Starting phenix.real_space_refine on Sun Jun 15 16:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2x_38021/06_2025/8x2x_38021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2x_38021/06_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_38021/06_2025/8x2x_38021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2x_38021/06_2025/8x2x_38021.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2x_38021/06_2025/8x2x_38021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2x_38021/06_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-5710/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: 10.77, per 1000 atoms: 0.64 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: 4.60 Conformation dependent library (CDL) restraints added in 1.6 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: 7.60 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: 7.14 Time building geometry restraints manager: 5.36 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: 3.430 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: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 47.270 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 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:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.920 ------------------------------------------------------------------------------- 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 : 1.587 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: 0.4672 time to fit residues: 346.2017 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 : 1.648 ------------------------------------------------------------------------------- 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 = 0.102740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.087699 restraints weight = 53996.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089712 restraints weight = 27260.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.091089 restraints weight = 17002.004| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17850 Z= 0.207 Angle : 0.832 11.141 25340 Z= 0.463 Chirality : 0.046 0.393 2858 Planarity : 0.007 0.067 2190 Dihedral : 29.290 125.473 4780 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.02 % Allowed : 20.32 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (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: -1.38 (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 4.38798 ( 2011) covalent geometry : bond 0.00447 (17850) covalent geometry : angle 0.83233 (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 : 1.366 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: 0.7718 (tm-30) cc_final: 0.7505 (tm-30) REVERT: N 91 ASN cc_start: 0.8133 (t0) cc_final: 0.7917 (t0) REVERT: K 289 TYR cc_start: 0.7341 (p90) cc_final: 0.6783 (p90) REVERT: K 353 TRP cc_start: 0.8238 (m-10) cc_final: 0.7852 (m-10) REVERT: K 357 LEU cc_start: 0.7855 (mt) cc_final: 0.7546 (mt) REVERT: K 377 THR cc_start: 0.8939 (p) cc_final: 0.7733 (t) REVERT: K 379 MET cc_start: 0.6644 (mpp) cc_final: 0.5953 (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: 0.4176 (tt) REVERT: M 135 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7446 (ptpp) REVERT: M 161 ASN cc_start: 0.6868 (p0) cc_final: 0.6327 (p0) REVERT: M 168 ASP cc_start: 0.7803 (t0) cc_final: 0.7121 (t0) REVERT: M 197 GLU cc_start: 0.6720 (tp30) cc_final: 0.6503 (tp30) REVERT: M 200 ILE cc_start: 0.8293 (pp) cc_final: 0.8083 (mm) REVERT: M 249 PHE cc_start: 0.7837 (t80) cc_final: 0.7472 (t80) REVERT: M 342 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8156 (pttm) REVERT: A 42 LYS cc_start: 0.6536 (tptt) cc_final: 0.6332 (tptt) REVERT: A 64 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7943 (mmmm) REVERT: A 65 LEU cc_start: 0.8225 (mm) cc_final: 0.7989 (mm) REVERT: A 81 ASP cc_start: 0.7500 (t0) cc_final: 0.7261 (t70) REVERT: A 102 SER cc_start: 0.7451 (p) cc_final: 0.7172 (p) REVERT: B 26 ILE cc_start: 0.8561 (tp) cc_final: 0.8251 (tp) REVERT: B 44 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8010 (mmmm) REVERT: B 97 LEU cc_start: 0.7862 (tp) cc_final: 0.7661 (tp) REVERT: C 28 VAL cc_start: 0.8715 (t) cc_final: 0.8385 (p) REVERT: C 52 TYR cc_start: 0.6838 (t80) cc_final: 0.6504 (t80) REVERT: C 63 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7174 (tm-30) REVERT: C 66 GLU cc_start: 0.7576 (pp20) cc_final: 0.6976 (pp20) REVERT: C 87 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.5642 (pp) REVERT: D 41 SER cc_start: 0.8576 (t) cc_final: 0.8126 (t) REVERT: D 43 TYR cc_start: 0.7728 (m-80) cc_final: 0.7502 (m-80) REVERT: D 73 PHE cc_start: 0.8726 (t80) cc_final: 0.8414 (t80) REVERT: D 101 VAL cc_start: 0.8881 (t) cc_final: 0.8594 (p) REVERT: D 116 GLU cc_start: 0.7331 (tm-30) cc_final: 0.5528 (tm-30) REVERT: E 57 SER cc_start: 0.8734 (t) cc_final: 0.8419 (p) REVERT: E 76 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6453 (pm20) REVERT: F 53 GLU cc_start: 0.7408 (mp0) cc_final: 0.7056 (mp0) REVERT: F 93 GLN cc_start: 0.8528 (tp40) cc_final: 0.8313 (tp40) REVERT: H 86 TYR cc_start: 0.7012 (p90) cc_final: 0.6729 (p90) REVERT: H 97 ILE cc_start: 0.8742 (tp) cc_final: 0.8457 (tp) REVERT: H 123 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8202 (tppp) outliers start: 60 outliers final: 27 residues processed: 521 average time/residue: 0.4573 time to fit residues: 327.8739 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 : 1.590 ------------------------------------------------------------------------------- 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: 0.8980 chunk 130 optimal weight: 0.0020 chunk 106 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 138 optimal weight: 0.0020 chunk 155 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.104272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089034 restraints weight = 54830.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091167 restraints weight = 27445.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092558 restraints weight = 16896.263| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17850 Z= 0.175 Angle : 0.792 10.913 25340 Z= 0.433 Chirality : 0.044 0.423 2858 Planarity : 0.006 0.057 2190 Dihedral : 28.997 122.273 4770 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.85 % Allowed : 23.08 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (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: -3.06 (0.21), residues: 1319 helix: -1.60 (0.17), residues: 714 sheet: -1.51 (1.27), residues: 19 loop : -2.55 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 247 HIS 0.011 0.001 HIS M 240 PHE 0.057 0.003 PHE M 189 TYR 0.032 0.002 TYR G 52 ARG 0.009 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 796) hydrogen bonds : angle 4.12657 ( 2011) covalent geometry : bond 0.00383 (17850) covalent geometry : angle 0.79155 (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 546 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 476 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.7980 (tt) cc_final: 0.7657 (mt) REVERT: K 212 GLU cc_start: 0.8001 (pp20) cc_final: 0.7658 (pt0) REVERT: K 266 TYR cc_start: 0.6489 (t80) cc_final: 0.5758 (t80) REVERT: K 289 TYR cc_start: 0.7484 (p90) cc_final: 0.7098 (p90) REVERT: K 334 VAL cc_start: 0.7623 (p) cc_final: 0.7131 (p) REVERT: K 353 TRP cc_start: 0.8388 (m-10) cc_final: 0.7960 (m-10) REVERT: K 357 LEU cc_start: 0.7911 (mt) cc_final: 0.7678 (mt) REVERT: K 376 MET cc_start: 0.8184 (tpp) cc_final: 0.7961 (tpp) REVERT: K 383 ASP cc_start: 0.7940 (t0) cc_final: 0.6189 (t0) REVERT: K 386 HIS cc_start: 0.6876 (m90) cc_final: 0.6443 (m90) REVERT: K 408 ASP cc_start: 0.8659 (p0) cc_final: 0.8407 (p0) REVERT: K 409 ILE cc_start: 0.7558 (mt) cc_final: 0.7234 (mp) REVERT: M 70 LEU cc_start: 0.4846 (OUTLIER) cc_final: 0.4152 (tt) REVERT: M 74 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7568 (mm) REVERT: M 161 ASN cc_start: 0.6747 (p0) cc_final: 0.6336 (p0) REVERT: M 167 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7301 (ttp80) REVERT: M 169 GLU cc_start: 0.6164 (pp20) cc_final: 0.4829 (tm-30) REVERT: M 189 PHE cc_start: 0.7761 (m-80) cc_final: 0.7005 (m-80) REVERT: M 249 PHE cc_start: 0.7805 (t80) cc_final: 0.7494 (t80) REVERT: M 267 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6206 (mt) REVERT: M 342 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8229 (pttm) REVERT: A 81 ASP cc_start: 0.7662 (t0) cc_final: 0.7315 (t70) REVERT: A 83 ARG cc_start: 0.7691 (mmp80) cc_final: 0.7144 (mmp80) REVERT: A 124 ILE cc_start: 0.8137 (mm) cc_final: 0.7876 (mm) REVERT: B 35 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7352 (ttt90) REVERT: B 36 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7465 (mtm180) REVERT: B 44 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8070 (mmmm) REVERT: B 67 ARG cc_start: 0.7369 (ttp80) cc_final: 0.7015 (ttp80) REVERT: B 79 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7973 (ttmt) REVERT: C 28 VAL cc_start: 0.8887 (t) cc_final: 0.8541 (p) REVERT: C 30 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7639 (mtp85) REVERT: C 48 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7410 (ptmm) REVERT: C 52 TYR cc_start: 0.6904 (t80) cc_final: 0.6609 (t80) REVERT: D 86 TYR cc_start: 0.6960 (p90) cc_final: 0.6751 (p90) REVERT: D 98 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7372 (tm-30) REVERT: D 101 VAL cc_start: 0.8918 (t) cc_final: 0.8615 (p) REVERT: D 111 LYS cc_start: 0.8132 (ptpp) cc_final: 0.7678 (ptpp) REVERT: E 57 SER cc_start: 0.8753 (t) cc_final: 0.8330 (p) REVERT: E 106 ASP cc_start: 0.7729 (p0) cc_final: 0.7516 (p0) REVERT: F 53 GLU cc_start: 0.7336 (mp0) cc_final: 0.7051 (mp0) REVERT: G 81 THR cc_start: 0.7847 (p) cc_final: 0.7601 (p) REVERT: G 94 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6378 (tm-30) REVERT: H 62 MET cc_start: 0.8062 (mmm) cc_final: 0.7808 (tpp) REVERT: H 88 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7928 (mmpt) REVERT: H 97 ILE cc_start: 0.8885 (tp) cc_final: 0.8614 (tp) REVERT: H 123 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8295 (tppp) outliers start: 70 outliers final: 31 residues processed: 504 average time/residue: 0.4225 time to fit residues: 289.3287 Evaluate side-chains 499 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 461 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 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 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 44 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain 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: 3.9990 chunk 130 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 332 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.103670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088238 restraints weight = 55204.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090382 restraints weight = 27806.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.091747 restraints weight = 17184.725| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17850 Z= 0.182 Angle : 0.797 12.770 25340 Z= 0.435 Chirality : 0.044 0.460 2858 Planarity : 0.005 0.058 2190 Dihedral : 28.760 120.970 4768 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.02 % Allowed : 25.59 % Favored : 68.39 % 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: -2.74 (0.21), residues: 1319 helix: -1.30 (0.18), residues: 711 sheet: -1.08 (1.20), residues: 20 loop : -2.46 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 247 HIS 0.010 0.001 HIS D 112 PHE 0.040 0.003 PHE K 323 TYR 0.033 0.002 TYR G 52 ARG 0.016 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 796) hydrogen bonds : angle 4.07471 ( 2011) covalent geometry : bond 0.00404 (17850) covalent geometry : angle 0.79730 (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 558 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 486 time to evaluate : 1.681 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: 0.8192 (tt) cc_final: 0.7795 (mt) REVERT: N 91 ASN cc_start: 0.8049 (t0) cc_final: 0.7822 (t0) REVERT: K 212 GLU cc_start: 0.8013 (pp20) cc_final: 0.7808 (pt0) REVERT: K 266 TYR cc_start: 0.6525 (t80) cc_final: 0.5741 (t80) REVERT: K 289 TYR cc_start: 0.7573 (p90) cc_final: 0.7124 (p90) REVERT: K 352 TYR cc_start: 0.6881 (t80) cc_final: 0.6537 (t80) REVERT: K 357 LEU cc_start: 0.8012 (mt) cc_final: 0.7763 (mt) REVERT: K 377 THR cc_start: 0.8675 (p) cc_final: 0.8461 (p) REVERT: K 406 ASN cc_start: 0.6434 (p0) cc_final: 0.6172 (p0) REVERT: M 70 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4207 (tt) REVERT: M 74 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7503 (mm) REVERT: M 161 ASN cc_start: 0.6851 (p0) cc_final: 0.6581 (p0) REVERT: M 167 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7358 (ttp80) REVERT: M 169 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5412 (tm-30) REVERT: M 189 PHE cc_start: 0.7938 (m-80) cc_final: 0.7337 (m-80) REVERT: M 215 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7017 (tt) REVERT: M 267 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6424 (mt) REVERT: M 289 TYR cc_start: 0.6357 (m-10) cc_final: 0.5998 (m-10) REVERT: M 335 ARG cc_start: 0.8531 (mmp-170) cc_final: 0.8290 (mmp-170) REVERT: M 342 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8213 (pttm) REVERT: A 64 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7788 (mmmm) REVERT: A 81 ASP cc_start: 0.7880 (t0) cc_final: 0.7565 (t70) REVERT: A 83 ARG cc_start: 0.7636 (mmp80) cc_final: 0.6984 (mmp80) REVERT: A 93 GLN cc_start: 0.7886 (tp40) cc_final: 0.7562 (tp40) REVERT: A 97 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7692 (tp30) REVERT: B 35 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7491 (tpt170) REVERT: B 44 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8254 (mmmm) REVERT: B 46 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 79 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: B 88 TYR cc_start: 0.7059 (m-80) cc_final: 0.6741 (m-10) REVERT: C 28 VAL cc_start: 0.9026 (t) cc_final: 0.8685 (p) REVERT: C 30 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7731 (mtp85) REVERT: C 79 ARG cc_start: 0.6388 (pmm150) cc_final: 0.5818 (ptp90) REVERT: D 86 TYR cc_start: 0.6882 (p90) cc_final: 0.6497 (p90) REVERT: D 111 LYS cc_start: 0.8248 (ptpp) cc_final: 0.7914 (ptpp) REVERT: E 49 ARG cc_start: 0.8311 (ptp-110) cc_final: 0.8089 (ptp-110) REVERT: E 57 SER cc_start: 0.8706 (t) cc_final: 0.8408 (p) REVERT: E 94 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7827 (mm-30) REVERT: E 106 ASP cc_start: 0.7739 (p0) cc_final: 0.7353 (p0) REVERT: E 109 LEU cc_start: 0.9073 (mm) cc_final: 0.8804 (mt) REVERT: E 125 LYS cc_start: 0.8676 (mmtp) cc_final: 0.8430 (tppp) REVERT: F 29 ILE cc_start: 0.8084 (tt) cc_final: 0.7843 (pt) REVERT: F 39 ARG cc_start: 0.7961 (mmt90) cc_final: 0.7648 (mmt90) REVERT: F 85 ASP cc_start: 0.7370 (m-30) cc_final: 0.7149 (m-30) REVERT: F 91 LYS cc_start: 0.8674 (tptp) cc_final: 0.8395 (tptp) REVERT: G 30 ARG cc_start: 0.6860 (ttp-110) cc_final: 0.6610 (ttp-110) REVERT: G 81 THR cc_start: 0.7937 (p) cc_final: 0.7627 (p) REVERT: H 62 MET cc_start: 0.7996 (mmm) cc_final: 0.7732 (tpp) REVERT: H 88 LYS cc_start: 0.8330 (mmpt) cc_final: 0.7950 (mmpt) REVERT: H 97 ILE cc_start: 0.9108 (tp) cc_final: 0.8824 (tp) REVERT: H 123 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8368 (tppp) outliers start: 72 outliers final: 37 residues processed: 520 average time/residue: 0.4058 time to fit residues: 287.4542 Evaluate side-chains 514 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 468 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 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 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 332 GLN Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 46 ILE 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 77 VAL 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 E residue 46 VAL 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 57 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 41 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 0.0570 chunk 73 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 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** E 85 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.102888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087315 restraints weight = 55495.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089479 restraints weight = 27646.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090842 restraints weight = 17058.254| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17850 Z= 0.205 Angle : 0.829 12.327 25340 Z= 0.450 Chirality : 0.045 0.350 2858 Planarity : 0.005 0.057 2190 Dihedral : 28.683 126.068 4768 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.85 % Allowed : 28.09 % Favored : 66.05 % 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: -2.54 (0.22), residues: 1319 helix: -1.17 (0.18), residues: 709 sheet: -1.19 (1.20), residues: 20 loop : -2.32 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 247 HIS 0.010 0.001 HIS D 112 PHE 0.029 0.002 PHE K 323 TYR 0.037 0.002 TYR G 52 ARG 0.015 0.001 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 796) hydrogen bonds : angle 4.08515 ( 2011) covalent geometry : bond 0.00453 (17850) covalent geometry : angle 0.82873 (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 573 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 503 time to evaluate : 2.170 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: 0.8342 (tt) cc_final: 0.8002 (mt) REVERT: N 26 GLU cc_start: 0.7721 (mp0) cc_final: 0.7436 (mp0) REVERT: K 177 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6720 (tp) REVERT: K 238 GLU cc_start: 0.6723 (pp20) cc_final: 0.6459 (pp20) REVERT: K 266 TYR cc_start: 0.6486 (t80) cc_final: 0.5629 (t80) REVERT: K 314 MET cc_start: 0.6075 (tpt) cc_final: 0.5846 (tpt) REVERT: K 328 SER cc_start: 0.8947 (m) cc_final: 0.8358 (t) REVERT: K 353 TRP cc_start: 0.8542 (m-10) cc_final: 0.8164 (m-10) REVERT: K 372 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7456 (tm-30) REVERT: K 376 MET cc_start: 0.8244 (tpp) cc_final: 0.8037 (tpp) REVERT: K 377 THR cc_start: 0.8503 (p) cc_final: 0.8148 (p) REVERT: K 406 ASN cc_start: 0.6639 (p0) cc_final: 0.6146 (p0) REVERT: M 70 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4110 (tt) REVERT: M 74 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.7381 (mm) REVERT: M 161 ASN cc_start: 0.6976 (p0) cc_final: 0.6757 (p0) REVERT: M 215 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7191 (tt) REVERT: M 224 LEU cc_start: 0.8476 (pt) cc_final: 0.8099 (mp) REVERT: M 267 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6456 (tt) REVERT: M 289 TYR cc_start: 0.6372 (m-10) cc_final: 0.6053 (m-10) REVERT: M 342 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8240 (pttm) REVERT: A 69 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: A 81 ASP cc_start: 0.8288 (t0) cc_final: 0.7870 (t0) REVERT: A 93 GLN cc_start: 0.7654 (tp40) cc_final: 0.7218 (tp40) REVERT: A 121 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7703 (mmtt) REVERT: B 49 LEU cc_start: 0.6652 (pt) cc_final: 0.6447 (pt) REVERT: B 92 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8110 (tmm-80) REVERT: C 28 VAL cc_start: 0.9239 (t) cc_final: 0.8901 (p) REVERT: C 79 ARG cc_start: 0.6264 (pmm150) cc_final: 0.6033 (ptp90) REVERT: C 92 ASP cc_start: 0.8244 (t0) cc_final: 0.8032 (t0) REVERT: D 116 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7318 (tm-30) REVERT: E 103 LEU cc_start: 0.8794 (tp) cc_final: 0.8547 (tp) REVERT: E 106 ASP cc_start: 0.7818 (p0) cc_final: 0.6172 (p0) REVERT: E 109 LEU cc_start: 0.9082 (mm) cc_final: 0.8819 (mt) REVERT: F 84 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7797 (mm) REVERT: G 37 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7522 (mmm-85) REVERT: G 57 LEU cc_start: 0.8677 (tt) cc_final: 0.8455 (tp) REVERT: G 90 ARG cc_start: 0.8353 (ttt180) cc_final: 0.8114 (ttt180) REVERT: G 93 ASP cc_start: 0.8374 (m-30) cc_final: 0.8137 (m-30) REVERT: H 46 LYS cc_start: 0.8685 (tttp) cc_final: 0.8446 (tttp) REVERT: H 62 MET cc_start: 0.7898 (mmm) cc_final: 0.7674 (tpp) REVERT: H 76 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7826 (tt) REVERT: H 82 LYS cc_start: 0.8429 (pttm) cc_final: 0.8203 (pttm) REVERT: H 86 TYR cc_start: 0.7302 (p90) cc_final: 0.6975 (p90) REVERT: H 88 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7940 (mmpt) REVERT: H 123 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8396 (tptp) outliers start: 70 outliers final: 41 residues processed: 534 average time/residue: 0.4705 time to fit residues: 344.5688 Evaluate side-chains 534 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 484 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 304 CYS Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 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 109 LEU Chi-restraints excluded: chain A residue 129 ARG 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 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 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain 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 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 Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 130 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS ** 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.103517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.087991 restraints weight = 55724.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090135 restraints weight = 27962.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091490 restraints weight = 17356.255| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17850 Z= 0.187 Angle : 0.829 12.462 25340 Z= 0.448 Chirality : 0.044 0.267 2858 Planarity : 0.006 0.062 2190 Dihedral : 28.626 124.568 4764 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.44 % Allowed : 30.94 % Favored : 62.63 % 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: -2.44 (0.22), residues: 1319 helix: -1.07 (0.18), residues: 713 sheet: -1.28 (1.18), residues: 20 loop : -2.29 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 247 HIS 0.007 0.001 HIS D 112 PHE 0.057 0.003 PHE M 189 TYR 0.037 0.002 TYR G 52 ARG 0.015 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 796) hydrogen bonds : angle 4.15563 ( 2011) covalent geometry : bond 0.00419 (17850) covalent geometry : angle 0.82887 (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 574 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 497 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8435 (tt) cc_final: 0.8017 (mt) REVERT: N 26 GLU cc_start: 0.7814 (mp0) cc_final: 0.7484 (mp0) REVERT: K 238 GLU cc_start: 0.6843 (pp20) cc_final: 0.6470 (pp20) REVERT: K 243 LYS cc_start: 0.8567 (tppt) cc_final: 0.8326 (tptp) REVERT: K 266 TYR cc_start: 0.6601 (t80) cc_final: 0.5756 (t80) REVERT: K 377 THR cc_start: 0.8356 (p) cc_final: 0.8015 (p) REVERT: M 70 LEU cc_start: 0.4724 (OUTLIER) cc_final: 0.3965 (tt) REVERT: M 74 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7416 (mm) REVERT: M 141 PHE cc_start: 0.7610 (t80) cc_final: 0.7324 (m-80) REVERT: M 162 TYR cc_start: 0.6057 (t80) cc_final: 0.5810 (t80) REVERT: M 168 ASP cc_start: 0.8506 (t0) cc_final: 0.8025 (m-30) REVERT: M 172 LEU cc_start: 0.7718 (mt) cc_final: 0.7275 (pp) REVERT: M 175 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7516 (mm-40) REVERT: M 215 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7265 (tt) REVERT: M 224 LEU cc_start: 0.8298 (pt) cc_final: 0.8028 (mp) REVERT: M 267 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6210 (tt) REVERT: M 289 TYR cc_start: 0.6530 (m-10) cc_final: 0.6159 (m-10) REVERT: M 339 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7729 (tp40) REVERT: A 81 ASP cc_start: 0.8080 (t0) cc_final: 0.7867 (t0) REVERT: A 128 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8331 (mtm-85) REVERT: B 68 ASP cc_start: 0.7679 (p0) cc_final: 0.7426 (p0) REVERT: B 88 TYR cc_start: 0.7103 (m-80) cc_final: 0.6758 (m-10) REVERT: B 92 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8192 (tmm-80) REVERT: C 28 VAL cc_start: 0.9212 (t) cc_final: 0.8846 (p) REVERT: C 44 ARG cc_start: 0.5355 (ptm-80) cc_final: 0.5094 (ptm-80) REVERT: C 79 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5849 (ptp90) REVERT: C 89 ILE cc_start: 0.7347 (mm) cc_final: 0.7137 (mm) REVERT: C 92 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8116 (t0) REVERT: D 46 LYS cc_start: 0.8645 (ptpp) cc_final: 0.8337 (ptmt) REVERT: D 89 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8195 (mmmm) REVERT: E 106 ASP cc_start: 0.7693 (p0) cc_final: 0.7489 (p0) REVERT: E 121 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8793 (ttpp) REVERT: F 67 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.7169 (mtm-85) REVERT: G 30 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7397 (mtm-85) REVERT: G 57 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8343 (tp) REVERT: G 79 ARG cc_start: 0.4882 (tpm170) cc_final: 0.4619 (tpm170) REVERT: H 43 TYR cc_start: 0.7128 (m-10) cc_final: 0.6915 (m-10) REVERT: H 46 LYS cc_start: 0.8724 (tttp) cc_final: 0.8363 (tttp) REVERT: H 49 LYS cc_start: 0.8586 (pttp) cc_final: 0.8183 (pttp) REVERT: H 62 MET cc_start: 0.8131 (mmm) cc_final: 0.7855 (tpp) REVERT: H 82 LYS cc_start: 0.8429 (pttm) cc_final: 0.8175 (pttm) REVERT: H 86 TYR cc_start: 0.7313 (p90) cc_final: 0.7067 (p90) REVERT: H 88 LYS cc_start: 0.8368 (mmpt) cc_final: 0.7965 (mmpt) REVERT: H 123 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8340 (tppp) outliers start: 77 outliers final: 42 residues processed: 528 average time/residue: 0.4107 time to fit residues: 295.0594 Evaluate side-chains 521 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 470 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 304 CYS Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 404 PHE Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 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 A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 53 GLU 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 B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain 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 98 TYR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 LEU 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: 0.0020 chunk 148 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN ** 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 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3765 r_free = 0.3765 target = 0.100971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085792 restraints weight = 54475.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087695 restraints weight = 28090.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088968 restraints weight = 17899.087| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 17850 Z= 0.244 Angle : 0.901 13.606 25340 Z= 0.486 Chirality : 0.049 0.281 2858 Planarity : 0.006 0.061 2190 Dihedral : 28.691 125.233 4761 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.60 % Allowed : 33.19 % Favored : 61.20 % 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: -2.54 (0.22), residues: 1319 helix: -1.16 (0.18), residues: 698 sheet: -2.30 (0.97), residues: 27 loop : -2.25 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP K 353 HIS 0.007 0.002 HIS M 240 PHE 0.055 0.003 PHE K 236 TYR 0.053 0.003 TYR G 52 ARG 0.012 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 796) hydrogen bonds : angle 4.40123 ( 2011) covalent geometry : bond 0.00554 (17850) covalent geometry : angle 0.90150 (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 563 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 496 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 17 LEU cc_start: 0.8646 (tt) cc_final: 0.8170 (mt) REVERT: K 209 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8211 (tppt) REVERT: K 352 TYR cc_start: 0.7326 (t80) cc_final: 0.6955 (t80) REVERT: K 371 ASP cc_start: 0.7888 (m-30) cc_final: 0.7472 (m-30) REVERT: K 377 THR cc_start: 0.8328 (p) cc_final: 0.8006 (p) REVERT: K 389 LYS cc_start: 0.8756 (pttp) cc_final: 0.8507 (pttm) REVERT: M 70 LEU cc_start: 0.4693 (OUTLIER) cc_final: 0.4018 (tt) REVERT: M 74 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.7496 (mm) REVERT: M 141 PHE cc_start: 0.7782 (t80) cc_final: 0.7411 (m-80) REVERT: M 162 TYR cc_start: 0.6487 (t80) cc_final: 0.6188 (t80) REVERT: M 175 GLN cc_start: 0.7639 (tp-100) cc_final: 0.7413 (mm-40) REVERT: M 215 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7804 (tt) REVERT: M 254 ASP cc_start: 0.7720 (t0) cc_final: 0.7508 (m-30) REVERT: M 267 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6702 (tt) REVERT: M 289 TYR cc_start: 0.6676 (m-10) cc_final: 0.6204 (m-10) REVERT: A 56 LYS cc_start: 0.9075 (tptp) cc_final: 0.8870 (tptp) REVERT: A 64 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8082 (mmmm) REVERT: A 81 ASP cc_start: 0.8375 (t0) cc_final: 0.7585 (t0) REVERT: A 93 GLN cc_start: 0.7810 (tp40) cc_final: 0.7425 (tp40) REVERT: A 123 ASP cc_start: 0.8151 (m-30) cc_final: 0.7884 (m-30) REVERT: A 128 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8462 (mtm-85) REVERT: B 68 ASP cc_start: 0.7545 (p0) cc_final: 0.7276 (p0) REVERT: B 88 TYR cc_start: 0.7134 (m-80) cc_final: 0.6881 (m-80) REVERT: B 92 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8223 (tmm-80) REVERT: C 28 VAL cc_start: 0.9271 (t) cc_final: 0.8961 (p) REVERT: C 79 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5862 (ptp90) REVERT: C 92 ASP cc_start: 0.8317 (t0) cc_final: 0.8006 (t0) REVERT: D 46 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8348 (ptmt) REVERT: D 88 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8254 (mmtt) REVERT: D 89 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8242 (mmmm) REVERT: D 123 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7895 (pttp) REVERT: E 121 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8630 (ttpp) REVERT: F 88 TYR cc_start: 0.8703 (m-80) cc_final: 0.8403 (m-80) REVERT: G 30 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7761 (mtp85) REVERT: G 90 ARG cc_start: 0.8234 (ttt180) cc_final: 0.7883 (ttt180) REVERT: G 93 ASP cc_start: 0.8037 (m-30) cc_final: 0.7750 (m-30) REVERT: H 74 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7182 (tm-30) REVERT: H 82 LYS cc_start: 0.8449 (pttm) cc_final: 0.8207 (pttm) REVERT: H 86 TYR cc_start: 0.7420 (p90) cc_final: 0.7099 (p90) REVERT: H 88 LYS cc_start: 0.8351 (mmpt) cc_final: 0.8070 (mmpt) REVERT: H 123 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8369 (tptp) outliers start: 67 outliers final: 40 residues processed: 520 average time/residue: 0.3863 time to fit residues: 271.3996 Evaluate side-chains 533 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 486 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 289 TYR 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 60 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 332 GLN Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 60 SER 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 B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 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 111 LYS Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 92 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 42 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 91 ASN ** K 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.103670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088543 restraints weight = 55164.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090444 restraints weight = 28788.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091689 restraints weight = 18504.716| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17850 Z= 0.188 Angle : 0.892 12.711 25340 Z= 0.474 Chirality : 0.046 0.314 2858 Planarity : 0.006 0.100 2190 Dihedral : 28.691 123.588 4761 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.85 % Allowed : 36.20 % Favored : 58.95 % 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: -2.63 (0.22), residues: 1319 helix: -1.23 (0.18), residues: 711 sheet: -0.99 (1.18), residues: 20 loop : -2.38 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP K 353 HIS 0.007 0.001 HIS M 240 PHE 0.052 0.003 PHE M 189 TYR 0.040 0.003 TYR G 52 ARG 0.012 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 796) hydrogen bonds : angle 4.37487 ( 2011) covalent geometry : bond 0.00430 (17850) covalent geometry : angle 0.89156 (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 559 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 501 time to evaluate : 1.549 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: N 17 LEU cc_start: 0.8561 (tt) cc_final: 0.8039 (mt) REVERT: K 209 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7887 (mmmt) REVERT: K 352 TYR cc_start: 0.7214 (t80) cc_final: 0.6980 (t80) REVERT: K 377 THR cc_start: 0.8165 (p) cc_final: 0.7789 (p) REVERT: K 389 LYS cc_start: 0.8712 (pttp) cc_final: 0.8475 (pttp) REVERT: M 70 LEU cc_start: 0.4687 (OUTLIER) cc_final: 0.3897 (tt) REVERT: M 74 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.7568 (mm) REVERT: M 168 ASP cc_start: 0.8172 (t0) cc_final: 0.7946 (m-30) REVERT: M 175 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7244 (mm-40) REVERT: M 215 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7620 (tt) REVERT: M 267 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6620 (tt) REVERT: M 289 TYR cc_start: 0.6580 (m-10) cc_final: 0.6145 (m-10) REVERT: M 298 GLU cc_start: 0.7338 (pm20) cc_final: 0.7003 (pm20) REVERT: A 64 LYS cc_start: 0.8399 (mmmt) cc_final: 0.7971 (mmmm) REVERT: A 81 ASP cc_start: 0.8356 (t0) cc_final: 0.7916 (t0) REVERT: A 93 GLN cc_start: 0.7680 (tp40) cc_final: 0.7396 (tp40) REVERT: A 123 ASP cc_start: 0.8078 (m-30) cc_final: 0.7870 (m-30) REVERT: B 39 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7342 (tpp-160) REVERT: B 51 TYR cc_start: 0.8295 (m-10) cc_final: 0.7737 (m-10) REVERT: B 80 THR cc_start: 0.8979 (t) cc_final: 0.8693 (p) REVERT: B 92 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8116 (tmm-80) REVERT: C 28 VAL cc_start: 0.9200 (t) cc_final: 0.8863 (p) REVERT: C 67 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7466 (mm) REVERT: C 79 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5840 (ptp90) REVERT: C 89 ILE cc_start: 0.7766 (mm) cc_final: 0.7546 (mm) REVERT: C 92 ASP cc_start: 0.8147 (t0) cc_final: 0.7881 (t0) REVERT: D 46 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8363 (ptmt) REVERT: D 88 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8251 (mmtt) REVERT: D 89 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8232 (mmmm) REVERT: D 123 LYS cc_start: 0.8256 (ptmm) cc_final: 0.8051 (pttt) REVERT: E 45 THR cc_start: 0.7976 (t) cc_final: 0.7773 (p) REVERT: F 67 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7278 (mtm-85) REVERT: F 88 TYR cc_start: 0.8533 (m-80) cc_final: 0.8109 (m-80) REVERT: G 93 ASP cc_start: 0.7816 (m-30) cc_final: 0.7336 (m-30) REVERT: H 49 LYS cc_start: 0.8582 (pttp) cc_final: 0.8276 (pttp) REVERT: H 82 LYS cc_start: 0.8392 (pttm) cc_final: 0.8122 (pttm) REVERT: H 86 TYR cc_start: 0.7276 (p90) cc_final: 0.6981 (p90) REVERT: H 88 LYS cc_start: 0.8399 (mmpt) cc_final: 0.8091 (mmpt) REVERT: H 89 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8173 (mmmm) REVERT: H 123 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8349 (tppt) outliers start: 58 outliers final: 32 residues processed: 522 average time/residue: 0.3838 time to fit residues: 272.1906 Evaluate side-chains 524 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 485 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 94 LEU Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 133 TYR 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 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 122 LYS Chi-restraints excluded: chain A residue 129 ARG 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 B residue 97 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 112 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 100 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 68 GLN ** 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** ** 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 = 0.3837 r_free = 0.3837 target = 0.104963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089649 restraints weight = 56031.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.091656 restraints weight = 28983.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092953 restraints weight = 18466.681| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.8254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17850 Z= 0.186 Angle : 0.892 13.885 25340 Z= 0.474 Chirality : 0.046 0.383 2858 Planarity : 0.005 0.060 2190 Dihedral : 28.603 120.443 4761 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.43 % Allowed : 36.62 % Favored : 58.95 % 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: -2.61 (0.22), residues: 1319 helix: -1.29 (0.18), residues: 719 sheet: -0.50 (1.22), residues: 20 loop : -2.29 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP K 353 HIS 0.012 0.001 HIS N 100 PHE 0.033 0.002 PHE K 404 TYR 0.048 0.003 TYR G 52 ARG 0.012 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 796) hydrogen bonds : angle 4.40497 ( 2011) covalent geometry : bond 0.00421 (17850) covalent geometry : angle 0.89207 (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 546 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 493 time to evaluate : 1.453 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: N 17 LEU cc_start: 0.8529 (tt) cc_final: 0.8118 (mt) REVERT: K 209 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7781 (mmmt) REVERT: K 352 TYR cc_start: 0.7164 (t80) cc_final: 0.6952 (t80) REVERT: K 383 ASP cc_start: 0.7758 (t0) cc_final: 0.6769 (t70) REVERT: K 389 LYS cc_start: 0.8692 (pttp) cc_final: 0.8479 (pttm) REVERT: M 74 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7389 (mt) REVERT: M 168 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: M 175 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7266 (mm-40) REVERT: M 215 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7590 (tt) REVERT: M 267 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6583 (tt) REVERT: M 289 TYR cc_start: 0.6467 (m-10) cc_final: 0.6029 (m-10) REVERT: M 294 GLN cc_start: 0.7548 (pm20) cc_final: 0.7303 (pm20) REVERT: A 64 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8158 (mmmt) REVERT: A 81 ASP cc_start: 0.8337 (t0) cc_final: 0.7932 (t0) REVERT: A 93 GLN cc_start: 0.7604 (tp40) cc_final: 0.7296 (tp40) REVERT: B 39 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7333 (tpp-160) REVERT: B 92 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8239 (tmm-80) REVERT: C 28 VAL cc_start: 0.9035 (t) cc_final: 0.8768 (p) REVERT: C 92 ASP cc_start: 0.8036 (t0) cc_final: 0.7824 (t0) REVERT: D 47 VAL cc_start: 0.8134 (t) cc_final: 0.7931 (t) REVERT: D 88 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8319 (mmtt) REVERT: D 89 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8223 (mmmm) REVERT: D 123 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7973 (pttt) REVERT: E 69 ARG cc_start: 0.8780 (ptp-110) cc_final: 0.8493 (ptp90) REVERT: F 52 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7957 (mp0) REVERT: G 30 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7759 (mtp85) REVERT: G 79 ARG cc_start: 0.4952 (tpm170) cc_final: 0.4348 (tpm170) REVERT: G 93 ASP cc_start: 0.7645 (m-30) cc_final: 0.6997 (m-30) REVERT: H 49 LYS cc_start: 0.8532 (pttp) cc_final: 0.8218 (pttp) REVERT: H 82 LYS cc_start: 0.8334 (pttm) cc_final: 0.8049 (pttm) REVERT: H 86 TYR cc_start: 0.7226 (p90) cc_final: 0.6985 (p90) REVERT: H 88 LYS cc_start: 0.8410 (mmpt) cc_final: 0.8125 (mmpt) REVERT: H 123 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8403 (tppt) outliers start: 53 outliers final: 35 residues processed: 510 average time/residue: 0.3921 time to fit residues: 270.8199 Evaluate side-chains 521 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 481 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 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 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 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 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 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 E residue 130 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 53 GLU 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 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 131 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 64 GLN M 236 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.104353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089261 restraints weight = 55510.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091193 restraints weight = 29278.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092442 restraints weight = 18941.748| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.8439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 17850 Z= 0.200 Angle : 0.932 16.276 25340 Z= 0.493 Chirality : 0.048 0.449 2858 Planarity : 0.006 0.060 2190 Dihedral : 28.553 119.311 4759 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.85 % Allowed : 38.04 % Favored : 58.11 % 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: -2.50 (0.22), residues: 1319 helix: -1.20 (0.18), residues: 701 sheet: -0.34 (1.25), residues: 20 loop : -2.23 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.005 TRP K 353 HIS 0.008 0.001 HIS M 240 PHE 0.033 0.002 PHE K 323 TYR 0.049 0.003 TYR K 175 ARG 0.011 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 796) hydrogen bonds : angle 4.42389 ( 2011) covalent geometry : bond 0.00461 (17850) covalent geometry : angle 0.93200 (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 530 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 484 time to evaluate : 1.411 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: N 17 LEU cc_start: 0.8533 (tt) cc_final: 0.8121 (mt) REVERT: K 209 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7888 (mmmt) REVERT: K 352 TYR cc_start: 0.7272 (t80) cc_final: 0.7023 (t80) REVERT: K 353 TRP cc_start: 0.8011 (m-10) cc_final: 0.7802 (m-10) REVERT: K 377 THR cc_start: 0.7862 (p) cc_final: 0.7436 (p) REVERT: K 383 ASP cc_start: 0.7742 (t0) cc_final: 0.7225 (t70) REVERT: K 389 LYS cc_start: 0.8690 (pttp) cc_final: 0.8478 (pttm) REVERT: M 74 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7593 (mm) REVERT: M 175 GLN cc_start: 0.7592 (tp-100) cc_final: 0.7265 (mm-40) REVERT: M 215 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7730 (tt) REVERT: M 289 TYR cc_start: 0.6449 (m-10) cc_final: 0.5991 (m-10) REVERT: M 294 GLN cc_start: 0.7464 (pm20) cc_final: 0.7184 (pm20) REVERT: A 64 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8174 (mmmm) REVERT: A 81 ASP cc_start: 0.8367 (t0) cc_final: 0.7836 (t0) REVERT: A 93 GLN cc_start: 0.7596 (tp40) cc_final: 0.7287 (tp40) REVERT: A 121 LYS cc_start: 0.7783 (mptt) cc_final: 0.7409 (mmtt) REVERT: B 92 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8266 (tmm-80) REVERT: C 94 GLU cc_start: 0.8224 (pt0) cc_final: 0.8004 (pt0) REVERT: D 47 VAL cc_start: 0.8119 (t) cc_final: 0.7888 (t) REVERT: D 88 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8370 (mmtt) REVERT: D 123 LYS cc_start: 0.8239 (ptmm) cc_final: 0.8017 (pttt) REVERT: F 52 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7935 (mp0) REVERT: G 79 ARG cc_start: 0.5095 (tpm170) cc_final: 0.4791 (tpm170) REVERT: G 94 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6923 (tm-30) REVERT: H 49 LYS cc_start: 0.8534 (pttp) cc_final: 0.8219 (pttp) REVERT: H 82 LYS cc_start: 0.8271 (pttm) cc_final: 0.7998 (pttm) REVERT: H 86 TYR cc_start: 0.7327 (p90) cc_final: 0.7029 (p90) REVERT: H 88 LYS cc_start: 0.8365 (mmpt) cc_final: 0.8099 (mmpt) REVERT: H 123 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8415 (tppt) outliers start: 46 outliers final: 35 residues processed: 498 average time/residue: 0.4056 time to fit residues: 271.7735 Evaluate side-chains 514 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 476 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 271 PHE Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 366 LYS Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 133 TYR Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 HIS Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.105122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090107 restraints weight = 55745.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092036 restraints weight = 29504.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093316 restraints weight = 19013.462| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.8633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17850 Z= 0.192 Angle : 0.939 17.036 25340 Z= 0.493 Chirality : 0.048 0.472 2858 Planarity : 0.005 0.050 2190 Dihedral : 28.527 118.009 4759 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.51 % Allowed : 38.71 % Favored : 57.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.55 (0.22), residues: 1319 helix: -1.21 (0.18), residues: 709 sheet: 0.15 (1.27), residues: 20 loop : -2.32 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP K 353 HIS 0.008 0.001 HIS M 240 PHE 0.030 0.002 PHE K 323 TYR 0.055 0.003 TYR G 59 ARG 0.010 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 796) hydrogen bonds : angle 4.41632 ( 2011) covalent geometry : bond 0.00438 (17850) covalent geometry : angle 0.93946 (25340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7575.31 seconds wall clock time: 135 minutes 29.99 seconds (8129.99 seconds total)