Starting phenix.real_space_refine on Sun Aug 24 06:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2x_38021/08_2025/8x2x_38021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2x_38021/08_2025/8x2x_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_2025/8x2x_38021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2x_38021/08_2025/8x2x_38021.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2x_38021/08_2025/8x2x_38021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2x_38021/08_2025/8x2x_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-2.0-5787/lib/python3.9/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: 4.04, per 1000 atoms: 0.24 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: 1.33 Conformation dependent library (CDL) restraints added in 532.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.53 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: 3.72 Time building geometry restraints manager: 1.84 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=" CB TYR G 52 " pdb=" CG TYR G 52 " ideal model delta sigma weight residual 1.512 1.449 0.063 2.20e-02 2.07e+03 8.25e+00 bond pdb=" C3' DA I 35 " pdb=" O3' DA I 35 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.87e+00 bond pdb=" CA PHE K 404 " pdb=" CB PHE K 404 " ideal model delta sigma weight residual 1.530 1.570 -0.040 1.69e-02 3.50e+03 5.48e+00 bond pdb=" CD1 TYR G 52 " pdb=" CE1 TYR G 52 " ideal model delta sigma weight residual 1.382 1.314 0.068 3.00e-02 1.11e+03 5.10e+00 bond pdb=" CD1 TYR C 52 " pdb=" CE1 TYR C 52 " ideal model delta sigma weight residual 1.382 1.316 0.066 3.00e-02 1.11e+03 4.83e+00 ... (remaining 17845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 24908 3.39 - 6.79: 387 6.79 - 10.18: 36 10.18 - 13.57: 4 13.57 - 16.96: 5 Bond angle restraints: 25340 Sorted by residual: 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=" CA LEU K 202 " pdb=" CB LEU K 202 " pdb=" CG LEU K 202 " ideal model delta sigma weight residual 116.30 133.26 -16.96 3.50e+00 8.16e-02 2.35e+01 angle pdb=" CA LEU C 67 " pdb=" CB LEU C 67 " pdb=" CG LEU C 67 " ideal model delta sigma weight residual 116.30 132.95 -16.65 3.50e+00 8.16e-02 2.26e+01 angle pdb=" CA LEU G 67 " pdb=" CB LEU G 67 " pdb=" CG LEU G 67 " ideal model delta sigma weight residual 116.30 132.56 -16.26 3.50e+00 8.16e-02 2.16e+01 angle pdb=" CA TYR G 52 " pdb=" CB TYR G 52 " pdb=" CG TYR G 52 " ideal model delta sigma weight residual 113.90 106.02 7.88 1.80e+00 3.09e-01 1.92e+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: 2371 0.082 - 0.163: 433 0.163 - 0.245: 43 0.245 - 0.326: 7 0.326 - 0.408: 4 Chirality restraints: 2858 Sorted by residual: chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL K 287 " pdb=" CA VAL K 287 " pdb=" CG1 VAL K 287 " pdb=" CG2 VAL K 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL M 62 " pdb=" CA VAL M 62 " pdb=" CG1 VAL M 62 " pdb=" CG2 VAL M 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2855 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 404 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C PHE K 404 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE K 404 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU K 405 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 52 " -0.042 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR G 52 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR G 52 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR G 52 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR G 52 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR G 52 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 52 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 52 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " 0.039 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR F 98 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " 0.014 2.00e-02 2.50e+03 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3878 2.79 - 3.32: 15435 3.32 - 3.84: 33518 3.84 - 4.37: 37243 4.37 - 4.90: 52946 Nonbonded interactions: 143020 Sorted by model distance: nonbonded pdb=" OG1 THR M 185 " pdb=" OD1 ASP M 187 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR G 34 " pdb=" OE1 GLU H 38 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR M 144 " pdb=" O SER M 146 " model vdw 2.285 3.040 nonbonded pdb=" O ASP M 210 " pdb=" OG SER M 213 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR K 204 " pdb=" O GLN M 294 " model vdw 2.295 3.040 ... (remaining 143015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.700 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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= 0.348 Angle : 1.132 16.965 25340 Z= 0.621 Chirality : 0.064 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 aren 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 covalent geometry : bond 0.00777 (17850) covalent geometry : angle 1.13161 (25340) hydrogen bonds : bond 0.17021 ( 796) hydrogen bonds : angle 6.48210 ( 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 : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6926 (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: 0.7460 (t0) REVERT: K 223 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7471 (Cg_endo) REVERT: K 240 ASP cc_start: 0.6206 (p0) cc_final: 0.5916 (p0) REVERT: K 287 VAL cc_start: 0.8641 (p) cc_final: 0.8432 (m) REVERT: K 318 LYS cc_start: 0.8052 (tppt) cc_final: 0.7689 (mmmt) REVERT: K 322 GLU cc_start: 0.6530 (mp0) cc_final: 0.6172 (mp0) REVERT: K 377 THR cc_start: 0.7703 (p) cc_final: 0.6832 (t) REVERT: K 379 MET cc_start: 0.6327 (mpp) cc_final: 0.5987 (mpp) REVERT: M 70 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4556 (tt) REVERT: M 147 TYR cc_start: 0.6264 (m-10) cc_final: 0.6001 (m-10) REVERT: M 161 ASN cc_start: 0.6925 (p0) cc_final: 0.6405 (p0) REVERT: M 200 ILE cc_start: 0.8471 (pp) cc_final: 0.8061 (mm) REVERT: M 241 GLU cc_start: 0.8312 (mp0) cc_final: 0.8049 (mp0) REVERT: A 77 ASP cc_start: 0.7545 (p0) cc_final: 0.6895 (p0) REVERT: A 81 ASP cc_start: 0.7194 (t0) cc_final: 0.6897 (t70) REVERT: A 89 ILE cc_start: 0.8559 (mm) cc_final: 0.8249 (tp) REVERT: A 123 ASP cc_start: 0.7744 (m-30) cc_final: 0.7155 (m-30) REVERT: A 124 ILE cc_start: 0.7770 (mt) cc_final: 0.7514 (mm) REVERT: B 49 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.5044 (pp) REVERT: C 48 LYS cc_start: 0.8285 (pptt) cc_final: 0.7484 (pptt) REVERT: C 93 ASP cc_start: 0.7275 (p0) cc_final: 0.6588 (p0) REVERT: D 38 GLU cc_start: 0.7198 (tp30) cc_final: 0.6932 (tp30) REVERT: D 46 LYS cc_start: 0.8330 (pttm) cc_final: 0.8106 (ptpp) REVERT: D 116 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6400 (tm-30) REVERT: E 61 LEU cc_start: 0.7720 (mm) cc_final: 0.7089 (mt) REVERT: G 60 LEU cc_start: 0.8088 (tp) cc_final: 0.7746 (tt) REVERT: H 46 LYS cc_start: 0.8044 (ptmm) cc_final: 0.7812 (ttpp) REVERT: H 47 VAL cc_start: 0.7605 (t) cc_final: 0.7394 (t) REVERT: H 82 LYS cc_start: 0.7879 (pttm) cc_final: 0.7666 (ptmm) REVERT: H 88 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7936 (mmpt) REVERT: H 97 ILE cc_start: 0.8388 (tp) cc_final: 0.8171 (tp) outliers start: 16 outliers final: 5 residues processed: 552 average time/residue: 0.2082 time to fit residues: 152.5878 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 : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain F residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 91 ASN ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN K 301 ASN K 401 HIS ** 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 ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 111 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 93 GLN G 16 GLN H 87 ASN H 98 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.102248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087075 restraints weight = 53977.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089117 restraints weight = 27536.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090481 restraints weight = 17250.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091353 restraints weight = 12630.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091907 restraints weight = 10364.228| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 17850 Z= 0.253 Angle : 0.863 11.063 25340 Z= 0.486 Chirality : 0.048 0.402 2858 Planarity : 0.007 0.067 2190 Dihedral : 29.224 124.270 4780 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.02 % Allowed : 20.32 % Favored : 74.67 % 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 aren not related in a simple way. whole: -3.68 (0.20), residues: 1319 helix: -2.22 (0.16), residues: 732 sheet: -1.38 (1.36), residues: 19 loop : -2.68 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 40 TYR 0.031 0.003 TYR G 52 PHE 0.025 0.003 PHE M 189 TRP 0.025 0.003 TRP M 361 HIS 0.024 0.002 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00533 (17850) covalent geometry : angle 0.86335 (25340) hydrogen bonds : bond 0.06167 ( 796) hydrogen bonds : angle 4.38979 ( 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 574 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 514 time to evaluate : 0.367 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: 0.7681 (tm-30) cc_final: 0.7367 (tp30) REVERT: N 17 LEU cc_start: 0.8340 (tt) cc_final: 0.7746 (mt) REVERT: N 91 ASN cc_start: 0.8208 (t0) cc_final: 0.7970 (t0) REVERT: K 286 LEU cc_start: 0.8350 (tp) cc_final: 0.8093 (tp) REVERT: K 289 TYR cc_start: 0.7379 (p90) cc_final: 0.6841 (p90) REVERT: K 290 PHE cc_start: 0.7835 (p90) cc_final: 0.7591 (p90) REVERT: K 308 LEU cc_start: 0.6690 (pt) cc_final: 0.6480 (pp) REVERT: K 353 TRP cc_start: 0.8213 (m-10) cc_final: 0.7954 (m-10) REVERT: K 357 LEU cc_start: 0.8010 (mt) cc_final: 0.7746 (mt) REVERT: K 377 THR cc_start: 0.9047 (p) cc_final: 0.7932 (p) REVERT: K 379 MET cc_start: 0.6854 (mpp) cc_final: 0.6165 (mpp) REVERT: K 386 HIS cc_start: 0.6855 (m90) cc_final: 0.6321 (m90) REVERT: K 402 ILE cc_start: 0.8007 (mm) cc_final: 0.7401 (mp) REVERT: M 70 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4372 (tt) REVERT: M 161 ASN cc_start: 0.7082 (p0) cc_final: 0.6601 (p0) REVERT: M 167 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7311 (ttp80) REVERT: M 168 ASP cc_start: 0.7990 (t0) cc_final: 0.7670 (t0) REVERT: M 200 ILE cc_start: 0.8306 (pp) cc_final: 0.8076 (mm) REVERT: M 249 PHE cc_start: 0.7955 (t80) cc_final: 0.7560 (t80) REVERT: M 342 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8219 (pttm) REVERT: A 64 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8065 (mmmm) REVERT: A 65 LEU cc_start: 0.8377 (mm) cc_final: 0.8122 (mm) REVERT: A 68 GLN cc_start: 0.8911 (mt0) cc_final: 0.8662 (mt0) REVERT: A 77 ASP cc_start: 0.8178 (p0) cc_final: 0.7919 (p0) REVERT: A 81 ASP cc_start: 0.7698 (t0) cc_final: 0.7495 (t0) REVERT: B 35 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7448 (tpt170) REVERT: B 36 ARG cc_start: 0.7608 (mtm180) cc_final: 0.7354 (mtm-85) REVERT: B 44 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8283 (mmmm) REVERT: B 52 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 79 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: C 28 VAL cc_start: 0.8797 (t) cc_final: 0.8457 (p) REVERT: C 52 TYR cc_start: 0.6973 (t80) cc_final: 0.6743 (t80) REVERT: C 87 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6210 (pp) REVERT: C 94 GLU cc_start: 0.8109 (tt0) cc_final: 0.7857 (pt0) REVERT: D 101 VAL cc_start: 0.9027 (t) cc_final: 0.8790 (p) REVERT: D 111 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7814 (ptpp) REVERT: D 116 GLU cc_start: 0.7736 (tm-30) cc_final: 0.6127 (tm-30) REVERT: E 57 SER cc_start: 0.8766 (t) cc_final: 0.8260 (p) REVERT: E 76 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7273 (pm20) REVERT: F 53 GLU cc_start: 0.7440 (mp0) cc_final: 0.7162 (mp0) REVERT: F 91 LYS cc_start: 0.8679 (tptp) cc_final: 0.8366 (tptp) REVERT: H 62 MET cc_start: 0.8085 (mmm) cc_final: 0.7790 (tpp) REVERT: H 86 TYR cc_start: 0.7106 (p90) cc_final: 0.6871 (p90) REVERT: H 97 ILE cc_start: 0.8904 (tp) cc_final: 0.8592 (tp) REVERT: H 108 GLU cc_start: 0.7287 (pm20) cc_final: 0.6895 (pm20) REVERT: H 123 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8324 (tppp) outliers start: 60 outliers final: 28 residues processed: 538 average time/residue: 0.1945 time to fit residues: 142.3567 Evaluate side-chains 509 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 475 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 13 ASP 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 341 LEU Chi-restraints excluded: chain K residue 366 LYS 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 M residue 342 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 100 HIS ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** M 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 233 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN M 363 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 111 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.102811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087619 restraints weight = 54550.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089721 restraints weight = 27423.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091097 restraints weight = 16914.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091970 restraints weight = 12242.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092508 restraints weight = 9987.384| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17850 Z= 0.189 Angle : 0.814 10.764 25340 Z= 0.445 Chirality : 0.045 0.415 2858 Planarity : 0.006 0.060 2190 Dihedral : 29.092 125.263 4770 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.77 % Allowed : 24.16 % Favored : 70.07 % 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 aren not related in a simple way. whole: -3.09 (0.21), residues: 1319 helix: -1.68 (0.17), residues: 706 sheet: -1.64 (1.28), residues: 19 loop : -2.48 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 395 TYR 0.022 0.002 TYR D 86 PHE 0.029 0.003 PHE M 189 TRP 0.022 0.002 TRP K 247 HIS 0.014 0.002 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00418 (17850) covalent geometry : angle 0.81380 (25340) hydrogen bonds : bond 0.05167 ( 796) hydrogen bonds : angle 4.16902 ( 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 : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7307 (tp30) REVERT: N 17 LEU cc_start: 0.8284 (tt) cc_final: 0.7755 (mt) REVERT: K 209 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7455 (tppt) REVERT: K 236 PHE cc_start: 0.6794 (m-80) cc_final: 0.6484 (m-10) REVERT: K 266 TYR cc_start: 0.6348 (t80) cc_final: 0.5622 (t80) REVERT: K 357 LEU cc_start: 0.7979 (mt) cc_final: 0.7769 (mt) REVERT: K 370 ILE cc_start: 0.7716 (tt) cc_final: 0.7330 (pt) REVERT: K 386 HIS cc_start: 0.6875 (m90) cc_final: 0.6648 (m90) REVERT: K 408 ASP cc_start: 0.8654 (p0) cc_final: 0.8408 (p0) REVERT: K 409 ILE cc_start: 0.7499 (mt) cc_final: 0.7152 (mp) REVERT: M 70 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4315 (tt) REVERT: M 74 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7539 (mm) REVERT: M 161 ASN cc_start: 0.7033 (p0) cc_final: 0.6710 (p0) REVERT: M 249 PHE cc_start: 0.7984 (t80) cc_final: 0.7602 (t80) REVERT: M 339 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7451 (tp40) REVERT: M 342 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8281 (pttm) REVERT: A 64 LYS cc_start: 0.8485 (mmmm) cc_final: 0.7916 (mmmm) REVERT: A 65 LEU cc_start: 0.8353 (mm) cc_final: 0.8120 (mm) REVERT: A 68 GLN cc_start: 0.8987 (mt0) cc_final: 0.8682 (mt0) REVERT: A 69 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8147 (mtp180) REVERT: A 74 ILE cc_start: 0.8802 (tt) cc_final: 0.8599 (tt) REVERT: A 81 ASP cc_start: 0.8044 (t0) cc_final: 0.7496 (t0) REVERT: A 83 ARG cc_start: 0.7638 (mmp80) cc_final: 0.7007 (mmp80) REVERT: A 93 GLN cc_start: 0.7832 (tp40) cc_final: 0.7621 (tp40) REVERT: B 35 ARG cc_start: 0.7910 (ttt90) cc_final: 0.7603 (tpt170) REVERT: B 44 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8394 (mmmm) REVERT: B 79 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7858 (mtpt) REVERT: C 28 VAL cc_start: 0.9002 (t) cc_final: 0.8701 (p) REVERT: C 48 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7662 (ptmm) REVERT: C 63 GLU cc_start: 0.7678 (tp30) cc_final: 0.7466 (tp30) REVERT: D 111 LYS cc_start: 0.8304 (ptpp) cc_final: 0.8060 (ptpp) REVERT: E 57 SER cc_start: 0.8835 (t) cc_final: 0.8208 (p) REVERT: E 106 ASP cc_start: 0.7766 (p0) cc_final: 0.7437 (p0) REVERT: F 34 ILE cc_start: 0.8692 (mp) cc_final: 0.8487 (mm) REVERT: F 39 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7683 (mmt90) REVERT: F 53 GLU cc_start: 0.7383 (mp0) cc_final: 0.7102 (mp0) REVERT: F 55 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7615 (mtt180) REVERT: F 91 LYS cc_start: 0.8739 (tptp) cc_final: 0.8529 (tptp) REVERT: G 57 LEU cc_start: 0.8719 (tt) cc_final: 0.8482 (tp) REVERT: H 62 MET cc_start: 0.8051 (mmm) cc_final: 0.7689 (tpp) REVERT: H 88 LYS cc_start: 0.8270 (mmpt) cc_final: 0.8001 (mmpt) REVERT: H 97 ILE cc_start: 0.9055 (tp) cc_final: 0.8777 (tp) REVERT: H 123 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8437 (tppp) outliers start: 69 outliers final: 35 residues processed: 518 average time/residue: 0.1970 time to fit residues: 137.4366 Evaluate side-chains 511 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 470 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain 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 247 THR Chi-restraints excluded: chain M residue 332 GLN Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 44 LYS 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 48 LYS 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 119 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 59 TYR 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 58 SER Chi-restraints excluded: chain H residue 104 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 173 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.101843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086555 restraints weight = 55112.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088602 restraints weight = 27784.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089932 restraints weight = 17371.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090769 restraints weight = 12792.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.091315 restraints weight = 10551.514| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17850 Z= 0.208 Angle : 0.828 12.493 25340 Z= 0.452 Chirality : 0.045 0.394 2858 Planarity : 0.006 0.060 2190 Dihedral : 28.908 124.350 4768 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 6.61 % Allowed : 25.92 % Favored : 67.47 % 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 aren not related in a simple way. whole: -2.70 (0.22), residues: 1319 helix: -1.34 (0.18), residues: 702 sheet: -1.23 (1.13), residues: 20 loop : -2.32 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 67 TYR 0.036 0.002 TYR G 52 PHE 0.049 0.002 PHE M 189 TRP 0.026 0.002 TRP K 247 HIS 0.020 0.002 HIS G 111 Details of bonding type rmsd covalent geometry : bond 0.00465 (17850) covalent geometry : angle 0.82773 (25340) hydrogen bonds : bond 0.05259 ( 796) hydrogen bonds : angle 4.12004 ( 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 580 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 501 time to evaluate : 0.525 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: L 35 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7633 (tp30) REVERT: N 17 LEU cc_start: 0.8341 (tt) cc_final: 0.7922 (mt) REVERT: N 91 ASN cc_start: 0.8242 (t0) cc_final: 0.8031 (t0) REVERT: K 212 GLU cc_start: 0.8190 (pp20) cc_final: 0.7789 (pt0) REVERT: K 213 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7928 (mmm160) REVERT: K 238 GLU cc_start: 0.6689 (pp20) cc_final: 0.6432 (pp20) REVERT: K 266 TYR cc_start: 0.6446 (t80) cc_final: 0.5596 (t80) REVERT: K 272 LEU cc_start: 0.8180 (tp) cc_final: 0.7870 (tp) REVERT: K 289 TYR cc_start: 0.7534 (p90) cc_final: 0.7296 (p90) REVERT: K 352 TYR cc_start: 0.7151 (t80) cc_final: 0.6839 (t80) REVERT: K 353 TRP cc_start: 0.8573 (m-10) cc_final: 0.8299 (m-10) REVERT: K 357 LEU cc_start: 0.8070 (mt) cc_final: 0.7840 (mt) REVERT: K 377 THR cc_start: 0.8547 (p) cc_final: 0.8273 (p) REVERT: K 383 ASP cc_start: 0.8055 (t0) cc_final: 0.7466 (t0) REVERT: K 386 HIS cc_start: 0.7059 (m90) cc_final: 0.6855 (m90) REVERT: K 391 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8195 (tp) REVERT: K 406 ASN cc_start: 0.6810 (p0) cc_final: 0.6596 (p0) REVERT: K 408 ASP cc_start: 0.8568 (p0) cc_final: 0.8293 (p0) REVERT: M 70 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4250 (tt) REVERT: M 74 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.7589 (mt) REVERT: M 161 ASN cc_start: 0.7001 (p0) cc_final: 0.6728 (p0) REVERT: M 168 ASP cc_start: 0.8267 (t0) cc_final: 0.7701 (t0) REVERT: M 189 PHE cc_start: 0.7819 (m-80) cc_final: 0.7390 (m-80) REVERT: M 215 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6964 (tt) REVERT: M 224 LEU cc_start: 0.8238 (pt) cc_final: 0.7825 (mp) REVERT: M 342 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (pttm) REVERT: M 345 LYS cc_start: 0.8024 (tptp) cc_final: 0.7817 (tppt) REVERT: A 69 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8181 (mtp180) REVERT: A 81 ASP cc_start: 0.8210 (t0) cc_final: 0.7771 (t0) REVERT: A 93 GLN cc_start: 0.7747 (tp40) cc_final: 0.7430 (tp40) REVERT: A 121 LYS cc_start: 0.8490 (mptt) cc_final: 0.8255 (mptt) REVERT: A 122 LYS cc_start: 0.8309 (pmtt) cc_final: 0.8102 (pmtt) REVERT: A 123 ASP cc_start: 0.8162 (m-30) cc_final: 0.7884 (m-30) REVERT: B 35 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7881 (tpt170) REVERT: B 44 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8691 (mmmm) REVERT: B 67 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6888 (ttp80) REVERT: B 79 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7922 (mtmt) REVERT: C 28 VAL cc_start: 0.9167 (t) cc_final: 0.8806 (p) REVERT: C 63 GLU cc_start: 0.8138 (tp30) cc_final: 0.7932 (tp30) REVERT: D 116 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 57 SER cc_start: 0.8545 (t) cc_final: 0.8152 (p) REVERT: E 62 ILE cc_start: 0.8192 (mm) cc_final: 0.7977 (mt) REVERT: E 74 ILE cc_start: 0.8502 (tt) cc_final: 0.8173 (tp) REVERT: E 103 LEU cc_start: 0.8759 (tp) cc_final: 0.8487 (tp) REVERT: E 106 ASP cc_start: 0.7769 (p0) cc_final: 0.6552 (p0) REVERT: E 109 LEU cc_start: 0.9048 (mm) cc_final: 0.8838 (mt) REVERT: E 131 ARG cc_start: 0.7574 (ptp-110) cc_final: 0.7214 (ttm110) REVERT: F 29 ILE cc_start: 0.7922 (tt) cc_final: 0.7680 (pt) REVERT: F 53 GLU cc_start: 0.7424 (mp0) cc_final: 0.7028 (mp0) REVERT: F 63 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: F 67 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: F 84 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7830 (mm) REVERT: H 46 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8410 (ttmm) REVERT: H 88 LYS cc_start: 0.8398 (mmpt) cc_final: 0.8038 (mmpt) REVERT: H 123 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8369 (tppp) outliers start: 79 outliers final: 40 residues processed: 536 average time/residue: 0.1928 time to fit residues: 139.5637 Evaluate side-chains 540 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 489 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR 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 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU 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 53 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 97 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 0.0010 chunk 14 optimal weight: 0.0040 chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 107 ASN ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.103876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088519 restraints weight = 54869.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090684 restraints weight = 27149.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092062 restraints weight = 16599.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092943 restraints weight = 12003.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093492 restraints weight = 9783.974| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17850 Z= 0.171 Angle : 0.813 12.217 25340 Z= 0.438 Chirality : 0.043 0.377 2858 Planarity : 0.005 0.058 2190 Dihedral : 28.777 122.245 4768 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.60 % Allowed : 29.85 % Favored : 64.55 % 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 aren not related in a simple way. whole: -2.59 (0.22), residues: 1319 helix: -1.21 (0.18), residues: 712 sheet: -1.55 (1.15), residues: 20 loop : -2.32 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 395 TYR 0.047 0.002 TYR G 52 PHE 0.041 0.003 PHE K 323 TRP 0.028 0.002 TRP K 247 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (17850) covalent geometry : angle 0.81307 (25340) hydrogen bonds : bond 0.04607 ( 796) hydrogen bonds : angle 4.16587 ( 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 565 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 498 time to evaluate : 0.517 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: 0.7891 (tm-30) cc_final: 0.7641 (tp30) REVERT: N 17 LEU cc_start: 0.8327 (tt) cc_final: 0.7852 (mt) REVERT: K 212 GLU cc_start: 0.8083 (pp20) cc_final: 0.7681 (pt0) REVERT: K 238 GLU cc_start: 0.6890 (pp20) cc_final: 0.6432 (pp20) REVERT: K 243 LYS cc_start: 0.8659 (tppt) cc_final: 0.8352 (tppt) REVERT: K 266 TYR cc_start: 0.6372 (t80) cc_final: 0.5534 (t80) REVERT: K 272 LEU cc_start: 0.8027 (tp) cc_final: 0.7729 (tp) REVERT: K 352 TYR cc_start: 0.7103 (t80) cc_final: 0.6741 (t80) REVERT: K 357 LEU cc_start: 0.8083 (mt) cc_final: 0.7882 (mt) REVERT: K 370 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6019 (pt) REVERT: K 377 THR cc_start: 0.8470 (p) cc_final: 0.8199 (p) REVERT: K 383 ASP cc_start: 0.7932 (t0) cc_final: 0.7261 (t0) REVERT: K 386 HIS cc_start: 0.7139 (m90) cc_final: 0.6894 (m90) REVERT: K 405 LEU cc_start: 0.1941 (OUTLIER) cc_final: 0.1091 (tp) REVERT: M 70 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.3742 (tt) REVERT: M 74 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7622 (mt) REVERT: M 141 PHE cc_start: 0.7360 (t80) cc_final: 0.7131 (m-80) REVERT: M 215 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6813 (tt) REVERT: M 224 LEU cc_start: 0.8218 (pt) cc_final: 0.7964 (mp) REVERT: M 342 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8214 (pttm) REVERT: A 64 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8234 (mmmt) REVERT: A 68 GLN cc_start: 0.8843 (mt0) cc_final: 0.8548 (mt0) REVERT: A 81 ASP cc_start: 0.8247 (t0) cc_final: 0.7673 (t0) REVERT: B 45 ARG cc_start: 0.8282 (tpt170) cc_final: 0.7965 (mmm160) REVERT: B 79 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7907 (mtmt) REVERT: B 92 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8087 (tmm-80) REVERT: C 28 VAL cc_start: 0.9181 (t) cc_final: 0.8765 (p) REVERT: C 30 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7629 (mtp85) REVERT: C 89 ILE cc_start: 0.7655 (mm) cc_final: 0.7366 (mm) REVERT: E 45 THR cc_start: 0.7816 (t) cc_final: 0.7610 (p) REVERT: E 57 SER cc_start: 0.8577 (t) cc_final: 0.8263 (p) REVERT: E 62 ILE cc_start: 0.8204 (mm) cc_final: 0.7947 (mt) REVERT: E 74 ILE cc_start: 0.8410 (tt) cc_final: 0.8122 (tp) REVERT: E 103 LEU cc_start: 0.8730 (tp) cc_final: 0.8407 (tp) REVERT: E 106 ASP cc_start: 0.7808 (p0) cc_final: 0.7406 (p0) REVERT: E 109 LEU cc_start: 0.9045 (mm) cc_final: 0.8796 (mt) REVERT: F 67 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7209 (mtm110) REVERT: G 30 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7315 (ttp80) REVERT: G 93 ASP cc_start: 0.8452 (m-30) cc_final: 0.8149 (m-30) REVERT: H 46 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8213 (ttmm) REVERT: H 49 LYS cc_start: 0.8584 (pttp) cc_final: 0.8125 (pttp) REVERT: H 62 MET cc_start: 0.8001 (tpp) cc_final: 0.7777 (tpp) REVERT: H 88 LYS cc_start: 0.8427 (mmpt) cc_final: 0.8040 (mmpt) REVERT: H 123 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8422 (tppp) outliers start: 67 outliers final: 38 residues processed: 526 average time/residue: 0.1916 time to fit residues: 136.3245 Evaluate side-chains 527 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 479 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 304 CYS Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 334 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 342 LYS 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 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 130 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 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 = 0.3804 r_free = 0.3804 target = 0.103579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088240 restraints weight = 55115.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090384 restraints weight = 27260.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.091744 restraints weight = 16741.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092600 restraints weight = 12141.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.093145 restraints weight = 9925.567| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6958 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= 0.182 Angle : 0.808 11.673 25340 Z= 0.440 Chirality : 0.044 0.207 2858 Planarity : 0.006 0.115 2190 Dihedral : 28.674 121.179 4768 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.93 % Allowed : 32.61 % Favored : 62.46 % 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 aren not related in a simple way. whole: -2.43 (0.22), residues: 1319 helix: -1.08 (0.18), residues: 716 sheet: -1.73 (1.13), residues: 20 loop : -2.23 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 40 TYR 0.061 0.002 TYR G 52 PHE 0.039 0.003 PHE K 323 TRP 0.033 0.003 TRP K 247 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00413 (17850) covalent geometry : angle 0.80819 (25340) hydrogen bonds : bond 0.04760 ( 796) hydrogen bonds : angle 4.16752 ( 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 550 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 491 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8364 (tt) cc_final: 0.8161 (mt) REVERT: N 20 GLU cc_start: 0.7137 (pp20) cc_final: 0.6653 (pp20) REVERT: N 21 PHE cc_start: 0.7820 (t80) cc_final: 0.7369 (t80) REVERT: K 238 GLU cc_start: 0.7090 (pp20) cc_final: 0.6652 (pp20) REVERT: K 266 TYR cc_start: 0.6590 (t80) cc_final: 0.5777 (t80) REVERT: K 272 LEU cc_start: 0.8129 (tp) cc_final: 0.7832 (tp) REVERT: K 352 TYR cc_start: 0.7170 (t80) cc_final: 0.6944 (t80) REVERT: K 377 THR cc_start: 0.8258 (p) cc_final: 0.7953 (p) REVERT: K 383 ASP cc_start: 0.7860 (t0) cc_final: 0.7574 (t0) REVERT: K 405 LEU cc_start: 0.1919 (OUTLIER) cc_final: 0.0523 (tp) REVERT: M 70 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.3789 (tt) REVERT: M 74 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.7563 (mt) REVERT: M 141 PHE cc_start: 0.7435 (t80) cc_final: 0.7185 (m-80) REVERT: M 168 ASP cc_start: 0.8240 (t0) cc_final: 0.7495 (m-30) REVERT: M 215 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7029 (tt) REVERT: M 338 HIS cc_start: 0.6394 (t70) cc_final: 0.6024 (t-90) REVERT: A 64 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8211 (mmmt) REVERT: A 68 GLN cc_start: 0.8792 (mt0) cc_final: 0.8368 (mt0) REVERT: A 81 ASP cc_start: 0.8182 (t0) cc_final: 0.7759 (t0) REVERT: A 93 GLN cc_start: 0.7816 (tp40) cc_final: 0.7444 (tp40) REVERT: B 68 ASP cc_start: 0.7677 (p0) cc_final: 0.7442 (p0) REVERT: B 79 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: B 92 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8197 (tmm-80) REVERT: C 28 VAL cc_start: 0.9164 (t) cc_final: 0.8803 (p) REVERT: C 30 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8062 (ttm-80) REVERT: C 48 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7899 (tptt) REVERT: C 89 ILE cc_start: 0.7721 (mm) cc_final: 0.7504 (mm) REVERT: D 89 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8209 (mmmm) REVERT: E 103 LEU cc_start: 0.8825 (tp) cc_final: 0.8511 (tp) REVERT: E 106 ASP cc_start: 0.7715 (p0) cc_final: 0.7301 (p0) REVERT: E 109 LEU cc_start: 0.9069 (mm) cc_final: 0.8821 (mm) REVERT: E 121 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8626 (ttpp) REVERT: F 53 GLU cc_start: 0.7574 (mp0) cc_final: 0.7336 (mp0) REVERT: G 30 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7379 (mtm-85) REVERT: H 43 TYR cc_start: 0.7039 (m-10) cc_final: 0.6769 (m-10) REVERT: H 46 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8152 (ttmm) REVERT: H 49 LYS cc_start: 0.8600 (pttp) cc_final: 0.8144 (pttp) REVERT: H 62 MET cc_start: 0.8058 (tpp) cc_final: 0.7679 (tpp) REVERT: H 86 TYR cc_start: 0.7352 (p90) cc_final: 0.6848 (p90) REVERT: H 88 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8095 (mmpt) REVERT: H 123 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8396 (tppp) outliers start: 59 outliers final: 38 residues processed: 512 average time/residue: 0.1938 time to fit residues: 134.0235 Evaluate side-chains 525 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 478 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS 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 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 65 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 72 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 91 ASN ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.104039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.088715 restraints weight = 55808.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090790 restraints weight = 27994.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.092162 restraints weight = 17345.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093029 restraints weight = 12665.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093592 restraints weight = 10373.920| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17850 Z= 0.183 Angle : 0.832 11.815 25340 Z= 0.450 Chirality : 0.044 0.224 2858 Planarity : 0.006 0.092 2190 Dihedral : 28.633 120.478 4765 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.27 % Allowed : 32.36 % Favored : 61.37 % 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 aren not related in a simple way. whole: -2.42 (0.22), residues: 1319 helix: -1.06 (0.18), residues: 710 sheet: -1.95 (1.02), residues: 20 loop : -2.23 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 83 TYR 0.056 0.003 TYR G 52 PHE 0.042 0.002 PHE K 404 TRP 0.034 0.003 TRP K 353 HIS 0.007 0.001 HIS K 386 Details of bonding type rmsd covalent geometry : bond 0.00414 (17850) covalent geometry : angle 0.83168 (25340) hydrogen bonds : bond 0.04710 ( 796) hydrogen bonds : angle 4.24361 ( 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 584 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 509 time to evaluate : 0.580 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: 0.8391 (tt) cc_final: 0.7882 (mt) REVERT: N 105 GLU cc_start: 0.6053 (mm-30) cc_final: 0.5491 (mm-30) REVERT: K 238 GLU cc_start: 0.7201 (pp20) cc_final: 0.6665 (pp20) REVERT: K 266 TYR cc_start: 0.6735 (t80) cc_final: 0.5899 (t80) REVERT: K 272 LEU cc_start: 0.8109 (tp) cc_final: 0.7827 (tp) REVERT: K 331 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: K 352 TYR cc_start: 0.7191 (t80) cc_final: 0.6974 (t80) REVERT: K 377 THR cc_start: 0.8165 (p) cc_final: 0.7872 (p) REVERT: K 383 ASP cc_start: 0.7895 (t0) cc_final: 0.7192 (t70) REVERT: K 396 TYR cc_start: 0.5787 (t80) cc_final: 0.5293 (t80) REVERT: K 404 PHE cc_start: 0.4234 (OUTLIER) cc_final: 0.3941 (p90) REVERT: K 428 ARG cc_start: 0.5022 (tmt-80) cc_final: 0.4576 (tmt-80) REVERT: K 430 ILE cc_start: 0.8703 (pt) cc_final: 0.8473 (mm) REVERT: M 70 LEU cc_start: 0.4406 (OUTLIER) cc_final: 0.3662 (tt) REVERT: M 74 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.7678 (mm) REVERT: M 141 PHE cc_start: 0.7374 (t80) cc_final: 0.7158 (m-80) REVERT: M 162 TYR cc_start: 0.6326 (t80) cc_final: 0.5988 (t80) REVERT: M 169 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6158 (pp20) REVERT: M 215 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7204 (tt) REVERT: M 338 HIS cc_start: 0.6139 (t70) cc_final: 0.5858 (t-90) REVERT: A 64 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8224 (mmmt) REVERT: A 68 GLN cc_start: 0.8723 (mt0) cc_final: 0.8283 (mt0) REVERT: A 81 ASP cc_start: 0.8292 (t0) cc_final: 0.7926 (t0) REVERT: A 93 GLN cc_start: 0.7736 (tp40) cc_final: 0.7405 (tp40) REVERT: B 51 TYR cc_start: 0.8257 (m-10) cc_final: 0.8038 (m-10) REVERT: B 79 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7732 (mtmm) REVERT: B 92 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8296 (tmm-80) REVERT: C 28 VAL cc_start: 0.9180 (t) cc_final: 0.8798 (p) REVERT: C 89 ILE cc_start: 0.7728 (mm) cc_final: 0.7466 (mm) REVERT: D 59 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7751 (tp40) REVERT: D 88 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8263 (mmtt) REVERT: D 89 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8204 (mmmm) REVERT: D 116 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 105 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7421 (mm-30) REVERT: E 106 ASP cc_start: 0.7700 (p0) cc_final: 0.7367 (p0) REVERT: E 121 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8787 (ttpp) REVERT: E 123 ASP cc_start: 0.7867 (m-30) cc_final: 0.7550 (t0) REVERT: F 53 GLU cc_start: 0.7561 (mp0) cc_final: 0.7176 (mp0) REVERT: G 30 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7458 (mtm-85) REVERT: H 43 TYR cc_start: 0.7055 (m-10) cc_final: 0.6786 (m-10) REVERT: H 46 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8329 (ttmm) REVERT: H 86 TYR cc_start: 0.7285 (p90) cc_final: 0.6568 (p90) REVERT: H 88 LYS cc_start: 0.8439 (mmpt) cc_final: 0.8051 (mmpt) REVERT: H 123 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8343 (tppt) outliers start: 75 outliers final: 43 residues processed: 534 average time/residue: 0.1940 time to fit residues: 140.3878 Evaluate side-chains 534 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 481 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 404 PHE 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 144 THR Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 342 LYS 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 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 91 ASN N 107 ASN ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.103162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087861 restraints weight = 56094.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089979 restraints weight = 27831.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091351 restraints weight = 17164.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.092214 restraints weight = 12460.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092752 restraints weight = 10212.117| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17850 Z= 0.197 Angle : 0.876 14.428 25340 Z= 0.468 Chirality : 0.045 0.297 2858 Planarity : 0.006 0.107 2190 Dihedral : 28.625 120.186 4765 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.69 % Allowed : 33.95 % Favored : 60.37 % 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 aren not related in a simple way. whole: -2.37 (0.22), residues: 1319 helix: -1.12 (0.18), residues: 691 sheet: -1.42 (1.11), residues: 20 loop : -2.07 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 395 TYR 0.056 0.003 TYR G 52 PHE 0.035 0.003 PHE K 323 TRP 0.051 0.004 TRP K 353 HIS 0.007 0.001 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00451 (17850) covalent geometry : angle 0.87555 (25340) hydrogen bonds : bond 0.04966 ( 796) hydrogen bonds : angle 4.34885 ( 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 559 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 491 time to evaluate : 0.524 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: N 17 LEU cc_start: 0.8483 (tt) cc_final: 0.7972 (mt) REVERT: K 209 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7183 (mmmt) REVERT: K 238 GLU cc_start: 0.7192 (pp20) cc_final: 0.6684 (pp20) REVERT: K 272 LEU cc_start: 0.8214 (tp) cc_final: 0.7978 (tp) REVERT: K 353 TRP cc_start: 0.8005 (m-10) cc_final: 0.7791 (m-10) REVERT: K 377 THR cc_start: 0.8146 (p) cc_final: 0.7797 (p) REVERT: K 389 LYS cc_start: 0.8712 (pttp) cc_final: 0.8451 (pttm) REVERT: K 430 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8530 (mm) REVERT: M 70 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.3635 (tt) REVERT: M 74 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7325 (mm) REVERT: M 141 PHE cc_start: 0.7577 (t80) cc_final: 0.7328 (m-80) REVERT: M 168 ASP cc_start: 0.8313 (t0) cc_final: 0.7861 (m-30) REVERT: M 294 GLN cc_start: 0.7422 (pm20) cc_final: 0.6401 (pp30) REVERT: M 295 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6209 (mt) REVERT: A 64 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8412 (mmmt) REVERT: A 69 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8426 (mtm-85) REVERT: A 81 ASP cc_start: 0.8352 (t0) cc_final: 0.7900 (t0) REVERT: A 83 ARG cc_start: 0.7853 (mmp-170) cc_final: 0.7323 (mmp-170) REVERT: A 93 GLN cc_start: 0.7708 (tp40) cc_final: 0.7370 (tp40) REVERT: A 131 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.8027 (mtp85) REVERT: B 79 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7730 (mtmm) REVERT: B 80 THR cc_start: 0.8919 (t) cc_final: 0.8657 (p) REVERT: B 92 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8299 (tmm-80) REVERT: C 28 VAL cc_start: 0.9159 (t) cc_final: 0.8811 (p) REVERT: C 30 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8056 (mtp-110) REVERT: C 48 LYS cc_start: 0.7882 (tptp) cc_final: 0.7648 (tptp) REVERT: C 81 THR cc_start: 0.8095 (p) cc_final: 0.7790 (p) REVERT: D 49 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8126 (ptpp) REVERT: D 82 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8300 (ttmt) REVERT: D 88 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8230 (mmtt) REVERT: D 89 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8207 (mmmm) REVERT: D 98 GLN cc_start: 0.8266 (tp40) cc_final: 0.8015 (tp40) REVERT: D 123 LYS cc_start: 0.8214 (ptmm) cc_final: 0.7931 (pttp) REVERT: E 105 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7432 (mm-30) REVERT: E 106 ASP cc_start: 0.7708 (p0) cc_final: 0.7429 (p0) REVERT: E 109 LEU cc_start: 0.9104 (mm) cc_final: 0.8828 (mt) REVERT: E 121 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8878 (ttpp) REVERT: E 123 ASP cc_start: 0.7900 (m-30) cc_final: 0.7607 (t0) REVERT: F 53 GLU cc_start: 0.7545 (mp0) cc_final: 0.7170 (mp0) REVERT: G 30 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7405 (mtm-85) REVERT: G 90 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7513 (ttt180) REVERT: H 43 TYR cc_start: 0.7227 (m-10) cc_final: 0.6954 (m-10) REVERT: H 46 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8513 (ttmm) REVERT: H 49 LYS cc_start: 0.8573 (pttp) cc_final: 0.8231 (pttp) REVERT: H 62 MET cc_start: 0.8123 (tpp) cc_final: 0.7516 (tpp) REVERT: H 86 TYR cc_start: 0.7207 (p90) cc_final: 0.6689 (p90) REVERT: H 88 LYS cc_start: 0.8392 (mmpt) cc_final: 0.8044 (mmpt) REVERT: H 123 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8367 (tppt) outliers start: 68 outliers final: 46 residues processed: 512 average time/residue: 0.1941 time to fit residues: 134.5709 Evaluate side-chains 535 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 481 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 430 ILE Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 342 LYS 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 65 LEU Chi-restraints excluded: chain A residue 80 THR 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 54 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 91 ASN M 64 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.104914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089610 restraints weight = 55482.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091749 restraints weight = 27535.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.093133 restraints weight = 16994.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094022 restraints weight = 12318.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.094590 restraints weight = 10048.800| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.7979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17850 Z= 0.183 Angle : 0.888 13.350 25340 Z= 0.472 Chirality : 0.044 0.209 2858 Planarity : 0.006 0.080 2190 Dihedral : 28.586 118.962 4765 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.68 % Allowed : 35.95 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.22), residues: 1319 helix: -1.12 (0.18), residues: 686 sheet: -1.22 (1.13), residues: 20 loop : -2.07 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 395 TYR 0.053 0.003 TYR G 52 PHE 0.061 0.003 PHE K 404 TRP 0.047 0.004 TRP K 353 HIS 0.007 0.001 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00416 (17850) covalent geometry : angle 0.88813 (25340) hydrogen bonds : bond 0.04620 ( 796) hydrogen bonds : angle 4.32620 ( 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 547 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 491 time to evaluate : 0.544 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: 0.8506 (tt) cc_final: 0.7930 (mt) REVERT: K 238 GLU cc_start: 0.7206 (pp20) cc_final: 0.6842 (pp20) REVERT: K 243 LYS cc_start: 0.8172 (tptp) cc_final: 0.7859 (tptt) REVERT: K 377 THR cc_start: 0.8132 (p) cc_final: 0.7926 (p) REVERT: K 389 LYS cc_start: 0.8747 (pttp) cc_final: 0.8444 (pttp) REVERT: K 392 ASN cc_start: 0.8324 (p0) cc_final: 0.8089 (t0) REVERT: K 405 LEU cc_start: 0.2355 (OUTLIER) cc_final: 0.0926 (tp) REVERT: M 70 LEU cc_start: 0.3975 (OUTLIER) cc_final: 0.3310 (tt) REVERT: M 74 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.7325 (mm) REVERT: M 141 PHE cc_start: 0.7554 (t80) cc_final: 0.7330 (m-80) REVERT: M 168 ASP cc_start: 0.8296 (t0) cc_final: 0.8035 (m-30) REVERT: M 172 LEU cc_start: 0.7985 (mm) cc_final: 0.7519 (pp) REVERT: M 258 GLN cc_start: 0.7867 (mp10) cc_final: 0.7612 (pm20) REVERT: M 295 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.6040 (mt) REVERT: M 338 HIS cc_start: 0.6399 (t70) cc_final: 0.6180 (t-90) REVERT: A 56 LYS cc_start: 0.9101 (tptp) cc_final: 0.8877 (tptp) REVERT: A 64 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8244 (mmmt) REVERT: A 68 GLN cc_start: 0.8653 (mt0) cc_final: 0.8396 (mt0) REVERT: A 69 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.7838 (mtm-85) REVERT: A 81 ASP cc_start: 0.8302 (t0) cc_final: 0.7791 (t0) REVERT: A 83 ARG cc_start: 0.7908 (mmp-170) cc_final: 0.7309 (mmp-170) REVERT: A 93 GLN cc_start: 0.7747 (tp40) cc_final: 0.7423 (tp40) REVERT: B 31 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6905 (tptp) REVERT: B 39 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7393 (tpp-160) REVERT: B 44 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8663 (tppp) REVERT: B 80 THR cc_start: 0.8922 (t) cc_final: 0.8677 (p) REVERT: B 92 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8293 (tmm-80) REVERT: C 25 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7409 (mm-40) REVERT: C 28 VAL cc_start: 0.9156 (t) cc_final: 0.8808 (p) REVERT: C 63 GLU cc_start: 0.8116 (tp30) cc_final: 0.7906 (tp30) REVERT: C 81 THR cc_start: 0.7884 (p) cc_final: 0.7606 (p) REVERT: D 46 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8256 (ptmt) REVERT: D 49 LYS cc_start: 0.8523 (ptpp) cc_final: 0.8142 (ptpp) REVERT: D 82 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8249 (ttmt) REVERT: D 87 ASN cc_start: 0.8291 (m-40) cc_final: 0.8039 (m-40) REVERT: D 88 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8299 (mmtt) REVERT: D 89 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8219 (mmmm) REVERT: E 105 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7478 (mm-30) REVERT: E 106 ASP cc_start: 0.7675 (p0) cc_final: 0.7431 (p0) REVERT: E 109 LEU cc_start: 0.9106 (mm) cc_final: 0.8837 (mt) REVERT: E 123 ASP cc_start: 0.7951 (m-30) cc_final: 0.7624 (t0) REVERT: F 53 GLU cc_start: 0.7530 (mp0) cc_final: 0.7129 (mp0) REVERT: G 30 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7339 (mtm-85) REVERT: G 90 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7631 (ttt180) REVERT: H 46 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8439 (ttmm) REVERT: H 49 LYS cc_start: 0.8535 (pttp) cc_final: 0.8174 (pttp) REVERT: H 62 MET cc_start: 0.8136 (tpp) cc_final: 0.7501 (tpp) REVERT: H 86 TYR cc_start: 0.7143 (p90) cc_final: 0.6627 (p90) REVERT: H 88 LYS cc_start: 0.8377 (mmpt) cc_final: 0.8054 (mmpt) REVERT: H 123 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8384 (tppt) outliers start: 56 outliers final: 30 residues processed: 510 average time/residue: 0.1927 time to fit residues: 132.9398 Evaluate side-chains 517 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 479 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 21 PHE Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 366 LYS 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 262 ARG Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 65 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 45 TYR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS K 392 ASN M 236 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 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 = 0.3811 r_free = 0.3811 target = 0.103832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088547 restraints weight = 55484.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090727 restraints weight = 27594.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092114 restraints weight = 16981.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092996 restraints weight = 12295.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093544 restraints weight = 10046.087| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.8195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17850 Z= 0.201 Angle : 0.933 13.709 25340 Z= 0.493 Chirality : 0.046 0.231 2858 Planarity : 0.006 0.071 2190 Dihedral : 28.546 117.413 4761 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.26 % Allowed : 37.96 % Favored : 57.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.22), residues: 1319 helix: -1.16 (0.18), residues: 687 sheet: -1.12 (1.18), residues: 20 loop : -2.06 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 395 TYR 0.054 0.003 TYR G 52 PHE 0.080 0.003 PHE K 404 TRP 0.074 0.005 TRP K 353 HIS 0.007 0.001 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00464 (17850) covalent geometry : angle 0.93337 (25340) hydrogen bonds : bond 0.04903 ( 796) hydrogen bonds : angle 4.38383 ( 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 528 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 477 time to evaluate : 0.523 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: N 17 LEU cc_start: 0.8565 (tt) cc_final: 0.8015 (mt) REVERT: K 314 MET cc_start: 0.6017 (tpt) cc_final: 0.5760 (tpt) REVERT: K 405 LEU cc_start: 0.2543 (OUTLIER) cc_final: 0.1157 (tp) REVERT: M 74 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7650 (mm) REVERT: M 141 PHE cc_start: 0.7614 (t80) cc_final: 0.7404 (m-80) REVERT: M 168 ASP cc_start: 0.8333 (t0) cc_final: 0.7802 (m-30) REVERT: M 172 LEU cc_start: 0.8124 (mm) cc_final: 0.7695 (pp) REVERT: M 295 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6040 (mt) REVERT: M 353 LYS cc_start: 0.8477 (tppt) cc_final: 0.8233 (mttm) REVERT: A 56 LYS cc_start: 0.9086 (tptp) cc_final: 0.8880 (tptp) REVERT: A 64 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8314 (mmmt) REVERT: A 68 GLN cc_start: 0.8682 (mt0) cc_final: 0.8449 (mt0) REVERT: A 69 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: A 81 ASP cc_start: 0.8379 (t0) cc_final: 0.7891 (t0) REVERT: A 83 ARG cc_start: 0.7938 (mmp-170) cc_final: 0.7420 (mmp-170) REVERT: A 93 GLN cc_start: 0.7741 (tp40) cc_final: 0.7416 (tp40) REVERT: B 31 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6794 (tptp) REVERT: B 44 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8692 (tppp) REVERT: B 80 THR cc_start: 0.8912 (t) cc_final: 0.8645 (p) REVERT: B 92 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8332 (tmm-80) REVERT: C 28 VAL cc_start: 0.9142 (t) cc_final: 0.8804 (p) REVERT: C 81 THR cc_start: 0.7926 (p) cc_final: 0.7624 (p) REVERT: D 49 LYS cc_start: 0.8553 (ptpp) cc_final: 0.8136 (ptpp) REVERT: D 82 LYS cc_start: 0.8537 (ttmm) cc_final: 0.8295 (ttmt) REVERT: D 87 ASN cc_start: 0.8235 (m-40) cc_final: 0.8010 (m-40) REVERT: D 88 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8301 (mmtt) REVERT: D 89 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8204 (mmmm) REVERT: D 111 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: E 106 ASP cc_start: 0.7665 (p0) cc_final: 0.7449 (p0) REVERT: E 123 ASP cc_start: 0.7942 (m-30) cc_final: 0.7603 (t0) REVERT: F 53 GLU cc_start: 0.7549 (mp0) cc_final: 0.7108 (mp0) REVERT: G 90 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7643 (ttt180) REVERT: H 46 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (ptmm) REVERT: H 49 LYS cc_start: 0.8591 (pttp) cc_final: 0.8221 (pttp) REVERT: H 86 TYR cc_start: 0.7159 (p90) cc_final: 0.6708 (p90) REVERT: H 88 LYS cc_start: 0.8368 (mmpt) cc_final: 0.8036 (mmpt) REVERT: H 123 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8425 (tppt) outliers start: 51 outliers final: 31 residues processed: 495 average time/residue: 0.1882 time to fit residues: 126.5532 Evaluate side-chains 517 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 478 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 21 PHE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 366 LYS 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 74 LEU Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 342 LYS 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 65 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 21 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 143 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.102859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087304 restraints weight = 55575.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089492 restraints weight = 27811.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090887 restraints weight = 17209.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.091770 restraints weight = 12526.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092324 restraints weight = 10239.368| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.8495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17850 Z= 0.216 Angle : 0.952 14.079 25340 Z= 0.505 Chirality : 0.048 0.394 2858 Planarity : 0.006 0.066 2190 Dihedral : 28.553 118.114 4759 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.01 % Allowed : 38.38 % Favored : 57.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.22), residues: 1319 helix: -1.15 (0.18), residues: 679 sheet: -0.88 (1.18), residues: 20 loop : -2.14 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 395 TYR 0.054 0.003 TYR G 52 PHE 0.077 0.003 PHE K 404 TRP 0.091 0.005 TRP K 353 HIS 0.007 0.001 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00496 (17850) covalent geometry : angle 0.95159 (25340) hydrogen bonds : bond 0.05120 ( 796) hydrogen bonds : angle 4.39014 ( 2011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.56 seconds wall clock time: 68 minutes 14.65 seconds (4094.65 seconds total)