Starting phenix.real_space_refine on Sun May 18 22:07:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2x_38021/05_2025/8x2x_38021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2x_38021/05_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_38021/05_2025/8x2x_38021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2x_38021/05_2025/8x2x_38021.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2x_38021/05_2025/8x2x_38021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2x_38021/05_2025/8x2x_38021.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.72, per 1000 atoms: 0.57 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: 4.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.98 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: 7.25 Time building geometry restraints manager: 5.17 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.140 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.005 TRP M 361 HIS 0.022 0.003 HIS D 112 PHE 0.036 0.004 PHE K 237 TYR 0.048 0.004 TYR F 98 ARG 0.013 0.001 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.17021 ( 796) hydrogen bonds : angle 6.48210 ( 2011) covalent geometry : bond 0.00777 (17850) covalent geometry : angle 1.13161 (25340) *********************** 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 : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6927 (tp30) REVERT: N 17 LEU cc_start: 0.8161 (tt) cc_final: 0.7828 (tt) REVERT: N 91 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7461 (t0) REVERT: K 223 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7472 (Cg_endo) REVERT: K 240 ASP cc_start: 0.6206 (p0) cc_final: 0.5917 (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: 0.6409 (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: 0.4072 time to fit residues: 298.7432 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 : 1.453 ------------------------------------------------------------------------------- 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 132 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 142 optimal weight: 0.7980 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 392 ASN K 401 HIS ** M 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 245 HIS M 338 HIS A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 111 HIS D 87 ASN E 55 GLN E 93 GLN G 16 GLN H 87 ASN H 98 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.102742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087610 restraints weight = 54000.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089668 restraints weight = 26935.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.091050 restraints weight = 16722.095| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3635 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= 0.206 Angle : 0.832 11.144 25340 Z= 0.463 Chirality : 0.046 0.393 2858 Planarity : 0.007 0.067 2190 Dihedral : 29.291 125.479 4780 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.02 % Allowed : 20.40 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.20), residues: 1319 helix: -2.23 (0.16), residues: 735 sheet: -1.39 (1.35), residues: 19 loop : -2.77 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 361 HIS 0.009 0.002 HIS D 112 PHE 0.015 0.002 PHE K 404 TYR 0.031 0.002 TYR G 52 ARG 0.029 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.05601 ( 796) hydrogen bonds : angle 4.38831 ( 2011) covalent geometry : bond 0.00446 (17850) covalent geometry : angle 0.83217 (25340) *********************** 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 556 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 496 time to evaluate : 1.356 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: L 35 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7509 (tm-30) REVERT: N 91 ASN cc_start: 0.8140 (t0) cc_final: 0.7923 (t0) REVERT: K 289 TYR cc_start: 0.7344 (p90) cc_final: 0.6788 (p90) REVERT: K 353 TRP cc_start: 0.8238 (m-10) cc_final: 0.7853 (m-10) REVERT: K 357 LEU cc_start: 0.7855 (mt) cc_final: 0.7546 (mt) REVERT: K 377 THR cc_start: 0.8940 (p) cc_final: 0.7734 (t) REVERT: K 379 MET cc_start: 0.6645 (mpp) cc_final: 0.5949 (mpp) REVERT: K 383 ASP cc_start: 0.7974 (t0) cc_final: 0.7214 (t0) REVERT: M 70 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4175 (tt) REVERT: M 135 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7449 (ptpp) REVERT: M 161 ASN cc_start: 0.6877 (p0) cc_final: 0.6335 (p0) REVERT: M 168 ASP cc_start: 0.7799 (t0) cc_final: 0.7119 (t0) REVERT: M 197 GLU cc_start: 0.6729 (tp30) cc_final: 0.6510 (tp30) REVERT: M 200 ILE cc_start: 0.8298 (pp) cc_final: 0.8088 (mm) REVERT: M 249 PHE cc_start: 0.7838 (t80) cc_final: 0.7476 (t80) REVERT: M 342 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8158 (pttm) REVERT: A 42 LYS cc_start: 0.6537 (tptt) cc_final: 0.6332 (tptt) REVERT: A 64 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7945 (mmmm) REVERT: A 65 LEU cc_start: 0.8225 (mm) cc_final: 0.7989 (mm) REVERT: A 81 ASP cc_start: 0.7508 (t0) cc_final: 0.7262 (t70) REVERT: A 102 SER cc_start: 0.7451 (p) cc_final: 0.7166 (p) REVERT: B 26 ILE cc_start: 0.8564 (tp) cc_final: 0.8253 (tp) REVERT: B 44 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8011 (mmmm) REVERT: B 97 LEU cc_start: 0.7864 (tp) cc_final: 0.7661 (tp) REVERT: C 28 VAL cc_start: 0.8715 (t) cc_final: 0.8386 (p) REVERT: C 52 TYR cc_start: 0.6837 (t80) cc_final: 0.6509 (t80) REVERT: C 63 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7172 (tm-30) REVERT: C 66 GLU cc_start: 0.7579 (pp20) cc_final: 0.6978 (pp20) REVERT: C 87 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5644 (pp) REVERT: D 41 SER cc_start: 0.8577 (t) cc_final: 0.8129 (t) REVERT: D 43 TYR cc_start: 0.7726 (m-80) cc_final: 0.7499 (m-80) REVERT: D 73 PHE cc_start: 0.8726 (t80) cc_final: 0.8413 (t80) REVERT: D 101 VAL cc_start: 0.8879 (t) cc_final: 0.8592 (p) REVERT: D 116 GLU cc_start: 0.7330 (tm-30) cc_final: 0.5530 (tm-30) REVERT: E 57 SER cc_start: 0.8738 (t) cc_final: 0.8419 (p) REVERT: E 76 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6456 (pm20) REVERT: F 53 GLU cc_start: 0.7411 (mp0) cc_final: 0.7061 (mp0) REVERT: F 93 GLN cc_start: 0.8530 (tp40) cc_final: 0.8315 (tp40) REVERT: H 86 TYR cc_start: 0.7017 (p90) cc_final: 0.6735 (p90) REVERT: H 88 LYS cc_start: 0.8122 (mmpt) cc_final: 0.7919 (mmpt) REVERT: H 97 ILE cc_start: 0.8741 (tp) cc_final: 0.8456 (tp) REVERT: H 123 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8202 (tppp) outliers start: 60 outliers final: 27 residues processed: 521 average time/residue: 0.3759 time to fit residues: 266.2903 Evaluate side-chains 500 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 467 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 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 135 LYS 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 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 76 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 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 116 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 138 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 301 ASN M 233 ASN M 332 GLN M 363 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.103926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.088615 restraints weight = 54812.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090785 restraints weight = 27362.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.092154 restraints weight = 16881.547| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17850 Z= 0.179 Angle : 0.794 10.951 25340 Z= 0.435 Chirality : 0.044 0.417 2858 Planarity : 0.006 0.057 2190 Dihedral : 29.001 123.098 4770 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.94 % Allowed : 22.66 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.21), residues: 1319 helix: -1.56 (0.17), residues: 709 sheet: -1.51 (1.30), residues: 19 loop : -2.49 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 247 HIS 0.011 0.001 HIS M 240 PHE 0.067 0.003 PHE M 189 TYR 0.025 0.002 TYR G 52 ARG 0.010 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 796) hydrogen bonds : angle 4.12353 ( 2011) covalent geometry : bond 0.00394 (17850) covalent geometry : angle 0.79445 (25340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 480 time to evaluate : 1.434 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: 0.8079 (tt) cc_final: 0.7742 (mt) REVERT: K 212 GLU cc_start: 0.8022 (pp20) cc_final: 0.7703 (pt0) REVERT: K 266 TYR cc_start: 0.6499 (t80) cc_final: 0.5760 (t80) REVERT: K 289 TYR cc_start: 0.7481 (p90) cc_final: 0.7092 (p90) REVERT: K 334 VAL cc_start: 0.7691 (p) cc_final: 0.7203 (p) REVERT: K 353 TRP cc_start: 0.8424 (m-10) cc_final: 0.8039 (m-10) REVERT: K 357 LEU cc_start: 0.7824 (mt) cc_final: 0.7592 (mt) REVERT: K 376 MET cc_start: 0.8207 (tpp) cc_final: 0.7968 (tpp) REVERT: K 383 ASP cc_start: 0.8008 (t0) cc_final: 0.6070 (t0) REVERT: K 386 HIS cc_start: 0.6946 (m90) cc_final: 0.6518 (m90) REVERT: K 408 ASP cc_start: 0.8640 (p0) cc_final: 0.8358 (p0) REVERT: K 409 ILE cc_start: 0.7554 (mt) cc_final: 0.7221 (mp) REVERT: M 70 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4044 (tt) REVERT: M 74 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7560 (mm) REVERT: M 161 ASN cc_start: 0.6823 (p0) cc_final: 0.6434 (p0) REVERT: M 167 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7318 (ttp80) REVERT: M 169 GLU cc_start: 0.6164 (pp20) cc_final: 0.5167 (tm-30) REVERT: M 189 PHE cc_start: 0.7737 (m-80) cc_final: 0.7374 (m-80) REVERT: M 224 LEU cc_start: 0.8224 (pt) cc_final: 0.7803 (mp) REVERT: M 249 PHE cc_start: 0.7838 (t80) cc_final: 0.7547 (t80) REVERT: M 267 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6291 (mt) REVERT: M 342 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8272 (pttm) REVERT: A 81 ASP cc_start: 0.7742 (t0) cc_final: 0.7451 (t70) REVERT: A 83 ARG cc_start: 0.7642 (mmp80) cc_final: 0.7090 (mmp80) REVERT: A 124 ILE cc_start: 0.8208 (mm) cc_final: 0.7930 (mm) REVERT: B 35 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7454 (ttt90) REVERT: B 36 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7516 (mtm180) REVERT: B 44 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8084 (mmmm) REVERT: B 79 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7962 (ttmt) REVERT: C 28 VAL cc_start: 0.8950 (t) cc_final: 0.8615 (p) REVERT: C 30 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7629 (mtp85) REVERT: C 52 TYR cc_start: 0.6934 (t80) cc_final: 0.6633 (t80) REVERT: C 87 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6580 (pp) REVERT: D 86 TYR cc_start: 0.6918 (p90) cc_final: 0.6688 (p90) REVERT: D 101 VAL cc_start: 0.8941 (t) cc_final: 0.8640 (p) REVERT: D 111 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7739 (ptpp) REVERT: E 57 SER cc_start: 0.8774 (t) cc_final: 0.8379 (p) REVERT: E 106 ASP cc_start: 0.7767 (p0) cc_final: 0.7535 (p0) REVERT: F 53 GLU cc_start: 0.7354 (mp0) cc_final: 0.7043 (mp0) REVERT: F 91 LYS cc_start: 0.8637 (tptp) cc_final: 0.8319 (tptp) REVERT: G 21 ARG cc_start: 0.6677 (mtm-85) cc_final: 0.6444 (mtt90) REVERT: G 81 THR cc_start: 0.7880 (p) cc_final: 0.7625 (p) REVERT: G 94 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6374 (tm-30) REVERT: H 62 MET cc_start: 0.8020 (mmm) cc_final: 0.7771 (tpp) REVERT: H 88 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7977 (mmpt) REVERT: H 97 ILE cc_start: 0.8941 (tp) cc_final: 0.8670 (tp) REVERT: H 123 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8326 (tppp) outliers start: 71 outliers final: 33 residues processed: 509 average time/residue: 0.3824 time to fit residues: 262.7981 Evaluate side-chains 501 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 462 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 305 ILE 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 267 LEU Chi-restraints excluded: chain M residue 332 GLN 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 79 LYS Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 95 LEU 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 E residue 46 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 98 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 41 SER Chi-restraints excluded: chain H residue 98 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 107 ASN ** K 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 175 GLN ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086510 restraints weight = 54373.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.088621 restraints weight = 27324.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089969 restraints weight = 16933.272| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5944 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= 0.223 Angle : 0.833 12.770 25340 Z= 0.455 Chirality : 0.046 0.459 2858 Planarity : 0.006 0.059 2190 Dihedral : 28.854 125.792 4770 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.69 % Allowed : 25.33 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.22), residues: 1319 helix: -1.33 (0.18), residues: 717 sheet: -1.30 (1.19), residues: 20 loop : -2.40 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 247 HIS 0.011 0.002 HIS D 112 PHE 0.040 0.003 PHE M 189 TYR 0.035 0.002 TYR G 52 ARG 0.011 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.05367 ( 796) hydrogen bonds : angle 4.14288 ( 2011) covalent geometry : bond 0.00502 (17850) covalent geometry : angle 0.83339 (25340) *********************** 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 575 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 495 time to evaluate : 1.306 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: N 17 LEU cc_start: 0.8387 (tt) cc_final: 0.7981 (mt) REVERT: K 177 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6405 (tp) REVERT: K 213 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8012 (mmm160) REVERT: K 266 TYR cc_start: 0.6457 (t80) cc_final: 0.5661 (t80) REVERT: K 289 TYR cc_start: 0.7660 (p90) cc_final: 0.7332 (p90) REVERT: K 344 LEU cc_start: 0.7971 (tp) cc_final: 0.7699 (mm) REVERT: K 353 TRP cc_start: 0.8462 (m-10) cc_final: 0.8103 (m-10) REVERT: K 377 THR cc_start: 0.8551 (p) cc_final: 0.8310 (p) REVERT: K 383 ASP cc_start: 0.7980 (t0) cc_final: 0.6745 (t0) REVERT: M 70 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.4261 (tt) REVERT: M 74 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7419 (mm) REVERT: M 161 ASN cc_start: 0.6845 (p0) cc_final: 0.6538 (p0) REVERT: M 169 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5500 (tm-30) REVERT: M 189 PHE cc_start: 0.7963 (m-80) cc_final: 0.7261 (m-80) REVERT: M 215 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7074 (tt) REVERT: M 224 LEU cc_start: 0.8243 (pt) cc_final: 0.7848 (mp) REVERT: M 267 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6387 (mt) REVERT: M 289 TYR cc_start: 0.6417 (m-10) cc_final: 0.6200 (m-10) REVERT: A 64 LYS cc_start: 0.8422 (mmmm) cc_final: 0.7876 (mmmm) REVERT: A 69 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: A 81 ASP cc_start: 0.8186 (t0) cc_final: 0.7692 (t0) REVERT: A 93 GLN cc_start: 0.7877 (tp40) cc_final: 0.7517 (tp40) REVERT: B 25 ASN cc_start: 0.8136 (t0) cc_final: 0.7900 (t0) REVERT: B 35 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7792 (tpt170) REVERT: B 39 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7361 (tpp-160) REVERT: B 79 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: C 28 VAL cc_start: 0.9107 (t) cc_final: 0.8799 (p) REVERT: C 30 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7765 (mtp85) REVERT: C 36 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8198 (mmtt) REVERT: C 48 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7699 (ptmm) REVERT: C 66 GLU cc_start: 0.7388 (pp20) cc_final: 0.7071 (pp20) REVERT: C 79 ARG cc_start: 0.6459 (pmm150) cc_final: 0.5914 (ptp90) REVERT: C 87 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6900 (pp) REVERT: C 95 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8160 (tp) REVERT: D 86 TYR cc_start: 0.6916 (p90) cc_final: 0.6578 (p90) REVERT: E 45 THR cc_start: 0.7802 (t) cc_final: 0.7592 (p) REVERT: E 49 ARG cc_start: 0.8366 (ptp-110) cc_final: 0.8158 (ptp-110) REVERT: E 57 SER cc_start: 0.8667 (t) cc_final: 0.8434 (p) REVERT: E 73 GLU cc_start: 0.5827 (tp30) cc_final: 0.5623 (tp30) REVERT: E 106 ASP cc_start: 0.7872 (p0) cc_final: 0.7472 (p0) REVERT: F 29 ILE cc_start: 0.8215 (tt) cc_final: 0.7979 (pt) REVERT: F 34 ILE cc_start: 0.8953 (mp) cc_final: 0.8737 (mm) REVERT: F 39 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7828 (mmt90) REVERT: F 53 GLU cc_start: 0.7475 (mp0) cc_final: 0.7010 (mp0) REVERT: G 30 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.7024 (ttm110) REVERT: G 57 LEU cc_start: 0.8686 (tt) cc_final: 0.8460 (tp) REVERT: G 93 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: H 62 MET cc_start: 0.7954 (mmm) cc_final: 0.7617 (tpp) REVERT: H 123 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8389 (tppp) outliers start: 80 outliers final: 46 residues processed: 530 average time/residue: 0.3824 time to fit residues: 275.0670 Evaluate side-chains 537 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 480 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 N residue 89 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 268 VAL 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 379 MET 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 169 GLU Chi-restraints excluded: chain M residue 202 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 342 LYS 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 54 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 95 LEU 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 E residue 46 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 93 ASP 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 58 SER Chi-restraints excluded: chain H residue 104 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 0.0010 chunk 51 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 120 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.102786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087314 restraints weight = 55254.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089440 restraints weight = 27655.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090806 restraints weight = 16989.859| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17850 Z= 0.189 Angle : 0.814 12.116 25340 Z= 0.443 Chirality : 0.044 0.365 2858 Planarity : 0.005 0.059 2190 Dihedral : 28.805 123.806 4770 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.27 % Allowed : 29.35 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.22), residues: 1319 helix: -1.14 (0.18), residues: 721 sheet: -1.40 (1.21), residues: 20 loop : -2.51 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 247 HIS 0.006 0.001 HIS M 240 PHE 0.030 0.003 PHE K 323 TYR 0.040 0.002 TYR G 52 ARG 0.008 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 796) hydrogen bonds : angle 4.11773 ( 2011) covalent geometry : bond 0.00425 (17850) covalent geometry : angle 0.81407 (25340) *********************** 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 578 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 503 time to evaluate : 1.459 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: N 17 LEU cc_start: 0.8378 (tt) cc_final: 0.7938 (mt) REVERT: N 26 GLU cc_start: 0.7844 (mp0) cc_final: 0.7620 (mp0) REVERT: K 213 ARG cc_start: 0.8283 (mmm160) cc_final: 0.8040 (mmm160) REVERT: K 227 GLU cc_start: 0.7642 (mp0) cc_final: 0.7407 (mp0) REVERT: K 236 PHE cc_start: 0.7197 (m-80) cc_final: 0.6952 (m-10) REVERT: K 238 GLU cc_start: 0.6772 (pp20) cc_final: 0.6503 (pp20) REVERT: K 266 TYR cc_start: 0.6332 (t80) cc_final: 0.5428 (t80) REVERT: K 272 LEU cc_start: 0.8129 (tp) cc_final: 0.7817 (tp) REVERT: K 314 MET cc_start: 0.5921 (tpt) cc_final: 0.5573 (tpt) REVERT: K 328 SER cc_start: 0.8873 (m) cc_final: 0.8281 (t) REVERT: K 352 TYR cc_start: 0.7105 (t80) cc_final: 0.6816 (t80) REVERT: K 353 TRP cc_start: 0.8439 (m-10) cc_final: 0.8063 (m-10) REVERT: K 377 THR cc_start: 0.8338 (p) cc_final: 0.8017 (p) REVERT: M 70 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4217 (tt) REVERT: M 74 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7534 (mt) REVERT: M 141 PHE cc_start: 0.7592 (t80) cc_final: 0.7356 (m-80) REVERT: M 161 ASN cc_start: 0.6995 (p0) cc_final: 0.6789 (p0) REVERT: M 215 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7068 (tt) REVERT: M 262 ARG cc_start: 0.7063 (tmm-80) cc_final: 0.6704 (ttp-170) REVERT: M 267 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6610 (mt) REVERT: M 339 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7573 (tp40) REVERT: M 342 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8300 (pttm) REVERT: A 69 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.7684 (mtm-85) REVERT: A 81 ASP cc_start: 0.8240 (t0) cc_final: 0.7907 (t0) REVERT: A 93 GLN cc_start: 0.7687 (tp40) cc_final: 0.7305 (tp40) REVERT: A 128 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8366 (mtm-85) REVERT: B 31 LYS cc_start: 0.8239 (tptp) cc_final: 0.8037 (tptp) REVERT: B 39 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7408 (tpp-160) REVERT: B 65 VAL cc_start: 0.8620 (m) cc_final: 0.8329 (p) REVERT: B 92 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7310 (tmm-80) REVERT: C 28 VAL cc_start: 0.9202 (t) cc_final: 0.8791 (p) REVERT: C 31 ILE cc_start: 0.8915 (mm) cc_final: 0.8706 (mt) REVERT: C 66 GLU cc_start: 0.7080 (pp20) cc_final: 0.6424 (pp20) REVERT: C 79 ARG cc_start: 0.6288 (pmm150) cc_final: 0.5940 (ptp90) REVERT: C 87 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6956 (pp) REVERT: C 92 ASP cc_start: 0.8289 (t0) cc_final: 0.8045 (t0) REVERT: D 116 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 45 THR cc_start: 0.7942 (t) cc_final: 0.7708 (p) REVERT: E 49 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8210 (ptp-110) REVERT: E 106 ASP cc_start: 0.7782 (p0) cc_final: 0.7441 (p0) REVERT: F 53 GLU cc_start: 0.7465 (mp0) cc_final: 0.7041 (mp0) REVERT: G 37 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7559 (mmm-85) REVERT: G 57 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (tp) REVERT: G 93 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: H 62 MET cc_start: 0.8163 (mmm) cc_final: 0.7832 (tpp) REVERT: H 76 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7919 (tt) REVERT: H 88 LYS cc_start: 0.8423 (mmpt) cc_final: 0.8118 (mmpt) REVERT: H 108 GLU cc_start: 0.6740 (pm20) cc_final: 0.6505 (pp20) REVERT: H 123 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8383 (tppp) outliers start: 75 outliers final: 42 residues processed: 537 average time/residue: 0.3769 time to fit residues: 275.5423 Evaluate side-chains 544 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 492 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 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 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 202 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain M residue 362 ILE 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 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 54 VAL 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 77 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 95 LEU 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 E residue 46 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 76 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 107 ASN ** 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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.102157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.086880 restraints weight = 54715.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088939 restraints weight = 27626.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090265 restraints weight = 17199.027| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17850 Z= 0.203 Angle : 0.833 11.891 25340 Z= 0.451 Chirality : 0.045 0.202 2858 Planarity : 0.005 0.066 2190 Dihedral : 28.731 125.889 4766 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 6.94 % Allowed : 31.02 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.22), residues: 1319 helix: -1.03 (0.18), residues: 710 sheet: -2.25 (1.02), residues: 26 loop : -2.35 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 247 HIS 0.006 0.001 HIS M 65 PHE 0.040 0.003 PHE K 404 TYR 0.041 0.002 TYR G 52 ARG 0.010 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 796) hydrogen bonds : angle 4.13597 ( 2011) covalent geometry : bond 0.00460 (17850) covalent geometry : angle 0.83308 (25340) *********************** 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 585 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 502 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8478 (tt) cc_final: 0.8011 (mt) REVERT: K 236 PHE cc_start: 0.7271 (m-80) cc_final: 0.7065 (m-10) REVERT: K 237 PHE cc_start: 0.6650 (m-10) cc_final: 0.6274 (m-10) REVERT: K 238 GLU cc_start: 0.6949 (pp20) cc_final: 0.6559 (pp20) REVERT: K 272 LEU cc_start: 0.8190 (tp) cc_final: 0.7887 (tp) REVERT: K 352 TYR cc_start: 0.7131 (t80) cc_final: 0.6828 (t80) REVERT: K 377 THR cc_start: 0.8249 (p) cc_final: 0.7707 (p) REVERT: K 389 LYS cc_start: 0.8759 (pttp) cc_final: 0.8507 (pttm) REVERT: K 408 ASP cc_start: 0.8532 (p0) cc_final: 0.8317 (p0) REVERT: M 70 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4059 (tt) REVERT: M 74 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7667 (mm) REVERT: M 162 TYR cc_start: 0.6228 (t80) cc_final: 0.5923 (t80) REVERT: M 168 ASP cc_start: 0.8529 (t0) cc_final: 0.8224 (m-30) REVERT: M 175 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7534 (mm-40) REVERT: M 215 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7368 (tt) REVERT: M 267 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6625 (mt) REVERT: A 81 ASP cc_start: 0.8196 (t0) cc_final: 0.7897 (t0) REVERT: A 128 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8423 (mtm-85) REVERT: B 39 ARG cc_start: 0.7648 (tpp80) cc_final: 0.7371 (tpp-160) REVERT: B 65 VAL cc_start: 0.8606 (m) cc_final: 0.8359 (p) REVERT: B 68 ASP cc_start: 0.7664 (p0) cc_final: 0.7416 (p0) REVERT: B 92 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8201 (tmm-80) REVERT: C 28 VAL cc_start: 0.9183 (t) cc_final: 0.8863 (p) REVERT: C 63 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7396 (tp30) REVERT: C 92 ASP cc_start: 0.8297 (t0) cc_final: 0.8039 (t0) REVERT: D 59 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7900 (tp40) REVERT: D 89 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8234 (mmmm) REVERT: E 50 GLU cc_start: 0.7804 (pt0) cc_final: 0.7595 (pt0) REVERT: E 106 ASP cc_start: 0.7789 (p0) cc_final: 0.7418 (p0) REVERT: E 121 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8886 (ttpp) REVERT: F 53 GLU cc_start: 0.7355 (mp0) cc_final: 0.7108 (mp0) REVERT: G 30 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7450 (mtp85) REVERT: G 57 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8300 (tp) REVERT: G 93 ASP cc_start: 0.8303 (m-30) cc_final: 0.8000 (m-30) REVERT: H 86 TYR cc_start: 0.7380 (p90) cc_final: 0.7145 (p90) REVERT: H 88 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8029 (mmpt) REVERT: H 108 GLU cc_start: 0.6805 (pm20) cc_final: 0.6419 (pp20) REVERT: H 123 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8368 (tppp) outliers start: 83 outliers final: 46 residues processed: 534 average time/residue: 0.3842 time to fit residues: 279.0106 Evaluate side-chains 529 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 476 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 268 VAL Chi-restraints excluded: chain K residue 287 VAL 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 369 THR 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 202 GLU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 54 VAL 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 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 E residue 64 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 108 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.103320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087900 restraints weight = 55274.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089960 restraints weight = 27911.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091328 restraints weight = 17356.442| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17850 Z= 0.186 Angle : 0.865 13.092 25340 Z= 0.460 Chirality : 0.045 0.335 2858 Planarity : 0.006 0.068 2190 Dihedral : 28.667 123.649 4764 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.93 % Allowed : 34.45 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.22), residues: 1319 helix: -1.08 (0.18), residues: 713 sheet: -1.54 (1.19), residues: 20 loop : -2.39 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 247 HIS 0.012 0.001 HIS M 338 PHE 0.050 0.003 PHE M 189 TYR 0.048 0.002 TYR G 52 ARG 0.015 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 796) hydrogen bonds : angle 4.22078 ( 2011) covalent geometry : bond 0.00425 (17850) covalent geometry : angle 0.86505 (25340) *********************** 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 547 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 488 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8477 (tt) cc_final: 0.7980 (mt) REVERT: N 105 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5774 (mm-30) REVERT: K 212 GLU cc_start: 0.7569 (pt0) cc_final: 0.7240 (pt0) REVERT: K 236 PHE cc_start: 0.7374 (m-80) cc_final: 0.7105 (m-10) REVERT: K 238 GLU cc_start: 0.6906 (pp20) cc_final: 0.6456 (pp20) REVERT: K 266 TYR cc_start: 0.6625 (t80) cc_final: 0.5584 (t80) REVERT: K 272 LEU cc_start: 0.8211 (tp) cc_final: 0.7914 (tp) REVERT: K 352 TYR cc_start: 0.7169 (t80) cc_final: 0.6891 (t80) REVERT: K 377 THR cc_start: 0.8261 (p) cc_final: 0.7642 (p) REVERT: K 389 LYS cc_start: 0.8764 (pttp) cc_final: 0.8493 (pttm) REVERT: M 70 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.3937 (tt) REVERT: M 74 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7291 (mm) REVERT: M 141 PHE cc_start: 0.7528 (t80) cc_final: 0.7223 (m-80) REVERT: M 162 TYR cc_start: 0.6304 (t80) cc_final: 0.6032 (t80) REVERT: M 167 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7609 (ttp80) REVERT: M 168 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: M 175 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7493 (mm-40) REVERT: M 215 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7440 (tt) REVERT: M 220 LEU cc_start: 0.6279 (mt) cc_final: 0.5758 (mt) REVERT: M 289 TYR cc_start: 0.6530 (m-10) cc_final: 0.6063 (m-10) REVERT: M 342 LYS cc_start: 0.8480 (pttp) cc_final: 0.8179 (mtmm) REVERT: A 41 TYR cc_start: 0.7976 (m-10) cc_final: 0.7570 (m-10) REVERT: A 69 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: A 81 ASP cc_start: 0.8235 (t0) cc_final: 0.7761 (t0) REVERT: A 93 GLN cc_start: 0.7618 (tp40) cc_final: 0.7348 (tp40) REVERT: A 128 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8393 (mtm-85) REVERT: B 31 LYS cc_start: 0.8040 (tptp) cc_final: 0.7781 (tptp) REVERT: B 51 TYR cc_start: 0.8263 (m-10) cc_final: 0.7956 (m-10) REVERT: B 65 VAL cc_start: 0.8611 (m) cc_final: 0.8378 (p) REVERT: B 79 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7701 (ptmt) REVERT: B 92 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8191 (tmm-80) REVERT: C 28 VAL cc_start: 0.9235 (t) cc_final: 0.8875 (p) REVERT: C 30 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: D 89 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8251 (mmmm) REVERT: D 123 LYS cc_start: 0.8142 (ptmm) cc_final: 0.7843 (pttp) REVERT: E 106 ASP cc_start: 0.7825 (p0) cc_final: 0.6252 (p0) REVERT: E 121 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8724 (ttpp) REVERT: F 67 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7374 (mtm-85) REVERT: G 30 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7659 (mtm-85) REVERT: H 49 LYS cc_start: 0.8596 (pttp) cc_final: 0.8225 (pttp) REVERT: H 62 MET cc_start: 0.8015 (tpp) cc_final: 0.7665 (tpp) REVERT: H 83 LEU cc_start: 0.8873 (tp) cc_final: 0.8672 (tp) REVERT: H 88 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8095 (mmpt) REVERT: H 123 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8341 (tppt) outliers start: 59 outliers final: 36 residues processed: 510 average time/residue: 0.3856 time to fit residues: 265.5782 Evaluate side-chains 514 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 472 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 287 VAL 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 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 168 ASP Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU 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 17 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE 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 90 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 141 optimal weight: 0.0870 chunk 123 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 91 ASN ** K 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.104922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089807 restraints weight = 55844.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091692 restraints weight = 29493.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092953 restraints weight = 19049.140| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.7833 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= 0.182 Angle : 0.869 12.367 25340 Z= 0.464 Chirality : 0.045 0.298 2858 Planarity : 0.006 0.123 2190 Dihedral : 28.608 124.449 4761 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.18 % Allowed : 35.37 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1319 helix: -1.08 (0.18), residues: 699 sheet: -2.63 (0.94), residues: 26 loop : -2.23 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 353 HIS 0.014 0.002 HIS M 338 PHE 0.037 0.002 PHE N 95 TYR 0.049 0.002 TYR G 52 ARG 0.015 0.001 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 796) hydrogen bonds : angle 4.26764 ( 2011) covalent geometry : bond 0.00414 (17850) covalent geometry : angle 0.86943 (25340) *********************** 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 546 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 484 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8464 (tt) cc_final: 0.7999 (mt) REVERT: K 238 GLU cc_start: 0.6797 (pp20) cc_final: 0.6595 (pp20) REVERT: K 272 LEU cc_start: 0.8143 (tp) cc_final: 0.7868 (tp) REVERT: K 352 TYR cc_start: 0.7169 (t80) cc_final: 0.6842 (t80) REVERT: K 377 THR cc_start: 0.7984 (p) cc_final: 0.7769 (p) REVERT: K 389 LYS cc_start: 0.8699 (pttp) cc_final: 0.8436 (pttm) REVERT: M 70 LEU cc_start: 0.4377 (OUTLIER) cc_final: 0.3612 (tt) REVERT: M 74 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7260 (mm) REVERT: M 141 PHE cc_start: 0.7599 (t80) cc_final: 0.7297 (m-80) REVERT: M 168 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: M 175 GLN cc_start: 0.7668 (tp-100) cc_final: 0.7324 (mm-40) REVERT: M 215 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7498 (tt) REVERT: M 295 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5792 (mt) REVERT: A 64 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8018 (mmmm) REVERT: A 69 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: A 81 ASP cc_start: 0.8120 (t0) cc_final: 0.7699 (t0) REVERT: A 116 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7747 (ptp-170) REVERT: A 128 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8248 (mtm-85) REVERT: B 31 LYS cc_start: 0.8020 (tptp) cc_final: 0.7712 (tptp) REVERT: B 51 TYR cc_start: 0.8303 (m-10) cc_final: 0.7859 (m-10) REVERT: B 65 VAL cc_start: 0.8653 (m) cc_final: 0.8406 (p) REVERT: B 92 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8237 (tmm-80) REVERT: C 28 VAL cc_start: 0.9127 (t) cc_final: 0.8751 (p) REVERT: C 30 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7772 (mtp-110) REVERT: D 89 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8244 (mmmm) REVERT: D 123 LYS cc_start: 0.8114 (ptmm) cc_final: 0.7864 (pttt) REVERT: E 63 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8683 (mmt-90) REVERT: E 121 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8730 (ttpp) REVERT: F 46 ILE cc_start: 0.8368 (pp) cc_final: 0.8161 (pp) REVERT: F 67 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7492 (mtm-85) REVERT: G 30 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7508 (mtm-85) REVERT: H 49 LYS cc_start: 0.8530 (pttp) cc_final: 0.8118 (pttp) REVERT: H 60 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8636 (mmmm) REVERT: H 86 TYR cc_start: 0.7312 (p90) cc_final: 0.6700 (p90) REVERT: H 88 LYS cc_start: 0.8376 (mmpt) cc_final: 0.8101 (mmpt) REVERT: H 123 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8367 (tppt) outliers start: 62 outliers final: 37 residues processed: 508 average time/residue: 0.3868 time to fit residues: 266.9295 Evaluate side-chains 516 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 471 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 VAL 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 369 THR 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 168 ASP Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 295 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 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU 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 17 SER Chi-restraints excluded: chain C residue 51 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 E residue 63 ARG Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN M 236 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** A 113 HIS ** 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 112 HIS ** 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 = 0.3812 r_free = 0.3812 target = 0.103799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088364 restraints weight = 55481.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090487 restraints weight = 27944.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091838 restraints weight = 17373.333| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.8108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17850 Z= 0.195 Angle : 0.891 12.756 25340 Z= 0.473 Chirality : 0.046 0.288 2858 Planarity : 0.006 0.099 2190 Dihedral : 28.561 121.575 4761 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.43 % Allowed : 36.87 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.22), residues: 1319 helix: -1.13 (0.18), residues: 707 sheet: -2.43 (0.95), residues: 26 loop : -2.30 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP K 353 HIS 0.008 0.001 HIS M 240 PHE 0.037 0.003 PHE K 323 TYR 0.048 0.003 TYR K 175 ARG 0.010 0.001 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 796) hydrogen bonds : angle 4.29056 ( 2011) covalent geometry : bond 0.00449 (17850) covalent geometry : angle 0.89068 (25340) *********************** 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 533 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 480 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8559 (tt) cc_final: 0.8034 (mt) REVERT: K 243 LYS cc_start: 0.8021 (tptp) cc_final: 0.7677 (tptt) REVERT: K 272 LEU cc_start: 0.8263 (tp) cc_final: 0.7951 (tp) REVERT: K 377 THR cc_start: 0.8132 (p) cc_final: 0.7896 (p) REVERT: K 389 LYS cc_start: 0.8733 (pttp) cc_final: 0.8500 (pttm) REVERT: M 70 LEU cc_start: 0.4263 (OUTLIER) cc_final: 0.3571 (tt) REVERT: M 74 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.7588 (mm) REVERT: M 141 PHE cc_start: 0.7692 (t80) cc_final: 0.7369 (m-80) REVERT: M 167 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7605 (ttp80) REVERT: M 168 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: M 175 GLN cc_start: 0.7649 (tp-100) cc_final: 0.7288 (mm-40) REVERT: M 215 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7697 (tt) REVERT: M 295 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5866 (mt) REVERT: A 64 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8000 (mmmm) REVERT: A 81 ASP cc_start: 0.8328 (t0) cc_final: 0.7815 (t0) REVERT: A 128 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8265 (mtm-85) REVERT: B 31 LYS cc_start: 0.8138 (tptp) cc_final: 0.7933 (tptp) REVERT: B 36 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7818 (mtm-85) REVERT: B 65 VAL cc_start: 0.8671 (m) cc_final: 0.8440 (p) REVERT: B 92 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8266 (tmm-80) REVERT: C 28 VAL cc_start: 0.9184 (t) cc_final: 0.8787 (p) REVERT: C 48 LYS cc_start: 0.8227 (pptt) cc_final: 0.7016 (pptt) REVERT: D 123 LYS cc_start: 0.8249 (ptmm) cc_final: 0.7988 (pttp) REVERT: E 45 THR cc_start: 0.8092 (t) cc_final: 0.7821 (p) REVERT: E 121 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8821 (ttpp) REVERT: F 27 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: F 88 TYR cc_start: 0.8447 (m-80) cc_final: 0.8226 (m-80) REVERT: G 30 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7615 (mtm-85) REVERT: G 90 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7487 (ttt90) REVERT: H 46 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8645 (ttmm) REVERT: H 49 LYS cc_start: 0.8599 (pttp) cc_final: 0.8176 (pttp) REVERT: H 86 TYR cc_start: 0.7426 (p90) cc_final: 0.6985 (p90) REVERT: H 88 LYS cc_start: 0.8359 (mmpt) cc_final: 0.8091 (mmpt) REVERT: H 123 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8359 (tppt) outliers start: 53 outliers final: 36 residues processed: 501 average time/residue: 0.3803 time to fit residues: 258.0598 Evaluate side-chains 519 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 475 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain K residue 308 LEU 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 369 THR 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 133 TYR Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 295 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 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU 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 51 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 76 ILE Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 50 ILE 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 96 GLU Chi-restraints excluded: chain H residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 131 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 173 ASN M 236 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.103135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087675 restraints weight = 55634.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089778 restraints weight = 27928.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.091140 restraints weight = 17391.268| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17850 Z= 0.204 Angle : 0.919 13.752 25340 Z= 0.487 Chirality : 0.046 0.272 2858 Planarity : 0.006 0.079 2190 Dihedral : 28.534 119.761 4761 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.60 % Allowed : 38.21 % Favored : 58.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.22), residues: 1319 helix: -1.17 (0.18), residues: 696 sheet: -2.46 (0.90), residues: 26 loop : -2.26 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP K 353 HIS 0.008 0.001 HIS M 240 PHE 0.039 0.002 PHE K 323 TYR 0.057 0.003 TYR G 52 ARG 0.010 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 796) hydrogen bonds : angle 4.36938 ( 2011) covalent geometry : bond 0.00472 (17850) covalent geometry : angle 0.91871 (25340) ********************** 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: 43 poor density : 485 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8619 (tt) cc_final: 0.8083 (mt) REVERT: K 209 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7010 (mmmt) REVERT: K 272 LEU cc_start: 0.8216 (tp) cc_final: 0.7922 (tp) REVERT: K 377 THR cc_start: 0.8097 (p) cc_final: 0.7864 (p) REVERT: K 389 LYS cc_start: 0.8761 (pttp) cc_final: 0.8512 (pttm) REVERT: M 70 LEU cc_start: 0.4237 (OUTLIER) cc_final: 0.3540 (tt) REVERT: M 74 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.7567 (mm) REVERT: M 141 PHE cc_start: 0.7771 (t80) cc_final: 0.7408 (m-80) REVERT: M 167 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7508 (ttp80) REVERT: M 168 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: M 175 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7283 (mm-40) REVERT: M 215 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7767 (tt) REVERT: M 295 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5751 (mt) REVERT: A 64 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8091 (mmmt) REVERT: A 81 ASP cc_start: 0.8343 (t0) cc_final: 0.7866 (t0) REVERT: B 31 LYS cc_start: 0.8030 (tptp) cc_final: 0.7693 (tptp) REVERT: B 51 TYR cc_start: 0.8215 (m-10) cc_final: 0.7790 (m-10) REVERT: B 65 VAL cc_start: 0.8653 (m) cc_final: 0.8441 (p) REVERT: B 92 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8231 (tmm-80) REVERT: C 28 VAL cc_start: 0.9152 (t) cc_final: 0.8713 (p) REVERT: C 36 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8334 (mmmt) REVERT: C 48 LYS cc_start: 0.8214 (pptt) cc_final: 0.8001 (tptt) REVERT: C 105 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8738 (p) REVERT: E 121 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8848 (tttm) REVERT: G 30 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7871 (mtm-85) REVERT: H 38 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6706 (tm-30) REVERT: H 86 TYR cc_start: 0.7515 (p90) cc_final: 0.7097 (p90) REVERT: H 88 LYS cc_start: 0.8441 (mmpt) cc_final: 0.8015 (mmpt) REVERT: H 89 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7992 (mmmm) REVERT: H 123 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8343 (tppt) outliers start: 43 outliers final: 29 residues processed: 498 average time/residue: 0.4067 time to fit residues: 278.4822 Evaluate side-chains 510 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 473 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 369 THR 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 133 TYR Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 58 LEU 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 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 E residue 121 LYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** A 68 GLN A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 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 = 0.3816 r_free = 0.3816 target = 0.104097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088515 restraints weight = 55738.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090644 restraints weight = 28201.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.092025 restraints weight = 17634.444| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.8588 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= 0.196 Angle : 0.943 13.450 25340 Z= 0.496 Chirality : 0.046 0.264 2858 Planarity : 0.006 0.094 2190 Dihedral : 28.516 119.288 4761 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.93 % Allowed : 38.96 % Favored : 57.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.22), residues: 1319 helix: -1.20 (0.18), residues: 706 sheet: -1.24 (1.11), residues: 20 loop : -2.29 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.004 TRP K 353 HIS 0.007 0.001 HIS M 240 PHE 0.031 0.002 PHE K 323 TYR 0.053 0.003 TYR K 175 ARG 0.014 0.001 ARG G 79 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 796) hydrogen bonds : angle 4.40166 ( 2011) covalent geometry : bond 0.00453 (17850) covalent geometry : angle 0.94310 (25340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6792.92 seconds wall clock time: 118 minutes 52.10 seconds (7132.10 seconds total)