328.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089562 restraints weight = 28091.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090906 restraints weight = 17588.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.091746 restraints weight = 12926.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.092292 restraints weight = 10659.186| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17850 Z= 0.190 Angle : 0.932 14.216 25340 Z= 0.499 Chirality : 0.051 0.399 2858 Planarity : 0.007 0.121 2190 Dihedral : 29.251 91.676 4770 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.18 % Allowed : 34.20 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.88 (0.21), residues: 1319 helix: -1.41 (0.17), residues: 728 sheet: -1.53 (1.26), residues: 20 loop : -2.55 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 167 TYR 0.065 0.003 TYR G 52 PHE 0.052 0.003 PHE K 236 TRP 0.012 0.001 TRP K 247 HIS 0.006 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (17850) covalent geometry : angle 0.93211 / 0.50 (25340) hydrogen bonds : bond 0.05577 / 3.51 ( 796) hydrogen bonds : angle 4.38525 / 2.99 ( 2011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 488 time to evaluate : 0.468 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: L 35 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7562 (tp30) REVERT: N 17 LEU cc_start: 0.8235 (tt) cc_final: 0.7937 (mt) REVERT: K 230 ARG cc_start: 0.6469 (tpm170) cc_final: 0.5855 (tpp-160) REVERT: K 272 LEU cc_start: 0.7973 (tp) cc_final: 0.7671 (tp) REVERT: K 322 GLU cc_start: 0.7257 (tt0) cc_final: 0.6901 (pt0) REVERT: K 352 TYR cc_start: 0.6942 (t80) cc_final: 0.6686 (t80) REVERT: K 353 TRP cc_start: 0.8450 (m-10) cc_final: 0.8189 (m-10) REVERT: K 357 LEU cc_start: 0.8137 (mt) cc_final: 0.7835 (mt) REVERT: K 383 ASP cc_start: 0.7969 (t0) cc_final: 0.7127 (t0) REVERT: M 70 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4150 (tt) REVERT: M 74 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7713 (mt) REVERT: M 141 PHE cc_start: 0.7562 (t80) cc_final: 0.7209 (m-80) REVERT: M 161 ASN cc_start: 0.6964 (p0) cc_final: 0.6678 (p0) REVERT: M 175 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7144 (mm-40) REVERT: M 215 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6947 (tt) REVERT: M 224 LEU cc_start: 0.8334 (pt) cc_final: 0.7704 (mp) REVERT: A 83 ARG cc_start: 0.7609 (mmp80) cc_final: 0.6875 (mmp80) REVERT: A 93 GLN cc_start: 0.7823 (tp40) cc_final: 0.7613 (tp40) REVERT: A 123 ASP cc_start: 0.8156 (m-30) cc_final: 0.7948 (m-30) REVERT: B 35 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7772 (tpt170) REVERT: B 44 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8615 (mmmm) REVERT: B 79 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: B 92 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.6774 (tmm-80) REVERT: C 28 VAL cc_start: 0.9010 (t) cc_final: 0.8632 (p) REVERT: C 66 GLU cc_start: 0.7147 (pp20) cc_final: 0.6582 (pp20) REVERT: C 87 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6754 (pp) REVERT: C 92 ASP cc_start: 0.8298 (t0) cc_final: 0.8036 (t0) REVERT: E 57 SER cc_start: 0.8690 (t) cc_final: 0.8344 (p) REVERT: F 39 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7610 (mmt90) REVERT: F 59 LYS cc_start: 0.8408 (tmtt) cc_final: 0.8092 (ttmm) REVERT: F 67 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6899 (mtm110) REVERT: G 30 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7229 (mtm-85) REVERT: G 57 LEU cc_start: 0.8700 (tt) cc_final: 0.8431 (tp) REVERT: H 49 LYS cc_start: 0.8478 (pttp) cc_final: 0.8041 (pttp) REVERT: H 62 MET cc_start: 0.8153 (tpp) cc_final: 0.7694 (tpp) REVERT: H 88 LYS cc_start: 0.8427 (mmpt) cc_final: 0.8028 (mmpt) REVERT: H 123 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8317 (tppp) outliers start: 62 outliers final: 46 residues processed: 511 average time/residue: 0.1726 time to fit residues: 121.2327 Evaluate side-chains 525 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 473 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 100 HIS Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 chunk 87 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 107 ASN ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.103936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088436 restraints weight = 55473.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090558 restraints weight = 27965.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091899 restraints weight = 17480.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092752 restraints weight = 12863.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093281 restraints weight = 10586.188| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17850 Z= 0.186 Angle : 0.955 16.536 25340 Z= 0.507 Chirality : 0.051 0.417 2858 Planarity : 0.007 0.139 2190 Dihedral : 29.196 92.526 4770 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.10 % Allowed : 34.62 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.85 (0.21), residues: 1319 helix: -1.43 (0.17), residues: 715 sheet: -1.50 (1.20), residues: 20 loop : -2.44 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 49 TYR 0.055 0.003 TYR G 52 PHE 0.054 0.003 PHE M 189 TRP 0.021 0.001 TRP K 247 HIS 0.013 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (17850) covalent geometry : angle 0.95517 / 0.51 (25340) hydrogen bonds : bond 0.05503 / 3.47 ( 796) hydrogen bonds : angle 4.36525 / 2.97 ( 2011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 484 time to evaluate : 0.520 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: L 35 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7573 (tp30) REVERT: N 17 LEU cc_start: 0.8320 (tt) cc_final: 0.7907 (mt) REVERT: K 272 LEU cc_start: 0.8006 (tp) cc_final: 0.7714 (tp) REVERT: K 322 GLU cc_start: 0.7135 (tt0) cc_final: 0.6857 (pt0) REVERT: K 352 TYR cc_start: 0.6964 (t80) cc_final: 0.6717 (t80) REVERT: K 353 TRP cc_start: 0.8443 (m-10) cc_final: 0.8161 (m-10) REVERT: K 357 LEU cc_start: 0.8144 (mt) cc_final: 0.7817 (mt) REVERT: K 370 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6543 (pt) REVERT: K 383 ASP cc_start: 0.7937 (t0) cc_final: 0.7060 (t0) REVERT: K 408 ASP cc_start: 0.8552 (p0) cc_final: 0.8280 (p0) REVERT: M 70 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4078 (tt) REVERT: M 74 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7717 (mt) REVERT: M 141 PHE cc_start: 0.7565 (t80) cc_final: 0.7233 (m-80) REVERT: M 161 ASN cc_start: 0.6817 (p0) cc_final: 0.6539 (p0) REVERT: M 189 PHE cc_start: 0.8019 (m-80) cc_final: 0.7346 (m-80) REVERT: M 193 CYS cc_start: 0.7528 (m) cc_final: 0.7170 (p) REVERT: M 215 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6949 (tt) REVERT: M 224 LEU cc_start: 0.8354 (pt) cc_final: 0.7737 (mp) REVERT: M 335 ARG cc_start: 0.8373 (mmp-170) cc_final: 0.8034 (mmp-170) REVERT: A 83 ARG cc_start: 0.7588 (mmp80) cc_final: 0.6856 (mmp80) REVERT: A 121 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7707 (mmtt) REVERT: B 63 GLU cc_start: 0.7581 (pp20) cc_final: 0.7269 (pp20) REVERT: B 67 ARG cc_start: 0.7261 (ttp80) cc_final: 0.6919 (ttp80) REVERT: B 92 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.6799 (tmm-80) REVERT: C 28 VAL cc_start: 0.9052 (t) cc_final: 0.8692 (p) REVERT: C 30 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7539 (mtp85) REVERT: C 66 GLU cc_start: 0.7007 (pp20) cc_final: 0.6426 (pp20) REVERT: C 87 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6875 (pp) REVERT: C 92 ASP cc_start: 0.8218 (t0) cc_final: 0.7948 (t0) REVERT: D 88 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8126 (mmtt) REVERT: D 89 LYS cc_start: 0.8518 (mmmm) cc_final: 0.7943 (mmmm) REVERT: E 57 SER cc_start: 0.8591 (t) cc_final: 0.8326 (p) REVERT: F 23 ARG cc_start: 0.7072 (mmp80) cc_final: 0.6869 (mmp80) REVERT: F 59 LYS cc_start: 0.8400 (tmtt) cc_final: 0.8078 (ttmm) REVERT: G 30 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7173 (mtm-85) REVERT: G 57 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8412 (tp) REVERT: G 93 ASP cc_start: 0.8191 (m-30) cc_final: 0.7921 (m-30) REVERT: H 49 LYS cc_start: 0.8478 (pttp) cc_final: 0.8026 (pttp) REVERT: H 62 MET cc_start: 0.8165 (tpp) cc_final: 0.7729 (tpp) REVERT: H 88 LYS cc_start: 0.8460 (mmpt) cc_final: 0.8076 (mmpt) REVERT: H 123 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8315 (tppp) outliers start: 61 outliers final: 45 residues processed: 511 average time/residue: 0.1689 time to fit residues: 119.4990 Evaluate side-chains 535 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 482 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 100 HIS Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 369 THR Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 83 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 141 optimal weight: 0.0070 chunk 70 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** 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 = 0.3807 r_free = 0.3807 target = 0.103354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.087764 restraints weight = 55626.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089905 restraints weight = 28198.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091267 restraints weight = 17570.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.092117 restraints weight = 12879.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092672 restraints weight = 10612.697| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17850 Z= 0.193 Angle : 0.957 15.328 25340 Z= 0.510 Chirality : 0.052 0.384 2858 Planarity : 0.007 0.132 2190 Dihedral : 29.121 93.726 4766 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.60 % Allowed : 35.12 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.21), residues: 1319 helix: -1.44 (0.18), residues: 711 sheet: -0.94 (1.21), residues: 20 loop : -2.38 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 44 TYR 0.062 0.003 TYR G 52 PHE 0.059 0.003 PHE M 189 TRP 0.011 0.001 TRP M 361 HIS 0.008 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (17850) covalent geometry : angle 0.95732 / 0.51 (25340) hydrogen bonds : bond 0.05601 / 3.52 ( 796) hydrogen bonds : angle 4.42083 / 3.01 ( 2011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.47 seconds wall clock time: 57 minutes 52.61 seconds (3472.61 seconds total)