Starting phenix.real_space_refine on Thu Aug 6 21:56:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2x_38021/08_2026/8x2x_38021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2x_38021/08_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_38021/08_2026/8x2x_38021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2x_38021/08_2026/8x2x_38021.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2x_38021/08_2026/8x2x_38021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2x_38021/08_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-2.2rc3-6140/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: 3.37, per 1000 atoms: 0.20 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: 1.07 Conformation dependent library (CDL) restraints added in 551.7 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: 2.18 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: 3.66 Time building geometry restraints manager: 1.42 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: 24858 3.39 - 6.79: 436 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.900 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- 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= 0.651 Angle : 1.217 16.965 25340 Z= 0.862 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 1.21691 / 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 : 0.522 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: L 35 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6926 (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: 0.7459 (t0) REVERT: K 223 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7470 (Cg_endo) REVERT: K 240 ASP cc_start: 0.6206 (p0) cc_final: 0.5915 (p0) REVERT: K 287 VAL cc_start: 0.8641 (p) cc_final: 0.8431 (m) REVERT: K 318 LYS cc_start: 0.8052 (tppt) cc_final: 0.7690 (mmmt) REVERT: K 322 GLU cc_start: 0.6530 (mp0) cc_final: 0.6173 (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: 0.5990 (mpp) REVERT: M 70 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4554 (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: 0.8050 (mp0) REVERT: A 77 ASP cc_start: 0.7545 (p0) cc_final: 0.6898 (p0) REVERT: A 81 ASP cc_start: 0.7194 (t0) cc_final: 0.6829 (t70) REVERT: A 89 ILE cc_start: 0.8559 (mm) cc_final: 0.8253 (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: 0.5052 (pp) REVERT: B 79 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7722 (ttmt) REVERT: C 48 LYS cc_start: 0.8285 (pptt) cc_final: 0.7482 (pptt) REVERT: C 93 ASP cc_start: 0.7275 (p0) cc_final: 0.6586 (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: 0.8107 (ptpp) REVERT: D 116 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6399 (tm-30) REVERT: E 61 LEU cc_start: 0.7720 (mm) cc_final: 0.7087 (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: 0.7813 (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: 0.7667 (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: 4 residues processed: 552 average time/residue: 0.1838 time to fit residues: 137.0350 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 : 0.526 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 91 ASN ** K 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN K 392 ASN K 401 HIS M 173 ASN ** M 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 245 HIS ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 84 HIS C 111 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS H 87 ASN H 98 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.099841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084732 restraints weight = 53976.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.086797 restraints weight = 27378.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088133 restraints weight = 17069.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.089005 restraints weight = 12503.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089531 restraints weight = 10249.016| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 17850 Z= 0.317 Angle : 1.053 10.202 25340 Z= 0.583 Chirality : 0.059 0.371 2858 Planarity : 0.008 0.094 2190 Dihedral : 29.867 126.633 4780 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.52 % Allowed : 20.65 % Favored : 73.83 % 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: -3.85 (0.20), residues: 1319 helix: -2.31 (0.16), residues: 720 sheet: -1.91 (1.32), residues: 19 loop : -2.81 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 40 TYR 0.054 0.004 TYR G 52 PHE 0.031 0.003 PHE K 182 TRP 0.025 0.003 TRP M 361 HIS 0.011 0.002 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.32 (17850) covalent geometry : angle 1.05299 / 0.58 (25340) hydrogen bonds : bond 0.07398 / 4.68 ( 796) hydrogen bonds : angle 4.71046 / 3.23 ( 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 570 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 504 time to evaluate : 0.471 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: L 35 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7626 (tp30) REVERT: N 17 LEU cc_start: 0.8332 (tt) cc_final: 0.7702 (mt) REVERT: N 91 ASN cc_start: 0.8311 (t0) cc_final: 0.8022 (t0) REVERT: K 220 LEU cc_start: 0.8631 (tp) cc_final: 0.8360 (tt) REVERT: K 289 TYR cc_start: 0.7396 (p90) cc_final: 0.6790 (p90) REVERT: K 290 PHE cc_start: 0.7815 (p90) cc_final: 0.7553 (p90) REVERT: K 331 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: K 352 TYR cc_start: 0.7036 (t80) cc_final: 0.6746 (t80) REVERT: K 357 LEU cc_start: 0.7909 (mt) cc_final: 0.7604 (mt) REVERT: K 377 THR cc_start: 0.8972 (p) cc_final: 0.7682 (t) REVERT: K 379 MET cc_start: 0.7211 (mpp) cc_final: 0.6566 (mpp) REVERT: K 386 HIS cc_start: 0.6830 (m90) cc_final: 0.6270 (m90) REVERT: M 70 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4560 (tt) REVERT: M 161 ASN cc_start: 0.7129 (p0) cc_final: 0.6671 (p0) REVERT: M 197 GLU cc_start: 0.6932 (tp30) cc_final: 0.6730 (tp30) REVERT: M 200 ILE cc_start: 0.8412 (pp) cc_final: 0.8064 (mm) REVERT: M 224 LEU cc_start: 0.8333 (pt) cc_final: 0.7725 (mp) REVERT: M 249 PHE cc_start: 0.8037 (t80) cc_final: 0.7593 (t80) REVERT: M 267 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6079 (mt) REVERT: A 81 ASP cc_start: 0.7649 (t0) cc_final: 0.7383 (t0) REVERT: A 85 GLN cc_start: 0.7317 (tp40) cc_final: 0.7068 (tp-100) REVERT: B 39 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7200 (tpp80) REVERT: B 88 TYR cc_start: 0.7660 (m-80) cc_final: 0.6990 (m-80) REVERT: B 97 LEU cc_start: 0.8411 (tp) cc_final: 0.8207 (tp) REVERT: C 28 VAL cc_start: 0.8822 (t) cc_final: 0.8503 (p) REVERT: C 30 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7585 (ttm170) REVERT: C 63 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7012 (tm-30) REVERT: C 66 GLU cc_start: 0.7514 (pp20) cc_final: 0.6936 (pp20) REVERT: C 87 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.5830 (pp) REVERT: D 72 ILE cc_start: 0.8755 (mm) cc_final: 0.8549 (mm) REVERT: D 73 PHE cc_start: 0.8813 (t80) cc_final: 0.8465 (t80) REVERT: D 86 TYR cc_start: 0.7306 (p90) cc_final: 0.7029 (p90) REVERT: D 101 VAL cc_start: 0.8895 (t) cc_final: 0.8651 (p) REVERT: D 116 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7451 (tm-30) REVERT: E 57 SER cc_start: 0.8747 (t) cc_final: 0.8322 (p) REVERT: E 64 LYS cc_start: 0.8474 (ptmm) cc_final: 0.8225 (ttpp) REVERT: E 76 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: E 109 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8894 (mt) REVERT: F 53 GLU cc_start: 0.7371 (mp0) cc_final: 0.7098 (mp0) REVERT: H 97 ILE cc_start: 0.8840 (tp) cc_final: 0.8535 (tp) REVERT: H 102 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: H 123 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8313 (tppp) outliers start: 66 outliers final: 30 residues processed: 535 average time/residue: 0.1603 time to fit residues: 118.7958 Evaluate side-chains 505 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 469 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 25 LEU 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 295 GLU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU 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 83 ARG 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 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 109 LEU 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 57 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ** M 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN M 363 ASN A 85 GLN A 93 GLN D 87 ASN E 55 GLN F 25 ASN G 16 GLN G 111 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.101119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.085722 restraints weight = 54481.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.087845 restraints weight = 27070.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089226 restraints weight = 16694.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090109 restraints weight = 12138.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090653 restraints weight = 9920.599| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4669 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= 0.204 Angle : 0.905 11.796 25340 Z= 0.497 Chirality : 0.053 0.400 2858 Planarity : 0.007 0.073 2190 Dihedral : 29.731 127.792 4770 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.77 % Allowed : 23.49 % Favored : 70.74 % 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: -3.43 (0.21), residues: 1319 helix: -1.81 (0.17), residues: 733 sheet: -3.17 (0.89), residues: 29 loop : -2.78 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 79 TYR 0.037 0.003 TYR G 52 PHE 0.035 0.003 PHE K 323 TRP 0.018 0.002 TRP K 247 HIS 0.007 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (17850) covalent geometry : angle 0.90462 / 0.50 (25340) hydrogen bonds : bond 0.06444 / 4.06 ( 796) hydrogen bonds : angle 4.45087 / 3.03 ( 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 558 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 489 time to evaluate : 0.403 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: N 12 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: N 17 LEU cc_start: 0.8194 (tt) cc_final: 0.7805 (mt) REVERT: N 91 ASN cc_start: 0.8301 (t0) cc_final: 0.7997 (t0) REVERT: N 100 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.6093 (m90) REVERT: K 236 PHE cc_start: 0.6612 (m-80) cc_final: 0.6411 (m-80) REVERT: K 289 TYR cc_start: 0.7408 (p90) cc_final: 0.6867 (p90) REVERT: K 331 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: K 334 VAL cc_start: 0.7803 (p) cc_final: 0.7393 (p) REVERT: K 349 TYR cc_start: 0.6853 (m-10) cc_final: 0.6647 (m-80) REVERT: K 353 TRP cc_start: 0.8415 (m-10) cc_final: 0.8059 (m-10) REVERT: K 357 LEU cc_start: 0.7896 (mt) cc_final: 0.7611 (mt) REVERT: K 377 THR cc_start: 0.9005 (p) cc_final: 0.7768 (p) REVERT: K 379 MET cc_start: 0.6954 (mpp) cc_final: 0.6314 (mpp) REVERT: K 383 ASP cc_start: 0.8091 (t0) cc_final: 0.7679 (t0) REVERT: K 409 ILE cc_start: 0.7517 (mt) cc_final: 0.7265 (mp) REVERT: M 70 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4515 (tt) REVERT: M 74 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7517 (mt) REVERT: M 161 ASN cc_start: 0.7002 (p0) cc_final: 0.6694 (p0) REVERT: M 200 ILE cc_start: 0.8366 (pp) cc_final: 0.7973 (mm) REVERT: M 249 PHE cc_start: 0.8046 (t80) cc_final: 0.7512 (t80) REVERT: M 267 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6549 (mt) REVERT: M 342 LYS cc_start: 0.8453 (pttm) cc_final: 0.8047 (pttm) REVERT: A 64 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7849 (mmmm) REVERT: A 65 LEU cc_start: 0.8443 (mm) cc_final: 0.8183 (mm) REVERT: A 68 GLN cc_start: 0.8913 (mt0) cc_final: 0.8622 (mt0) REVERT: A 81 ASP cc_start: 0.7752 (t0) cc_final: 0.7473 (t0) REVERT: A 121 LYS cc_start: 0.8279 (mttp) cc_final: 0.8075 (mptt) REVERT: C 28 VAL cc_start: 0.8928 (t) cc_final: 0.8636 (p) REVERT: C 52 TYR cc_start: 0.7119 (t80) cc_final: 0.6824 (t80) REVERT: C 66 GLU cc_start: 0.7176 (pp20) cc_final: 0.6751 (pp20) REVERT: C 87 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6584 (pp) REVERT: D 101 VAL cc_start: 0.8991 (t) cc_final: 0.8729 (p) REVERT: D 111 LYS cc_start: 0.8232 (ptpp) cc_final: 0.7812 (ptpp) REVERT: D 116 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7348 (tm-30) REVERT: E 57 SER cc_start: 0.8764 (t) cc_final: 0.8351 (p) REVERT: E 76 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7444 (pp30) REVERT: F 53 GLU cc_start: 0.7301 (mp0) cc_final: 0.6961 (mp0) REVERT: F 67 ARG cc_start: 0.7271 (mtm-85) cc_final: 0.6978 (mtm110) REVERT: F 91 LYS cc_start: 0.8752 (tptp) cc_final: 0.8485 (tptp) REVERT: G 30 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.6965 (mtm-85) REVERT: H 46 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8316 (ttmm) REVERT: H 62 MET cc_start: 0.8099 (mmm) cc_final: 0.7737 (tpp) REVERT: H 88 LYS cc_start: 0.8288 (mmpt) cc_final: 0.7908 (mmpt) REVERT: H 97 ILE cc_start: 0.8935 (tp) cc_final: 0.8678 (tp) REVERT: H 123 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8365 (tppp) outliers start: 69 outliers final: 40 residues processed: 519 average time/residue: 0.1495 time to fit residues: 106.7093 Evaluate side-chains 524 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 475 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain N residue 100 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 331 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 247 THR 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 83 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 78 ARG 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 87 LEU 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 71 VAL 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 130 LEU 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 111 HIS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 92 ILE 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: 0.8980 chunk 92 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 301 ASN M 175 GLN ** M 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 113 HIS ** 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** D 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.100428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085022 restraints weight = 55354.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087132 restraints weight = 27830.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088449 restraints weight = 17312.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089284 restraints weight = 12736.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089824 restraints weight = 10522.696| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 17850 Z= 0.217 Angle : 0.907 13.169 25340 Z= 0.492 Chirality : 0.053 0.397 2858 Planarity : 0.006 0.059 2190 Dihedral : 29.649 126.228 4770 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 6.52 % Allowed : 25.17 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.31 % 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: -3.20 (0.21), residues: 1319 helix: -1.63 (0.17), residues: 725 sheet: -2.57 (0.85), residues: 31 loop : -2.70 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 167 TYR 0.035 0.003 TYR G 52 PHE 0.038 0.003 PHE K 323 TRP 0.028 0.002 TRP K 247 HIS 0.012 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (17850) covalent geometry : angle 0.90723 / 0.49 (25340) hydrogen bonds : bond 0.06310 / 3.99 ( 796) hydrogen bonds : angle 4.42119 / 3.01 ( 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 566 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 488 time to evaluate : 0.388 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: N 12 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: N 17 LEU cc_start: 0.8268 (tt) cc_final: 0.7709 (mt) REVERT: N 91 ASN cc_start: 0.8368 (t0) cc_final: 0.8107 (t0) REVERT: K 176 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: K 266 TYR cc_start: 0.6336 (t80) cc_final: 0.6038 (t80) REVERT: K 272 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7895 (tp) REVERT: K 289 TYR cc_start: 0.7519 (p90) cc_final: 0.7138 (p90) REVERT: K 323 PHE cc_start: 0.7926 (t80) cc_final: 0.7709 (t80) REVERT: K 353 TRP cc_start: 0.8484 (m-10) cc_final: 0.8116 (m-10) REVERT: K 357 LEU cc_start: 0.8033 (mt) cc_final: 0.7748 (mt) REVERT: K 370 ILE cc_start: 0.7868 (tt) cc_final: 0.7461 (pt) REVERT: K 372 GLU cc_start: 0.7654 (pp20) cc_final: 0.7450 (tm-30) REVERT: K 377 THR cc_start: 0.8882 (p) cc_final: 0.8609 (p) REVERT: M 70 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.4505 (tt) REVERT: M 74 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7441 (mt) REVERT: M 161 ASN cc_start: 0.7045 (p0) cc_final: 0.6720 (p0) REVERT: M 162 TYR cc_start: 0.6410 (t80) cc_final: 0.5943 (t80) REVERT: M 169 GLU cc_start: 0.5870 (pp20) cc_final: 0.5390 (tm-30) REVERT: M 200 ILE cc_start: 0.8302 (pp) cc_final: 0.7961 (mm) REVERT: M 249 PHE cc_start: 0.8100 (t80) cc_final: 0.7619 (t80) REVERT: M 267 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6559 (mt) REVERT: A 64 LYS cc_start: 0.8422 (mmmm) cc_final: 0.7806 (mmmm) REVERT: A 68 GLN cc_start: 0.8956 (mt0) cc_final: 0.8585 (mt0) REVERT: A 81 ASP cc_start: 0.8004 (t0) cc_final: 0.7676 (t70) REVERT: A 100 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 39 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7419 (tpp-160) REVERT: B 68 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6852 (p0) REVERT: B 79 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7863 (mtpt) REVERT: C 28 VAL cc_start: 0.9019 (t) cc_final: 0.8691 (p) REVERT: C 30 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7479 (mmm-85) REVERT: C 66 GLU cc_start: 0.7179 (pp20) cc_final: 0.6958 (pp20) REVERT: C 87 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6729 (pp) REVERT: D 89 LYS cc_start: 0.8469 (mmmm) cc_final: 0.7970 (mmmm) REVERT: D 101 VAL cc_start: 0.9023 (t) cc_final: 0.8806 (p) REVERT: D 116 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7630 (tm-30) REVERT: E 57 SER cc_start: 0.8770 (t) cc_final: 0.8399 (p) REVERT: E 121 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8659 (ttpp) REVERT: F 53 GLU cc_start: 0.7265 (mp0) cc_final: 0.6955 (mp0) REVERT: F 55 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7645 (mtt180) REVERT: F 63 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6057 (mp0) REVERT: F 67 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6772 (mtm-85) REVERT: F 79 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7517 (tptp) REVERT: F 91 LYS cc_start: 0.8828 (tptp) cc_final: 0.8621 (tptp) REVERT: G 30 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7256 (mtm-85) REVERT: H 46 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8438 (ttmm) REVERT: H 62 MET cc_start: 0.8035 (mmm) cc_final: 0.7741 (tpp) REVERT: H 88 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7941 (mmpt) REVERT: H 97 ILE cc_start: 0.9083 (tp) cc_final: 0.8851 (tp) REVERT: H 123 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8376 (tppp) outliers start: 78 outliers final: 46 residues processed: 525 average time/residue: 0.1496 time to fit residues: 108.0525 Evaluate side-chains 537 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 479 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 25 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 176 GLU 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 272 LEU 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 K residue 405 LEU Chi-restraints excluded: chain K residue 416 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 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 80 THR Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 LEU 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 17 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 64 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 E residue 53 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 84 LEU 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 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 92 ILE 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: 0.8980 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 135 optimal weight: 0.0020 chunk 87 optimal weight: 0.0170 chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 100 HIS N 107 ASN ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 233 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS A 85 GLN ** 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** F 27 GLN G 111 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.102603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087121 restraints weight = 54249.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089173 restraints weight = 27076.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090516 restraints weight = 16846.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091372 restraints weight = 12320.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091908 restraints weight = 10121.458| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17850 Z= 0.177 Angle : 0.876 11.782 25340 Z= 0.476 Chirality : 0.051 0.384 2858 Planarity : 0.006 0.061 2190 Dihedral : 29.521 121.702 4770 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.19 % Allowed : 27.68 % Favored : 66.14 % 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: -2.87 (0.21), residues: 1319 helix: -1.36 (0.18), residues: 703 sheet: -1.73 (1.13), residues: 20 loop : -2.56 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 119 TYR 0.050 0.003 TYR G 52 PHE 0.047 0.003 PHE M 297 TRP 0.029 0.002 TRP K 247 HIS 0.005 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (17850) covalent geometry : angle 0.87606 / 0.48 (25340) hydrogen bonds : bond 0.05636 / 3.58 ( 796) hydrogen bonds : angle 4.39450 / 2.99 ( 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 572 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 498 time to evaluate : 0.590 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: N 17 LEU cc_start: 0.8220 (tt) cc_final: 0.7770 (mt) REVERT: N 91 ASN cc_start: 0.8277 (t0) cc_final: 0.8060 (t0) REVERT: K 176 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: K 183 SER cc_start: 0.4197 (OUTLIER) cc_final: 0.2713 (t) REVERT: K 212 GLU cc_start: 0.7854 (pp20) cc_final: 0.7579 (pt0) REVERT: K 226 ASN cc_start: 0.6965 (m-40) cc_final: 0.6695 (m-40) REVERT: K 266 TYR cc_start: 0.6276 (t80) cc_final: 0.5484 (t80) REVERT: K 272 LEU cc_start: 0.8032 (tp) cc_final: 0.7754 (tp) REVERT: K 289 TYR cc_start: 0.7453 (p90) cc_final: 0.7158 (p90) REVERT: K 352 TYR cc_start: 0.7013 (t80) cc_final: 0.6666 (t80) REVERT: K 353 TRP cc_start: 0.8519 (m-10) cc_final: 0.8116 (m-10) REVERT: K 357 LEU cc_start: 0.8012 (mt) cc_final: 0.7715 (mt) REVERT: K 377 THR cc_start: 0.8795 (p) cc_final: 0.8454 (p) REVERT: M 70 LEU cc_start: 0.5115 (OUTLIER) cc_final: 0.4117 (tt) REVERT: M 74 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7674 (mt) REVERT: M 161 ASN cc_start: 0.6881 (p0) cc_final: 0.6599 (p0) REVERT: M 162 TYR cc_start: 0.6382 (t80) cc_final: 0.6043 (t80) REVERT: M 200 ILE cc_start: 0.8291 (pp) cc_final: 0.8056 (mm) REVERT: M 249 PHE cc_start: 0.8018 (t80) cc_final: 0.7543 (t80) REVERT: M 267 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6478 (mt) REVERT: M 303 LYS cc_start: 0.4910 (tttt) cc_final: 0.4584 (tttt) REVERT: A 64 LYS cc_start: 0.8350 (mmmm) cc_final: 0.7674 (mmmm) REVERT: A 68 GLN cc_start: 0.8925 (mt0) cc_final: 0.8557 (mt0) REVERT: A 81 ASP cc_start: 0.7914 (t0) cc_final: 0.7586 (t70) REVERT: A 85 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7078 (tp-100) REVERT: A 93 GLN cc_start: 0.7868 (tp40) cc_final: 0.7643 (tp40) REVERT: A 100 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 121 LYS cc_start: 0.8393 (mptt) cc_final: 0.8130 (mmtm) REVERT: B 55 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7633 (mtt-85) REVERT: B 79 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: C 28 VAL cc_start: 0.8967 (t) cc_final: 0.8625 (p) REVERT: C 30 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7602 (mtp85) REVERT: C 87 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6482 (pp) REVERT: C 93 ASP cc_start: 0.6736 (t0) cc_final: 0.6391 (t0) REVERT: D 89 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7859 (mmmm) REVERT: D 101 VAL cc_start: 0.9031 (t) cc_final: 0.8823 (p) REVERT: D 116 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 57 SER cc_start: 0.8722 (t) cc_final: 0.8247 (p) REVERT: E 108 ASN cc_start: 0.8377 (t0) cc_final: 0.8104 (t0) REVERT: E 121 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8360 (ttpp) REVERT: F 53 GLU cc_start: 0.7229 (mp0) cc_final: 0.6862 (mp0) REVERT: F 59 LYS cc_start: 0.8301 (tmtt) cc_final: 0.7971 (ttmm) REVERT: F 67 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.6977 (mtm110) REVERT: F 91 LYS cc_start: 0.8791 (tptp) cc_final: 0.8563 (tptp) REVERT: F 92 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8350 (ttp80) REVERT: G 30 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7270 (mtm-85) REVERT: H 46 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8194 (ttmm) REVERT: H 49 LYS cc_start: 0.8400 (pttp) cc_final: 0.8078 (pttp) REVERT: H 62 MET cc_start: 0.8050 (mmm) cc_final: 0.7628 (tpp) REVERT: H 79 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7845 (tm-30) REVERT: H 86 TYR cc_start: 0.7286 (p90) cc_final: 0.6958 (p90) REVERT: H 88 LYS cc_start: 0.8368 (mmpt) cc_final: 0.7969 (mmpt) REVERT: H 97 ILE cc_start: 0.9105 (tp) cc_final: 0.8899 (tp) REVERT: H 123 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8368 (tppp) outliers start: 74 outliers final: 42 residues processed: 534 average time/residue: 0.1683 time to fit residues: 123.1717 Evaluate side-chains 534 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 482 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 K residue 176 GLU Chi-restraints excluded: chain K residue 183 SER 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 366 LYS Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 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 135 LYS 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 83 ARG Chi-restraints excluded: chain A residue 100 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 44 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 51 ILE 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 109 LEU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN 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 G residue 112 ILE Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 104 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 130 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.102030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086485 restraints weight = 54850.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088571 restraints weight = 27552.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089916 restraints weight = 17187.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.090774 restraints weight = 12612.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091296 restraints weight = 10389.838| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17850 Z= 0.178 Angle : 0.871 10.739 25340 Z= 0.474 Chirality : 0.050 0.394 2858 Planarity : 0.006 0.062 2190 Dihedral : 29.408 118.651 4770 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.94 % Allowed : 30.52 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -2.73 (0.22), residues: 1319 helix: -1.26 (0.18), residues: 702 sheet: -1.32 (1.17), residues: 20 loop : -2.48 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 119 TYR 0.060 0.003 TYR G 52 PHE 0.040 0.002 PHE K 323 TRP 0.029 0.002 TRP K 247 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (17850) covalent geometry : angle 0.87139 / 0.47 (25340) hydrogen bonds : bond 0.05692 / 3.60 ( 796) hydrogen bonds : angle 4.32422 / 2.93 ( 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 568 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 497 time to evaluate : 0.533 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: N 17 LEU cc_start: 0.8216 (tt) cc_final: 0.7747 (mt) REVERT: N 91 ASN cc_start: 0.8288 (t0) cc_final: 0.8070 (t0) REVERT: K 183 SER cc_start: 0.4226 (OUTLIER) cc_final: 0.3760 (t) REVERT: K 272 LEU cc_start: 0.8064 (tp) cc_final: 0.7821 (tp) REVERT: K 322 GLU cc_start: 0.7484 (tt0) cc_final: 0.7026 (pt0) REVERT: K 352 TYR cc_start: 0.7119 (t80) cc_final: 0.6816 (t80) REVERT: K 353 TRP cc_start: 0.8545 (m-10) cc_final: 0.8187 (m-10) REVERT: K 357 LEU cc_start: 0.7990 (mt) cc_final: 0.7712 (mt) REVERT: K 377 THR cc_start: 0.8765 (p) cc_final: 0.8451 (p) REVERT: M 70 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4210 (tt) REVERT: M 74 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7683 (mt) REVERT: M 161 ASN cc_start: 0.6922 (p0) cc_final: 0.6674 (p0) REVERT: M 162 TYR cc_start: 0.6626 (t80) cc_final: 0.6407 (t80) REVERT: M 175 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7494 (mm-40) REVERT: M 249 PHE cc_start: 0.8071 (t80) cc_final: 0.7557 (t80) REVERT: M 345 LYS cc_start: 0.8054 (tptp) cc_final: 0.7716 (mmtt) REVERT: A 64 LYS cc_start: 0.8346 (mmmm) cc_final: 0.7622 (mmmm) REVERT: A 65 LEU cc_start: 0.8407 (mm) cc_final: 0.7823 (mm) REVERT: A 68 GLN cc_start: 0.8909 (mt0) cc_final: 0.8489 (mt0) REVERT: A 69 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: A 81 ASP cc_start: 0.8015 (t0) cc_final: 0.7670 (t70) REVERT: A 93 GLN cc_start: 0.7747 (tp40) cc_final: 0.7500 (tp40) REVERT: A 100 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8666 (mm) REVERT: B 31 LYS cc_start: 0.8422 (tptp) cc_final: 0.8124 (tptp) REVERT: B 51 TYR cc_start: 0.8340 (m-10) cc_final: 0.8140 (m-10) REVERT: B 79 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (mtpt) REVERT: C 28 VAL cc_start: 0.9074 (t) cc_final: 0.8712 (p) REVERT: C 30 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7691 (mtp85) REVERT: C 66 GLU cc_start: 0.7419 (pp20) cc_final: 0.6372 (pp20) REVERT: C 87 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6686 (pp) REVERT: C 92 ASP cc_start: 0.8403 (t0) cc_final: 0.8105 (t0) REVERT: D 88 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8159 (mmtt) REVERT: D 101 VAL cc_start: 0.9096 (t) cc_final: 0.8892 (p) REVERT: D 116 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7782 (tm-30) REVERT: E 57 SER cc_start: 0.8667 (t) cc_final: 0.8405 (p) REVERT: F 67 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6790 (mtm-85) REVERT: F 91 LYS cc_start: 0.8806 (tptp) cc_final: 0.8596 (tptp) REVERT: G 30 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7383 (mtm-85) REVERT: G 57 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8436 (tp) REVERT: G 90 ARG cc_start: 0.7105 (ptt180) cc_final: 0.6528 (tmm-80) REVERT: G 93 ASP cc_start: 0.8356 (m-30) cc_final: 0.7480 (m-30) REVERT: H 49 LYS cc_start: 0.8396 (pttp) cc_final: 0.8044 (pttp) REVERT: H 62 MET cc_start: 0.8034 (mmm) cc_final: 0.7754 (tpp) REVERT: H 79 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7914 (tm-30) REVERT: H 86 TYR cc_start: 0.7294 (p90) cc_final: 0.7093 (p90) REVERT: H 88 LYS cc_start: 0.8371 (mmpt) cc_final: 0.8017 (mmpt) REVERT: H 123 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8345 (tppp) outliers start: 71 outliers final: 40 residues processed: 532 average time/residue: 0.1691 time to fit residues: 123.8163 Evaluate side-chains 532 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 485 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 K residue 183 SER 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 366 LYS Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 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 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 83 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 65 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 D residue 109 LEU 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 119 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN 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 104 ILE 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: 1.9990 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 0.0470 chunk 146 optimal weight: 0.2980 chunk 78 optimal weight: 9.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN A 113 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087343 restraints weight = 55235.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089421 restraints weight = 27818.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090767 restraints weight = 17362.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.091620 restraints weight = 12722.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092159 restraints weight = 10478.542| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17850 Z= 0.177 Angle : 0.893 10.983 25340 Z= 0.483 Chirality : 0.051 0.452 2858 Planarity : 0.006 0.151 2190 Dihedral : 29.323 112.256 4770 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.10 % Allowed : 33.19 % Favored : 61.71 % 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: -2.80 (0.21), residues: 1319 helix: -1.34 (0.18), residues: 710 sheet: -1.79 (1.11), residues: 20 loop : -2.48 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 203 TYR 0.058 0.003 TYR G 52 PHE 0.039 0.002 PHE K 323 TRP 0.026 0.002 TRP K 247 HIS 0.007 0.002 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (17850) covalent geometry : angle 0.89336 / 0.48 (25340) hydrogen bonds : bond 0.05431 / 3.43 ( 796) hydrogen bonds : angle 4.35020 / 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 559 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 498 time to evaluate : 0.501 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: N 12 GLN cc_start: 0.8250 (pm20) cc_final: 0.8041 (pm20) REVERT: N 17 LEU cc_start: 0.8212 (tt) cc_final: 0.7726 (mt) REVERT: N 89 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7373 (pt) REVERT: K 183 SER cc_start: 0.4199 (OUTLIER) cc_final: 0.3795 (t) REVERT: K 226 ASN cc_start: 0.7070 (m-40) cc_final: 0.6821 (m-40) REVERT: K 266 TYR cc_start: 0.6069 (t80) cc_final: 0.5372 (t80) REVERT: K 272 LEU cc_start: 0.8062 (tp) cc_final: 0.7774 (tp) REVERT: K 352 TYR cc_start: 0.7088 (t80) cc_final: 0.6822 (t80) REVERT: K 353 TRP cc_start: 0.8486 (m-10) cc_final: 0.8179 (m-10) REVERT: K 357 LEU cc_start: 0.7943 (mt) cc_final: 0.7694 (mt) REVERT: K 377 THR cc_start: 0.8744 (p) cc_final: 0.8430 (p) REVERT: M 70 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4154 (tt) REVERT: M 74 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7666 (mt) REVERT: M 161 ASN cc_start: 0.6905 (p0) cc_final: 0.6629 (p0) REVERT: M 162 TYR cc_start: 0.6516 (t80) cc_final: 0.6286 (t80) REVERT: M 249 PHE cc_start: 0.8032 (t80) cc_final: 0.7582 (t80) REVERT: M 345 LYS cc_start: 0.8040 (tptp) cc_final: 0.7743 (mmtt) REVERT: M 353 LYS cc_start: 0.8556 (tppt) cc_final: 0.8143 (mtmm) REVERT: A 64 LYS cc_start: 0.8336 (mmmm) cc_final: 0.7593 (mmmm) REVERT: A 68 GLN cc_start: 0.8886 (mt0) cc_final: 0.8488 (mt0) REVERT: A 81 ASP cc_start: 0.8017 (t0) cc_final: 0.7652 (t70) REVERT: A 85 GLN cc_start: 0.7463 (tp-100) cc_final: 0.6965 (tp-100) REVERT: A 97 GLU cc_start: 0.8070 (tp30) cc_final: 0.7835 (tp30) REVERT: B 31 LYS cc_start: 0.8406 (tptp) cc_final: 0.8086 (tptp) REVERT: B 35 ARG cc_start: 0.7971 (ttt90) cc_final: 0.7726 (tpt170) REVERT: B 44 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8688 (tppp) REVERT: B 53 GLU cc_start: 0.7061 (pm20) cc_final: 0.6809 (pm20) REVERT: B 67 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7275 (ttp80) REVERT: B 79 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (mtpt) REVERT: B 92 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6982 (tmm-80) REVERT: C 28 VAL cc_start: 0.9083 (t) cc_final: 0.8710 (p) REVERT: C 66 GLU cc_start: 0.7123 (pp20) cc_final: 0.6553 (pp20) REVERT: C 87 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6532 (pp) REVERT: C 92 ASP cc_start: 0.8273 (t0) cc_final: 0.7982 (t0) REVERT: D 116 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7728 (tm-30) REVERT: E 45 THR cc_start: 0.7804 (t) cc_final: 0.7577 (p) REVERT: E 57 SER cc_start: 0.8648 (t) cc_final: 0.8443 (p) REVERT: F 53 GLU cc_start: 0.7555 (mp0) cc_final: 0.7291 (mp0) REVERT: F 67 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: G 30 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7351 (mtm-85) REVERT: G 57 LEU cc_start: 0.8648 (tt) cc_final: 0.8421 (tp) REVERT: H 43 TYR cc_start: 0.6989 (m-10) cc_final: 0.6776 (m-10) REVERT: H 46 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8127 (ttmm) REVERT: H 49 LYS cc_start: 0.8427 (pttp) cc_final: 0.7984 (pttp) REVERT: H 62 MET cc_start: 0.8071 (mmm) cc_final: 0.7814 (tpp) REVERT: H 81 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.8024 (p) REVERT: H 88 LYS cc_start: 0.8384 (mmpt) cc_final: 0.7951 (mmpt) REVERT: H 123 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8331 (tppp) outliers start: 61 outliers final: 41 residues processed: 525 average time/residue: 0.1706 time to fit residues: 122.8133 Evaluate side-chains 534 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 483 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 K residue 183 SER 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 363 GLU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 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 135 LYS Chi-restraints excluded: chain M residue 248 HIS 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 53 ARG Chi-restraints excluded: chain A residue 83 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 44 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU 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 C residue 51 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 129 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 168 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.102390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.086843 restraints weight = 55164.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088955 restraints weight = 27696.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090303 restraints weight = 17241.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091155 restraints weight = 12649.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091703 restraints weight = 10429.899| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17850 Z= 0.191 Angle : 0.902 10.896 25340 Z= 0.487 Chirality : 0.050 0.421 2858 Planarity : 0.006 0.100 2190 Dihedral : 29.244 101.160 4770 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.69 % Allowed : 33.44 % Favored : 60.87 % 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: -2.77 (0.22), residues: 1319 helix: -1.31 (0.18), residues: 686 sheet: -1.80 (1.13), residues: 20 loop : -2.44 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 119 TYR 0.053 0.003 TYR G 52 PHE 0.054 0.003 PHE M 189 TRP 0.024 0.002 TRP K 247 HIS 0.006 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (17850) covalent geometry : angle 0.90242 / 0.49 (25340) hydrogen bonds : bond 0.05586 / 3.53 ( 796) hydrogen bonds : angle 4.35111 / 2.95 ( 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 555 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 487 time to evaluate : 0.362 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: N 17 LEU cc_start: 0.8267 (tt) cc_final: 0.7883 (mt) REVERT: K 183 SER cc_start: 0.4204 (OUTLIER) cc_final: 0.3802 (t) REVERT: K 272 LEU cc_start: 0.8089 (tp) cc_final: 0.7849 (tp) REVERT: K 352 TYR cc_start: 0.7209 (t80) cc_final: 0.6925 (t80) REVERT: K 353 TRP cc_start: 0.8497 (m-10) cc_final: 0.8143 (m-10) REVERT: K 377 THR cc_start: 0.8725 (p) cc_final: 0.8421 (p) REVERT: M 70 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.4115 (tt) REVERT: M 74 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7783 (mt) REVERT: M 162 TYR cc_start: 0.6655 (t80) cc_final: 0.6421 (t80) REVERT: M 267 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7495 (tt) REVERT: M 345 LYS cc_start: 0.8020 (tptp) cc_final: 0.7757 (mmtt) REVERT: A 64 LYS cc_start: 0.8415 (mmmm) cc_final: 0.7648 (mmmm) REVERT: A 68 GLN cc_start: 0.8928 (mt0) cc_final: 0.8498 (mt0) REVERT: A 69 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: A 81 ASP cc_start: 0.8107 (t0) cc_final: 0.7738 (t70) REVERT: A 85 GLN cc_start: 0.7453 (tp-100) cc_final: 0.7000 (tp-100) REVERT: B 35 ARG cc_start: 0.8027 (ttt90) cc_final: 0.7816 (tpt170) REVERT: B 36 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: B 44 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8740 (tppp) REVERT: B 51 TYR cc_start: 0.8439 (m-10) cc_final: 0.8030 (m-10) REVERT: B 67 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7288 (ttp80) REVERT: B 92 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.6990 (tmm-80) REVERT: C 28 VAL cc_start: 0.9057 (t) cc_final: 0.8706 (p) REVERT: C 92 ASP cc_start: 0.8261 (t0) cc_final: 0.8005 (t0) REVERT: C 93 ASP cc_start: 0.6544 (t0) cc_final: 0.6331 (t0) REVERT: D 46 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8317 (ptmt) REVERT: D 89 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8031 (mmmm) REVERT: D 116 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7843 (tm-30) REVERT: E 45 THR cc_start: 0.7847 (t) cc_final: 0.7627 (p) REVERT: E 57 SER cc_start: 0.8602 (t) cc_final: 0.8391 (p) REVERT: E 121 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8722 (tttm) REVERT: F 53 GLU cc_start: 0.7572 (mp0) cc_final: 0.7062 (mp0) REVERT: F 67 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7138 (mtm110) REVERT: G 30 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7380 (mtm-85) REVERT: G 57 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8368 (tp) REVERT: H 43 TYR cc_start: 0.7072 (m-10) cc_final: 0.6844 (m-10) REVERT: H 46 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8117 (ttmm) REVERT: H 49 LYS cc_start: 0.8448 (pttp) cc_final: 0.8026 (pttp) REVERT: H 62 MET cc_start: 0.8125 (mmm) cc_final: 0.7838 (tpp) REVERT: H 86 TYR cc_start: 0.7340 (p90) cc_final: 0.7014 (p90) REVERT: H 88 LYS cc_start: 0.8419 (mmpt) cc_final: 0.8067 (mmpt) REVERT: H 123 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8320 (tppp) outliers start: 68 outliers final: 42 residues processed: 519 average time/residue: 0.1607 time to fit residues: 115.2191 Evaluate side-chains 532 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 482 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 369 THR Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 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 135 LYS 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 80 THR Chi-restraints excluded: chain A residue 83 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 44 LYS Chi-restraints excluded: chain B residue 58 LEU 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 51 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 80 ILE 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 130 LEU 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 111 HIS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 104 ILE 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: 0.7980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 139 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.102971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087489 restraints weight = 55313.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089593 restraints weight = 27951.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090945 restraints weight = 17445.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091802 restraints weight = 12788.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092342 restraints weight = 10544.487| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6673 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= 0.185 Angle : 0.938 12.757 25340 Z= 0.502 Chirality : 0.051 0.404 2858 Planarity : 0.006 0.099 2190 Dihedral : 29.147 91.063 4764 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.77 % Allowed : 34.70 % Favored : 60.54 % 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: -1.40 (0.18), residues: 703 sheet: -2.16 (0.99), residues: 30 loop : -2.48 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 44 TYR 0.054 0.003 TYR G 52 PHE 0.050 0.003 PHE M 189 TRP 0.027 0.002 TRP K 247 HIS 0.007 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (17850) covalent geometry : angle 0.93786 / 0.50 (25340) hydrogen bonds : bond 0.05493 / 3.46 ( 796) hydrogen bonds : angle 4.37032 / 2.96 ( 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 544 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 487 time to evaluate : 0.413 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: N 17 LEU cc_start: 0.8330 (tt) cc_final: 0.7868 (mt) REVERT: K 171 ILE cc_start: 0.8665 (tp) cc_final: 0.8434 (tp) REVERT: K 176 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: K 183 SER cc_start: 0.4172 (OUTLIER) cc_final: 0.3847 (t) REVERT: K 272 LEU cc_start: 0.8130 (tp) cc_final: 0.7844 (tp) REVERT: K 322 GLU cc_start: 0.7535 (tt0) cc_final: 0.7170 (pt0) REVERT: K 352 TYR cc_start: 0.7259 (t80) cc_final: 0.6963 (t80) REVERT: K 353 TRP cc_start: 0.8467 (m-10) cc_final: 0.8172 (m-10) REVERT: K 377 THR cc_start: 0.8672 (p) cc_final: 0.8407 (p) REVERT: M 70 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4094 (tt) REVERT: M 74 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7798 (mt) REVERT: M 162 TYR cc_start: 0.6567 (t80) cc_final: 0.6362 (t80) REVERT: M 342 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8309 (ptpp) REVERT: M 353 LYS cc_start: 0.8540 (tppt) cc_final: 0.8047 (mtmm) REVERT: A 64 LYS cc_start: 0.8418 (mmmm) cc_final: 0.7994 (mmmm) REVERT: A 69 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: A 81 ASP cc_start: 0.8076 (t0) cc_final: 0.7707 (t70) REVERT: A 85 GLN cc_start: 0.7417 (tp-100) cc_final: 0.7000 (tp-100) REVERT: B 25 ASN cc_start: 0.8103 (t160) cc_final: 0.7858 (t0) REVERT: B 31 LYS cc_start: 0.8246 (tptp) cc_final: 0.7885 (tptp) REVERT: B 39 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.7368 (tpp-160) REVERT: B 44 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8754 (tppp) REVERT: B 67 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7354 (ttp80) REVERT: B 92 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7044 (tmm-80) REVERT: C 28 VAL cc_start: 0.9024 (t) cc_final: 0.8649 (p) REVERT: C 48 LYS cc_start: 0.7924 (pptt) cc_final: 0.7279 (ptmm) REVERT: C 92 ASP cc_start: 0.8238 (t0) cc_final: 0.7982 (t0) REVERT: D 89 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8085 (mmmm) REVERT: D 116 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 119 ARG cc_start: 0.7469 (mtm110) cc_final: 0.7035 (ptt90) REVERT: E 45 THR cc_start: 0.7950 (t) cc_final: 0.7666 (p) REVERT: E 57 SER cc_start: 0.8568 (t) cc_final: 0.8320 (p) REVERT: E 121 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8765 (tttm) REVERT: F 53 GLU cc_start: 0.7515 (mp0) cc_final: 0.7062 (mp0) REVERT: G 30 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7385 (mtm-85) REVERT: G 57 LEU cc_start: 0.8633 (tt) cc_final: 0.8380 (tp) REVERT: H 43 TYR cc_start: 0.6994 (m-10) cc_final: 0.6793 (m-10) REVERT: H 46 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8151 (ttmm) REVERT: H 49 LYS cc_start: 0.8465 (pttp) cc_final: 0.8063 (pttp) REVERT: H 62 MET cc_start: 0.8125 (mmm) cc_final: 0.7858 (tpp) REVERT: H 86 TYR cc_start: 0.7265 (p90) cc_final: 0.6986 (p90) REVERT: H 88 LYS cc_start: 0.8416 (mmpt) cc_final: 0.8067 (mmpt) REVERT: H 123 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8384 (tppp) outliers start: 57 outliers final: 40 residues processed: 512 average time/residue: 0.1593 time to fit residues: 112.1855 Evaluate side-chains 526 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 479 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain K residue 176 GLU Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 369 THR Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 LEU 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 135 LYS Chi-restraints excluded: chain M residue 168 ASP 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 80 THR Chi-restraints excluded: chain A residue 83 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 44 LYS Chi-restraints excluded: chain B residue 58 LEU 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 51 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 80 ILE 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 E residue 46 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.102107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086678 restraints weight = 55377.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088765 restraints weight = 27987.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090106 restraints weight = 17480.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090947 restraints weight = 12837.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.091455 restraints weight = 10601.544| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17850 Z= 0.201 Angle : 0.968 14.135 25340 Z= 0.515 Chirality : 0.052 0.346 2858 Planarity : 0.006 0.118 2190 Dihedral : 29.093 91.424 4764 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.77 % Allowed : 35.37 % Favored : 59.87 % 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: -2.84 (0.21), residues: 1319 helix: -1.38 (0.18), residues: 701 sheet: -1.32 (1.28), residues: 20 loop : -2.49 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 55 TYR 0.053 0.003 TYR G 52 PHE 0.048 0.002 PHE M 189 TRP 0.032 0.003 TRP M 130 HIS 0.006 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (17850) covalent geometry : angle 0.96756 / 0.52 (25340) hydrogen bonds : bond 0.05722 / 3.60 ( 796) hydrogen bonds : angle 4.40040 / 2.98 ( 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 556 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 499 time to evaluate : 0.394 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: N 17 LEU cc_start: 0.8452 (tt) cc_final: 0.7984 (mt) REVERT: K 171 ILE cc_start: 0.8745 (tp) cc_final: 0.8450 (mm) REVERT: K 183 SER cc_start: 0.4711 (OUTLIER) cc_final: 0.3760 (t) REVERT: K 272 LEU cc_start: 0.8213 (tp) cc_final: 0.7977 (tp) REVERT: K 322 GLU cc_start: 0.7548 (tt0) cc_final: 0.7229 (pt0) REVERT: K 352 TYR cc_start: 0.7317 (t80) cc_final: 0.7106 (t80) REVERT: K 353 TRP cc_start: 0.8429 (m-10) cc_final: 0.8115 (m-10) REVERT: K 376 MET cc_start: 0.7897 (ttm) cc_final: 0.7682 (ttp) REVERT: K 377 THR cc_start: 0.8623 (p) cc_final: 0.8272 (p) REVERT: M 70 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4195 (tt) REVERT: M 74 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8082 (pt) REVERT: M 168 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: M 342 LYS cc_start: 0.8369 (ptpp) cc_final: 0.8058 (pttm) REVERT: M 345 LYS cc_start: 0.7876 (tppt) cc_final: 0.7660 (tppt) REVERT: A 64 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7844 (mmmm) REVERT: A 69 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.7457 (mtm-85) REVERT: A 81 ASP cc_start: 0.8154 (t0) cc_final: 0.7781 (t70) REVERT: B 25 ASN cc_start: 0.8058 (t160) cc_final: 0.7752 (t0) REVERT: B 39 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.7398 (tpp-160) REVERT: B 44 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8771 (tppp) REVERT: B 51 TYR cc_start: 0.8328 (m-10) cc_final: 0.7956 (m-10) REVERT: B 67 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7415 (ttp80) REVERT: B 92 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7058 (tmm-80) REVERT: C 28 VAL cc_start: 0.9028 (t) cc_final: 0.8664 (p) REVERT: C 30 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7731 (mtp85) REVERT: C 36 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8154 (mmtt) REVERT: C 92 ASP cc_start: 0.8236 (t0) cc_final: 0.7948 (t0) REVERT: D 46 LYS cc_start: 0.8667 (ptpp) cc_final: 0.8417 (ptmt) REVERT: D 59 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7630 (tp40) REVERT: D 86 TYR cc_start: 0.7203 (p90) cc_final: 0.6970 (p90) REVERT: D 89 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8083 (mmmm) REVERT: D 116 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 45 THR cc_start: 0.7927 (t) cc_final: 0.7669 (p) REVERT: E 57 SER cc_start: 0.8537 (t) cc_final: 0.8302 (p) REVERT: E 73 GLU cc_start: 0.6531 (tp30) cc_final: 0.6252 (tp30) REVERT: E 121 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8754 (tttm) REVERT: F 27 GLN cc_start: 0.8129 (mp10) cc_final: 0.7786 (mp10) REVERT: F 53 GLU cc_start: 0.7541 (mp0) cc_final: 0.7102 (mp0) REVERT: G 57 LEU cc_start: 0.8576 (tt) cc_final: 0.8348 (tp) REVERT: H 46 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8461 (ttmm) REVERT: H 62 MET cc_start: 0.8116 (mmm) cc_final: 0.7807 (tpp) REVERT: H 86 TYR cc_start: 0.7326 (p90) cc_final: 0.7001 (p90) REVERT: H 88 LYS cc_start: 0.8408 (mmpt) cc_final: 0.8071 (mmpt) REVERT: H 123 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8389 (tppp) outliers start: 57 outliers final: 43 residues processed: 517 average time/residue: 0.1474 time to fit residues: 106.2065 Evaluate side-chains 536 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 486 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 369 THR Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 432 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 144 THR Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 290 GLU 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 80 THR Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 100 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 44 LYS Chi-restraints excluded: chain B residue 58 LEU 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 51 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 80 ILE 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 130 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU 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 111 HIS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 21 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 141 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 93 GLN ** 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 ** H 87 ASN ** 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 = 0.3785 r_free = 0.3785 target = 0.102191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.086625 restraints weight = 55921.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088784 restraints weight = 27951.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090145 restraints weight = 17241.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091030 restraints weight = 12540.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.091587 restraints weight = 10257.238| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17850 Z= 0.192 Angle : 0.966 13.021 25340 Z= 0.515 Chirality : 0.053 0.339 2858 Planarity : 0.007 0.149 2190 Dihedral : 29.063 93.332 4764 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.26 % Allowed : 36.62 % Favored : 59.11 % 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: -2.87 (0.22), residues: 1319 helix: -1.48 (0.18), residues: 713 sheet: -1.29 (1.28), residues: 20 loop : -2.41 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 119 TYR 0.053 0.003 TYR G 52 PHE 0.045 0.003 PHE M 189 TRP 0.035 0.002 TRP M 130 HIS 0.009 0.001 HIS M 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (17850) covalent geometry : angle 0.96577 / 0.51 (25340) hydrogen bonds : bond 0.05602 / 3.53 ( 796) hydrogen bonds : angle 4.45009 / 3.00 ( 2011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.91 seconds wall clock time: 58 minutes 48.15 seconds (3528.15 seconds total)