Starting phenix.real_space_refine on Wed Nov 19 05:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8e_31016/11_2025/7e8e_31016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8e_31016/11_2025/7e8e_31016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e8e_31016/11_2025/7e8e_31016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8e_31016/11_2025/7e8e_31016.map" model { file = "/net/cci-nas-00/data/ceres_data/7e8e_31016/11_2025/7e8e_31016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8e_31016/11_2025/7e8e_31016.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13764 2.51 5 N 3626 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21380 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Chain: "K" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 211 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "H" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "L" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 196 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "A" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Chain: "I" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 211 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "J" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 196 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 5.50, per 1000 atoms: 0.26 Number of scatterers: 21380 At special positions: 0 Unit cell: (155.415, 151.405, 129.346, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3870 8.00 N 3626 7.00 C 13764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 902.5 milliseconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 6 sheets defined 71.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'G' and resid 49 through 62 removed outlier: 3.635A pdb=" N VAL G 55 " --> pdb=" O ARG G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 80 removed outlier: 4.103A pdb=" N GLN G 76 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR G 78 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 99 removed outlier: 3.577A pdb=" N ASN G 96 " --> pdb=" O HIS G 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 97 " --> pdb=" O TYR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 removed outlier: 3.707A pdb=" N THR G 103 " --> pdb=" O THR G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100 through 103' Processing helix chain 'G' and resid 108 through 120 Processing helix chain 'G' and resid 122 through 135 removed outlier: 3.696A pdb=" N LEU G 127 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 128 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 156 removed outlier: 4.170A pdb=" N ASP G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 182 removed outlier: 4.408A pdb=" N ARG G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 199 Processing helix chain 'G' and resid 202 through 215 removed outlier: 3.617A pdb=" N MET G 206 " --> pdb=" O ASP G 202 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.562A pdb=" N VAL C 5 " --> pdb=" O ALA C 2 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA C 7 " --> pdb=" O GLY C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.710A pdb=" N ALA C 12 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 88 through 102 removed outlier: 4.058A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.513A pdb=" N ILE C 128 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 133 through 152 removed outlier: 3.897A pdb=" N ASP C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.754A pdb=" N ARG C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 removed outlier: 3.770A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.556A pdb=" N SER C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 251 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.787A pdb=" N TYR C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.626A pdb=" N LEU C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.798A pdb=" N ARG C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 318 removed outlier: 4.337A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 removed outlier: 4.068A pdb=" N GLY C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 367 removed outlier: 4.333A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.555A pdb=" N ILE C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 450 removed outlier: 3.819A pdb=" N ASN C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 489 Processing helix chain 'K' and resid 29 through 56 removed outlier: 3.526A pdb=" N ILE K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR K 56 " --> pdb=" O VAL K 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.778A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.629A pdb=" N THR H 103 " --> pdb=" O THR H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 103' Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 143 through 156 removed outlier: 3.847A pdb=" N MET H 147 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 182 removed outlier: 4.335A pdb=" N ARG H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 202 through 208 removed outlier: 3.560A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.861A pdb=" N ILE D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.710A pdb=" N LEU D 59 " --> pdb=" O TRP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.831A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.670A pdb=" N PHE D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 130 through 153 removed outlier: 4.116A pdb=" N GLU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU D 136 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 removed outlier: 4.097A pdb=" N ALA D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 207 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 228 through 250 removed outlier: 4.408A pdb=" N THR D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 235 " --> pdb=" O CYS D 231 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.761A pdb=" N ILE D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 307 through 320 removed outlier: 4.135A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.473A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.802A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 450 Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.905A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'E' and resid 49 through 62 removed outlier: 3.635A pdb=" N VAL E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.102A pdb=" N GLN E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.577A pdb=" N ASN E 96 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.707A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 122 through 135 removed outlier: 3.697A pdb=" N LEU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 128 " --> pdb=" O HIS E 124 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 removed outlier: 4.169A pdb=" N ASP E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 182 removed outlier: 4.408A pdb=" N ARG E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 199 Processing helix chain 'E' and resid 202 through 215 removed outlier: 3.617A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.570A pdb=" N VAL A 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALA A 7 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.712A pdb=" N ALA A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 88 through 102 removed outlier: 4.059A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.514A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 133 through 152 removed outlier: 3.890A pdb=" N ASP A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.753A pdb=" N ARG A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 removed outlier: 3.769A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.556A pdb=" N SER A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 251 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.788A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.626A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.804A pdb=" N ARG A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 4.333A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 346 removed outlier: 4.064A pdb=" N GLY A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.328A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.563A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 450 removed outlier: 3.819A pdb=" N ASN A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'I' and resid 29 through 55 removed outlier: 3.526A pdb=" N ILE I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 64 removed outlier: 3.778A pdb=" N GLU F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 87 through 99 Processing helix chain 'F' and resid 100 through 103 removed outlier: 3.628A pdb=" N THR F 103 " --> pdb=" O THR F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 100 through 103' Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 143 through 156 removed outlier: 3.855A pdb=" N MET F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 removed outlier: 4.353A pdb=" N ARG F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 200 Processing helix chain 'F' and resid 202 through 208 removed outlier: 3.569A pdb=" N MET F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.861A pdb=" N ILE B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.711A pdb=" N LEU B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.831A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.670A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 153 removed outlier: 4.116A pdb=" N GLU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 4.096A pdb=" N ALA B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 228 through 250 removed outlier: 4.409A pdb=" N THR B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.759A pdb=" N ILE B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.135A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.477A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.797A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 450 Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.905A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AA2, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.871A pdb=" N LEU C 45 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 54 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.636A pdb=" N GLN D 82 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS D 77 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.870A pdb=" N LEU A 45 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 54 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.635A pdb=" N GLN B 82 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 77 " --> pdb=" O GLN B 82 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6832 1.34 - 1.46: 5237 1.46 - 1.58: 9617 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 21878 Sorted by residual: bond pdb=" C THR J 56 " pdb=" N PRO J 57 " ideal model delta sigma weight residual 1.339 1.387 -0.048 3.40e-02 8.65e+02 1.99e+00 bond pdb=" C THR L 56 " pdb=" N PRO L 57 " ideal model delta sigma weight residual 1.339 1.387 -0.047 3.40e-02 8.65e+02 1.95e+00 bond pdb=" C SER F 208 " pdb=" N LEU F 209 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.45e+00 bond pdb=" C SER H 208 " pdb=" N LEU H 209 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.39e+00 bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.336 1.347 -0.012 9.80e-03 1.04e+04 1.39e+00 ... (remaining 21873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 28757 1.73 - 3.46: 676 3.46 - 5.20: 121 5.20 - 6.93: 39 6.93 - 8.66: 13 Bond angle restraints: 29606 Sorted by residual: angle pdb=" N LEU G 39 " pdb=" CA LEU G 39 " pdb=" C LEU G 39 " ideal model delta sigma weight residual 114.56 108.33 6.23 1.27e+00 6.20e-01 2.40e+01 angle pdb=" N LEU E 39 " pdb=" CA LEU E 39 " pdb=" C LEU E 39 " ideal model delta sigma weight residual 114.56 108.35 6.21 1.27e+00 6.20e-01 2.39e+01 angle pdb=" CA ARG H 172 " pdb=" CB ARG H 172 " pdb=" CG ARG H 172 " ideal model delta sigma weight residual 114.10 122.76 -8.66 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA ARG F 172 " pdb=" CB ARG F 172 " pdb=" CG ARG F 172 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" C MET G 206 " pdb=" N ARG G 207 " pdb=" CA ARG G 207 " ideal model delta sigma weight residual 122.56 115.51 7.05 1.72e+00 3.38e-01 1.68e+01 ... (remaining 29601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11632 17.79 - 35.58: 1079 35.58 - 53.37: 241 53.37 - 71.16: 28 71.16 - 88.95: 24 Dihedral angle restraints: 13004 sinusoidal: 5182 harmonic: 7822 Sorted by residual: dihedral pdb=" CA ARG C 108 " pdb=" C ARG C 108 " pdb=" N HIS C 109 " pdb=" CA HIS C 109 " ideal model delta harmonic sigma weight residual -180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ARG A 108 " pdb=" C ARG A 108 " pdb=" N HIS A 109 " pdb=" CA HIS A 109 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG F 172 " pdb=" C ARG F 172 " pdb=" N GLN F 173 " pdb=" CA GLN F 173 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 13001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2589 0.051 - 0.102: 587 0.102 - 0.153: 116 0.153 - 0.205: 2 0.205 - 0.256: 2 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CA ARG H 172 " pdb=" N ARG H 172 " pdb=" C ARG H 172 " pdb=" CB ARG H 172 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ARG F 172 " pdb=" N ARG F 172 " pdb=" C ARG F 172 " pdb=" CB ARG F 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA THR J 56 " pdb=" N THR J 56 " pdb=" C THR J 56 " pdb=" CB THR J 56 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 3293 not shown) Planarity restraints: 3766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 129 " -0.021 2.00e-02 2.50e+03 1.97e-02 9.72e+00 pdb=" CG TRP G 129 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP G 129 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP G 129 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 129 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 129 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 129 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 129 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 129 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 129 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 129 " 0.021 2.00e-02 2.50e+03 1.96e-02 9.62e+00 pdb=" CG TRP E 129 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP E 129 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 129 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 129 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 129 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 129 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 129 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 129 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 129 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 30 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO A 31 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " 0.040 5.00e-02 4.00e+02 ... (remaining 3763 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 495 2.68 - 3.24: 23872 3.24 - 3.79: 34703 3.79 - 4.35: 44092 4.35 - 4.90: 69574 Nonbonded interactions: 172736 Sorted by model distance: nonbonded pdb=" NH1 ARG H 172 " pdb=" OE1 GLN H 173 " model vdw 2.130 3.120 nonbonded pdb=" NH1 ARG F 172 " pdb=" OE1 GLN F 173 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR B 65 " pdb=" OH TYR B 99 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR D 65 " pdb=" OH TYR D 99 " model vdw 2.142 3.040 nonbonded pdb=" O MET B 238 " pdb=" OG1 THR B 241 " model vdw 2.152 3.040 ... (remaining 172731 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 218 or resid 224 through 495)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 218 or resid 224 through 495)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 37 through 216) selection = chain 'F' selection = (chain 'G' and resid 37 through 216) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 31 through 58) selection = chain 'J' selection = (chain 'K' and resid 31 through 58) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.880 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.004 0.048 21878 Z= 0.184 Angle : 0.683 8.660 29606 Z= 0.367 Chirality : 0.044 0.256 3296 Planarity : 0.005 0.073 3766 Dihedral : 14.763 88.953 7936 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2606 helix: 0.66 (0.13), residues: 1680 sheet: -1.51 (1.18), residues: 20 loop : -1.57 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 108 TYR 0.015 0.001 TYR F 57 PHE 0.027 0.002 PHE A 194 TRP 0.053 0.002 TRP G 129 HIS 0.007 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00402 (21878) covalent geometry : angle 0.68290 (29606) hydrogen bonds : bond 0.14598 ( 1244) hydrogen bonds : angle 5.72232 ( 3648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 634 time to evaluate : 0.825 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: G 204 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6445 (t0) REVERT: C 224 ARG cc_start: 0.4852 (mmt-90) cc_final: 0.4306 (mtp85) REVERT: C 238 MET cc_start: 0.5759 (mtt) cc_final: 0.5478 (ttm) REVERT: C 299 ARG cc_start: 0.7413 (mmt-90) cc_final: 0.7060 (mtm-85) REVERT: C 318 LYS cc_start: 0.7382 (mmpt) cc_final: 0.7142 (tppt) REVERT: C 485 LEU cc_start: 0.8635 (mm) cc_final: 0.8424 (tp) REVERT: H 76 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7532 (tp-100) REVERT: H 77 ILE cc_start: 0.8304 (mm) cc_final: 0.7917 (mm) REVERT: H 107 LYS cc_start: 0.7783 (tttt) cc_final: 0.7419 (tttt) REVERT: H 110 ASP cc_start: 0.7438 (m-30) cc_final: 0.7160 (t0) REVERT: H 186 LYS cc_start: 0.6338 (tptt) cc_final: 0.5773 (mmmt) REVERT: H 204 ASN cc_start: 0.7459 (m-40) cc_final: 0.7214 (m-40) REVERT: H 214 ASN cc_start: 0.7203 (p0) cc_final: 0.6887 (p0) REVERT: H 216 MET cc_start: 0.7319 (tpp) cc_final: 0.7077 (mtt) REVERT: D 83 TYR cc_start: 0.8390 (m-80) cc_final: 0.8001 (m-80) REVERT: D 243 GLU cc_start: 0.7204 (pm20) cc_final: 0.6534 (tt0) REVERT: D 368 MET cc_start: 0.8257 (mmm) cc_final: 0.8021 (mmm) REVERT: D 406 VAL cc_start: 0.8413 (p) cc_final: 0.8124 (t) REVERT: E 211 LEU cc_start: 0.7107 (mt) cc_final: 0.4675 (mt) REVERT: A 224 ARG cc_start: 0.4891 (mmt-90) cc_final: 0.4328 (mtp85) REVERT: A 238 MET cc_start: 0.5747 (mtt) cc_final: 0.5464 (ttm) REVERT: A 299 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.6923 (mtm-85) REVERT: A 318 LYS cc_start: 0.7410 (mmpt) cc_final: 0.7157 (tppt) REVERT: A 484 CYS cc_start: 0.8712 (t) cc_final: 0.8509 (t) REVERT: F 76 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7541 (tp-100) REVERT: F 77 ILE cc_start: 0.8285 (mm) cc_final: 0.7897 (mm) REVERT: F 107 LYS cc_start: 0.7804 (tttt) cc_final: 0.7424 (tttt) REVERT: F 110 ASP cc_start: 0.7444 (m-30) cc_final: 0.7147 (t0) REVERT: F 186 LYS cc_start: 0.6323 (tptt) cc_final: 0.5759 (mmmt) REVERT: F 191 THR cc_start: 0.6496 (m) cc_final: 0.6193 (m) REVERT: F 204 ASN cc_start: 0.7470 (m-40) cc_final: 0.7230 (m-40) REVERT: F 214 ASN cc_start: 0.7230 (p0) cc_final: 0.6919 (p0) REVERT: F 216 MET cc_start: 0.7317 (tpp) cc_final: 0.7081 (mtt) REVERT: B 83 TYR cc_start: 0.8364 (m-80) cc_final: 0.7992 (m-80) REVERT: B 243 GLU cc_start: 0.7242 (pm20) cc_final: 0.6679 (tt0) REVERT: B 406 VAL cc_start: 0.8417 (p) cc_final: 0.8138 (t) outliers start: 1 outliers final: 0 residues processed: 635 average time/residue: 0.1730 time to fit residues: 164.0431 Evaluate side-chains 397 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 124 HIS G 174 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS H 96 ASN ** H 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN D 33 GLN D 202 ASN E 124 HIS E 174 HIS ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 96 ASN F 124 HIS F 213 GLN B 33 GLN B 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106649 restraints weight = 51256.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105191 restraints weight = 34930.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105305 restraints weight = 45288.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106175 restraints weight = 29523.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106505 restraints weight = 24964.572| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21878 Z= 0.158 Angle : 0.682 9.926 29606 Z= 0.355 Chirality : 0.044 0.239 3296 Planarity : 0.005 0.062 3766 Dihedral : 4.562 26.814 2924 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.14 % Favored : 93.78 % Rotamer: Outliers : 2.09 % Allowed : 13.48 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2606 helix: 0.58 (0.12), residues: 1716 sheet: -1.00 (1.27), residues: 20 loop : -1.68 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 247 TYR 0.020 0.001 TYR B 137 PHE 0.022 0.002 PHE C 329 TRP 0.036 0.002 TRP A 19 HIS 0.006 0.001 HIS G 174 Details of bonding type rmsd covalent geometry : bond 0.00339 (21878) covalent geometry : angle 0.68167 (29606) hydrogen bonds : bond 0.05070 ( 1244) hydrogen bonds : angle 4.85586 ( 3648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 466 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 148 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7076 (tpp) REVERT: C 224 ARG cc_start: 0.4882 (mmt-90) cc_final: 0.4169 (mtp85) REVERT: C 238 MET cc_start: 0.6075 (mtt) cc_final: 0.5820 (ttm) REVERT: C 299 ARG cc_start: 0.7792 (mmt-90) cc_final: 0.7276 (mtm-85) REVERT: C 318 LYS cc_start: 0.7517 (mmpt) cc_final: 0.7242 (tppt) REVERT: C 404 VAL cc_start: 0.8824 (p) cc_final: 0.8593 (t) REVERT: H 76 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7782 (tp-100) REVERT: H 77 ILE cc_start: 0.8063 (mm) cc_final: 0.7694 (mm) REVERT: H 80 GLN cc_start: 0.8376 (tt0) cc_final: 0.7971 (tt0) REVERT: H 107 LYS cc_start: 0.8123 (tttt) cc_final: 0.7507 (ttpt) REVERT: H 110 ASP cc_start: 0.7757 (m-30) cc_final: 0.7345 (t0) REVERT: D 33 GLN cc_start: 0.4080 (OUTLIER) cc_final: 0.2560 (pm20) REVERT: D 83 TYR cc_start: 0.8408 (m-80) cc_final: 0.8144 (m-80) REVERT: D 368 MET cc_start: 0.8173 (mmm) cc_final: 0.7891 (mmm) REVERT: D 406 VAL cc_start: 0.8582 (p) cc_final: 0.8286 (t) REVERT: D 429 ARG cc_start: 0.7995 (mmp-170) cc_final: 0.6555 (tpp-160) REVERT: E 148 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7045 (tpp) REVERT: A 224 ARG cc_start: 0.4890 (mmt-90) cc_final: 0.4181 (mtp85) REVERT: A 238 MET cc_start: 0.6062 (mtt) cc_final: 0.5816 (ttm) REVERT: A 299 ARG cc_start: 0.7799 (mmt-90) cc_final: 0.7193 (mtm-85) REVERT: A 318 LYS cc_start: 0.7501 (mmpt) cc_final: 0.7263 (tppt) REVERT: A 404 VAL cc_start: 0.8822 (p) cc_final: 0.8586 (t) REVERT: F 76 GLN cc_start: 0.8321 (tp-100) cc_final: 0.7779 (tp-100) REVERT: F 77 ILE cc_start: 0.8070 (mm) cc_final: 0.7704 (mm) REVERT: F 80 GLN cc_start: 0.8364 (tt0) cc_final: 0.7988 (tt0) REVERT: F 90 TYR cc_start: 0.7655 (t80) cc_final: 0.7442 (t80) REVERT: F 107 LYS cc_start: 0.8106 (tttt) cc_final: 0.7519 (ttpt) REVERT: F 110 ASP cc_start: 0.7758 (m-30) cc_final: 0.7340 (t0) REVERT: F 148 MET cc_start: 0.6415 (mmm) cc_final: 0.6187 (mmm) REVERT: F 178 PHE cc_start: 0.8840 (t80) cc_final: 0.8527 (t80) REVERT: B 33 GLN cc_start: 0.4072 (OUTLIER) cc_final: 0.2543 (pm20) REVERT: B 83 TYR cc_start: 0.8404 (m-80) cc_final: 0.8140 (m-80) REVERT: B 406 VAL cc_start: 0.8577 (p) cc_final: 0.8275 (t) REVERT: B 429 ARG cc_start: 0.7994 (mmp-170) cc_final: 0.6553 (tpp-160) outliers start: 48 outliers final: 24 residues processed: 484 average time/residue: 0.1581 time to fit residues: 118.0645 Evaluate side-chains 439 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 411 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 193 optimal weight: 0.1980 chunk 217 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS C 416 ASN D 33 GLN D 202 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 416 ASN B 33 GLN B 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.135859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108060 restraints weight = 51387.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106751 restraints weight = 35867.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107051 restraints weight = 41119.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.107663 restraints weight = 28597.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108034 restraints weight = 24611.361| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21878 Z= 0.140 Angle : 0.638 9.323 29606 Z= 0.330 Chirality : 0.043 0.167 3296 Planarity : 0.004 0.050 3766 Dihedral : 4.406 23.467 2922 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 2.35 % Allowed : 15.96 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2606 helix: 0.65 (0.12), residues: 1716 sheet: -0.86 (1.39), residues: 20 loop : -1.66 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 247 TYR 0.022 0.001 TYR D 137 PHE 0.026 0.002 PHE D 175 TRP 0.042 0.002 TRP C 19 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00301 (21878) covalent geometry : angle 0.63767 (29606) hydrogen bonds : bond 0.04407 ( 1244) hydrogen bonds : angle 4.61733 ( 3648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 458 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 129 TRP cc_start: 0.7103 (t60) cc_final: 0.6878 (t60) REVERT: G 132 ASN cc_start: 0.7822 (m110) cc_final: 0.7237 (t0) REVERT: G 148 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7140 (tpp) REVERT: G 181 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7922 (mtmt) REVERT: C 60 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: C 224 ARG cc_start: 0.4913 (mmt-90) cc_final: 0.4222 (mtp85) REVERT: C 238 MET cc_start: 0.6100 (mtt) cc_final: 0.5859 (ttm) REVERT: C 299 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7196 (mtm-85) REVERT: C 318 LYS cc_start: 0.7491 (mmpt) cc_final: 0.7268 (tppt) REVERT: C 404 VAL cc_start: 0.8685 (p) cc_final: 0.8481 (t) REVERT: H 76 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7731 (tp-100) REVERT: H 77 ILE cc_start: 0.8043 (mm) cc_final: 0.7699 (mm) REVERT: H 107 LYS cc_start: 0.8032 (tttt) cc_final: 0.7441 (tttt) REVERT: H 110 ASP cc_start: 0.7629 (m-30) cc_final: 0.7252 (t0) REVERT: H 148 MET cc_start: 0.6513 (mmm) cc_final: 0.6218 (mmm) REVERT: D 83 TYR cc_start: 0.8375 (m-80) cc_final: 0.8159 (m-80) REVERT: D 202 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7903 (t0) REVERT: D 247 ARG cc_start: 0.5926 (mmt180) cc_final: 0.5674 (mmt180) REVERT: D 406 VAL cc_start: 0.8592 (p) cc_final: 0.8309 (t) REVERT: D 429 ARG cc_start: 0.7920 (mmp-170) cc_final: 0.6580 (ttm170) REVERT: E 129 TRP cc_start: 0.7094 (t60) cc_final: 0.6873 (t60) REVERT: E 132 ASN cc_start: 0.7818 (m110) cc_final: 0.7241 (t0) REVERT: E 148 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7121 (tpp) REVERT: E 181 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7924 (mtmt) REVERT: A 60 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: A 224 ARG cc_start: 0.4923 (mmt-90) cc_final: 0.4246 (mtp85) REVERT: A 238 MET cc_start: 0.6105 (mtt) cc_final: 0.5867 (ttm) REVERT: A 299 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7200 (mtm-85) REVERT: A 318 LYS cc_start: 0.7473 (mmpt) cc_final: 0.7254 (tppt) REVERT: A 404 VAL cc_start: 0.8677 (p) cc_final: 0.8463 (t) REVERT: F 76 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7739 (tp-100) REVERT: F 77 ILE cc_start: 0.8045 (mm) cc_final: 0.7695 (mm) REVERT: F 107 LYS cc_start: 0.8040 (tttt) cc_final: 0.7452 (tttt) REVERT: F 110 ASP cc_start: 0.7636 (m-30) cc_final: 0.7255 (t0) REVERT: F 148 MET cc_start: 0.6611 (mmm) cc_final: 0.6383 (mmm) REVERT: F 186 LYS cc_start: 0.5785 (tptt) cc_final: 0.5544 (tptt) REVERT: B 83 TYR cc_start: 0.8377 (m-80) cc_final: 0.8158 (m-80) REVERT: B 202 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7882 (t0) REVERT: B 406 VAL cc_start: 0.8588 (p) cc_final: 0.8306 (t) REVERT: B 429 ARG cc_start: 0.7922 (mmp-170) cc_final: 0.6575 (ttm170) outliers start: 54 outliers final: 23 residues processed: 486 average time/residue: 0.1631 time to fit residues: 120.6445 Evaluate side-chains 440 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 409 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 193 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 179 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS C 416 ASN D 202 ASN E 62 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 416 ASN B 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108467 restraints weight = 51236.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106979 restraints weight = 39474.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107385 restraints weight = 40066.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107809 restraints weight = 30158.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107998 restraints weight = 25630.885| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21878 Z= 0.140 Angle : 0.630 9.730 29606 Z= 0.323 Chirality : 0.043 0.343 3296 Planarity : 0.004 0.039 3766 Dihedral : 4.295 21.760 2922 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 2.43 % Allowed : 17.83 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2606 helix: 0.68 (0.12), residues: 1720 sheet: -1.02 (1.37), residues: 20 loop : -1.64 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 207 TYR 0.022 0.001 TYR D 137 PHE 0.034 0.001 PHE D 187 TRP 0.035 0.002 TRP A 19 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00304 (21878) covalent geometry : angle 0.62996 (29606) hydrogen bonds : bond 0.04191 ( 1244) hydrogen bonds : angle 4.52344 ( 3648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 455 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 42 LEU cc_start: 0.6184 (mt) cc_final: 0.5943 (tp) REVERT: G 76 GLN cc_start: 0.8495 (pm20) cc_final: 0.7969 (pm20) REVERT: G 148 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7170 (tpp) REVERT: G 181 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7890 (mtmt) REVERT: C 19 TRP cc_start: 0.7855 (p90) cc_final: 0.7434 (p90) REVERT: C 60 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: C 224 ARG cc_start: 0.4954 (mmt-90) cc_final: 0.4272 (mtp85) REVERT: C 238 MET cc_start: 0.6139 (mtt) cc_final: 0.5894 (ttm) REVERT: C 299 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7268 (mtm-85) REVERT: C 318 LYS cc_start: 0.7462 (mmpt) cc_final: 0.7253 (tppt) REVERT: H 76 GLN cc_start: 0.8358 (tp-100) cc_final: 0.7801 (tp-100) REVERT: H 80 GLN cc_start: 0.8330 (tt0) cc_final: 0.7979 (tt0) REVERT: H 107 LYS cc_start: 0.8001 (tttt) cc_final: 0.7467 (tttt) REVERT: H 110 ASP cc_start: 0.7696 (m-30) cc_final: 0.7294 (t0) REVERT: H 148 MET cc_start: 0.6717 (mmm) cc_final: 0.6421 (mmm) REVERT: H 181 LYS cc_start: 0.6127 (tptp) cc_final: 0.5738 (tptp) REVERT: H 207 ARG cc_start: 0.8551 (ptm160) cc_final: 0.8273 (tmm-80) REVERT: D 83 TYR cc_start: 0.8375 (m-80) cc_final: 0.8145 (m-80) REVERT: D 247 ARG cc_start: 0.5847 (mmt180) cc_final: 0.5487 (mmt180) REVERT: D 406 VAL cc_start: 0.8634 (p) cc_final: 0.8362 (t) REVERT: D 429 ARG cc_start: 0.7791 (mmp-170) cc_final: 0.6544 (ttm170) REVERT: E 42 LEU cc_start: 0.6170 (mt) cc_final: 0.5922 (tp) REVERT: E 148 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7154 (tpp) REVERT: E 181 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7893 (mtmt) REVERT: A 19 TRP cc_start: 0.7772 (p90) cc_final: 0.7368 (p90) REVERT: A 45 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8286 (pp) REVERT: A 60 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: A 193 PHE cc_start: 0.8019 (t80) cc_final: 0.7777 (t80) REVERT: A 224 ARG cc_start: 0.4972 (mmt-90) cc_final: 0.4279 (mtp85) REVERT: A 238 MET cc_start: 0.5948 (mtt) cc_final: 0.5695 (ttm) REVERT: A 299 ARG cc_start: 0.7918 (mmt-90) cc_final: 0.7159 (mtm-85) REVERT: A 329 PHE cc_start: 0.8672 (t80) cc_final: 0.8402 (t80) REVERT: F 76 GLN cc_start: 0.8349 (tp-100) cc_final: 0.7796 (tp-100) REVERT: F 80 GLN cc_start: 0.8325 (tt0) cc_final: 0.7969 (tt0) REVERT: F 90 TYR cc_start: 0.7431 (t80) cc_final: 0.7163 (t80) REVERT: F 107 LYS cc_start: 0.7997 (tttt) cc_final: 0.7475 (tttt) REVERT: F 110 ASP cc_start: 0.7685 (m-30) cc_final: 0.7289 (t0) REVERT: F 148 MET cc_start: 0.6802 (mmm) cc_final: 0.6531 (mmm) REVERT: F 186 LYS cc_start: 0.5826 (tptt) cc_final: 0.5599 (tptt) REVERT: F 207 ARG cc_start: 0.8559 (ptm160) cc_final: 0.8285 (tmm-80) REVERT: B 83 TYR cc_start: 0.8372 (m-80) cc_final: 0.8141 (m-80) REVERT: B 406 VAL cc_start: 0.8636 (p) cc_final: 0.8343 (t) REVERT: B 429 ARG cc_start: 0.7792 (mmp-170) cc_final: 0.6592 (ttm170) outliers start: 56 outliers final: 28 residues processed: 484 average time/residue: 0.1626 time to fit residues: 120.3645 Evaluate side-chains 449 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 414 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 193 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 204 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 204 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 70 ASN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.135086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107219 restraints weight = 50990.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105716 restraints weight = 40432.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106324 restraints weight = 38530.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106723 restraints weight = 29560.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.107148 restraints weight = 25403.035| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21878 Z= 0.153 Angle : 0.633 10.454 29606 Z= 0.329 Chirality : 0.043 0.204 3296 Planarity : 0.004 0.037 3766 Dihedral : 4.261 21.168 2922 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 2.91 % Allowed : 19.48 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2606 helix: 0.71 (0.12), residues: 1728 sheet: -1.19 (1.34), residues: 20 loop : -1.61 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 207 TYR 0.031 0.001 TYR B 137 PHE 0.053 0.002 PHE D 187 TRP 0.028 0.002 TRP E 129 HIS 0.005 0.001 HIS D 479 Details of bonding type rmsd covalent geometry : bond 0.00346 (21878) covalent geometry : angle 0.63326 (29606) hydrogen bonds : bond 0.04175 ( 1244) hydrogen bonds : angle 4.53299 ( 3648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 451 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 42 LEU cc_start: 0.6185 (mt) cc_final: 0.5934 (tp) REVERT: G 76 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: G 132 ASN cc_start: 0.7824 (m110) cc_final: 0.7197 (t0) REVERT: G 148 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7236 (tpp) REVERT: G 181 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7879 (mtmt) REVERT: G 193 ASP cc_start: 0.8717 (t0) cc_final: 0.8143 (p0) REVERT: C 60 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: C 224 ARG cc_start: 0.5088 (mmt-90) cc_final: 0.4456 (mtp85) REVERT: C 238 MET cc_start: 0.6141 (mtt) cc_final: 0.5893 (ttm) REVERT: C 299 ARG cc_start: 0.7794 (mmt-90) cc_final: 0.7213 (mtm-85) REVERT: C 318 LYS cc_start: 0.7471 (mmpt) cc_final: 0.7246 (tppt) REVERT: H 76 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7838 (tp-100) REVERT: H 84 HIS cc_start: 0.6373 (p-80) cc_final: 0.5633 (p-80) REVERT: H 107 LYS cc_start: 0.8093 (tttt) cc_final: 0.7528 (tttt) REVERT: H 110 ASP cc_start: 0.7661 (m-30) cc_final: 0.7319 (t0) REVERT: H 148 MET cc_start: 0.6714 (mmm) cc_final: 0.6430 (mmm) REVERT: H 172 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7412 (pmt-80) REVERT: H 181 LYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5848 (tptp) REVERT: H 186 LYS cc_start: 0.5620 (tptt) cc_final: 0.5287 (tptt) REVERT: H 207 ARG cc_start: 0.8532 (ptm160) cc_final: 0.8254 (tmm-80) REVERT: D 83 TYR cc_start: 0.8356 (m-80) cc_final: 0.8152 (m-80) REVERT: D 194 PHE cc_start: 0.7595 (m-80) cc_final: 0.7336 (m-80) REVERT: D 247 ARG cc_start: 0.5839 (mmt180) cc_final: 0.5504 (mmt180) REVERT: D 406 VAL cc_start: 0.8651 (p) cc_final: 0.8393 (t) REVERT: D 429 ARG cc_start: 0.7802 (mmp-170) cc_final: 0.6745 (ttm170) REVERT: D 445 MET cc_start: 0.7966 (tpp) cc_final: 0.7376 (mmt) REVERT: E 42 LEU cc_start: 0.6174 (mt) cc_final: 0.5930 (tp) REVERT: E 76 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: E 132 ASN cc_start: 0.7830 (m110) cc_final: 0.7206 (t0) REVERT: E 148 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7229 (tpp) REVERT: E 181 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7881 (mtmt) REVERT: E 193 ASP cc_start: 0.8726 (t0) cc_final: 0.8127 (p0) REVERT: E 206 MET cc_start: 0.6746 (mmp) cc_final: 0.6461 (mmp) REVERT: A 60 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: A 224 ARG cc_start: 0.5040 (mmt-90) cc_final: 0.4417 (mtp85) REVERT: A 238 MET cc_start: 0.5902 (mtt) cc_final: 0.5646 (ttm) REVERT: A 299 ARG cc_start: 0.7923 (mmt-90) cc_final: 0.7166 (mtm-85) REVERT: A 329 PHE cc_start: 0.8716 (t80) cc_final: 0.8386 (t80) REVERT: F 76 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7848 (tp-100) REVERT: F 84 HIS cc_start: 0.6378 (p-80) cc_final: 0.5665 (p-80) REVERT: F 90 TYR cc_start: 0.7479 (t80) cc_final: 0.7258 (t80) REVERT: F 107 LYS cc_start: 0.8091 (tttt) cc_final: 0.7548 (tttt) REVERT: F 110 ASP cc_start: 0.7655 (m-30) cc_final: 0.7301 (t0) REVERT: F 148 MET cc_start: 0.6851 (mmm) cc_final: 0.6579 (mmm) REVERT: F 172 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7402 (pmt-80) REVERT: F 186 LYS cc_start: 0.5756 (tptt) cc_final: 0.5512 (tptt) REVERT: F 200 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.6106 (mp10) REVERT: F 207 ARG cc_start: 0.8542 (ptm160) cc_final: 0.8262 (tmm-80) REVERT: B 83 TYR cc_start: 0.8350 (m-80) cc_final: 0.8149 (m-80) REVERT: B 183 MET cc_start: 0.4654 (OUTLIER) cc_final: 0.4426 (tpt) REVERT: B 194 PHE cc_start: 0.7585 (m-80) cc_final: 0.7311 (m-80) REVERT: B 406 VAL cc_start: 0.8641 (p) cc_final: 0.8392 (t) REVERT: B 429 ARG cc_start: 0.7816 (mmp-170) cc_final: 0.6760 (ttm170) REVERT: B 445 MET cc_start: 0.7955 (tpp) cc_final: 0.7376 (mmt) outliers start: 67 outliers final: 39 residues processed: 486 average time/residue: 0.1647 time to fit residues: 121.3896 Evaluate side-chains 464 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 412 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 28 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS H 41 GLN H 80 GLN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 80 GLN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.134412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106981 restraints weight = 51275.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105080 restraints weight = 43213.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105658 restraints weight = 39401.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106385 restraints weight = 28726.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106646 restraints weight = 25220.162| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21878 Z= 0.161 Angle : 0.648 10.660 29606 Z= 0.336 Chirality : 0.043 0.344 3296 Planarity : 0.004 0.050 3766 Dihedral : 4.269 21.406 2922 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 3.26 % Allowed : 20.52 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2606 helix: 0.71 (0.12), residues: 1726 sheet: -1.22 (1.32), residues: 20 loop : -1.60 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 100 TYR 0.035 0.001 TYR D 137 PHE 0.067 0.002 PHE B 187 TRP 0.060 0.003 TRP C 19 HIS 0.004 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00368 (21878) covalent geometry : angle 0.64790 (29606) hydrogen bonds : bond 0.04225 ( 1244) hydrogen bonds : angle 4.55077 ( 3648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 440 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: G 148 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7147 (tpp) REVERT: G 206 MET cc_start: 0.6712 (mmp) cc_final: 0.6368 (mmp) REVERT: C 60 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: C 224 ARG cc_start: 0.5067 (mmt-90) cc_final: 0.4491 (mtp85) REVERT: C 238 MET cc_start: 0.6104 (mtt) cc_final: 0.5866 (ttm) REVERT: C 299 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7235 (mtm-85) REVERT: C 318 LYS cc_start: 0.7564 (mmpt) cc_final: 0.7041 (tppt) REVERT: H 76 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7776 (tp-100) REVERT: H 77 ILE cc_start: 0.7969 (mm) cc_final: 0.7598 (mm) REVERT: H 80 GLN cc_start: 0.8361 (tt0) cc_final: 0.8083 (tt0) REVERT: H 84 HIS cc_start: 0.6280 (p-80) cc_final: 0.5522 (p-80) REVERT: H 107 LYS cc_start: 0.8061 (tttt) cc_final: 0.7517 (tttt) REVERT: H 110 ASP cc_start: 0.7627 (m-30) cc_final: 0.7319 (t0) REVERT: H 148 MET cc_start: 0.6753 (mmm) cc_final: 0.5802 (mmm) REVERT: H 152 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7763 (mmtp) REVERT: H 172 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7389 (pmt-80) REVERT: H 181 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5897 (tptp) REVERT: H 186 LYS cc_start: 0.5606 (tptt) cc_final: 0.5301 (tptt) REVERT: H 207 ARG cc_start: 0.8535 (ptm160) cc_final: 0.8233 (tmm-80) REVERT: D 83 TYR cc_start: 0.8320 (m-80) cc_final: 0.8106 (m-80) REVERT: D 247 ARG cc_start: 0.5702 (mmt180) cc_final: 0.5470 (mmt180) REVERT: D 406 VAL cc_start: 0.8640 (p) cc_final: 0.8367 (t) REVERT: D 429 ARG cc_start: 0.7824 (mmp-170) cc_final: 0.6803 (ttm170) REVERT: D 437 LYS cc_start: 0.8531 (tppt) cc_final: 0.8141 (mmmm) REVERT: E 76 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: E 148 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7185 (tpp) REVERT: E 193 ASP cc_start: 0.8719 (t0) cc_final: 0.8197 (p0) REVERT: A 60 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: A 193 PHE cc_start: 0.8170 (t80) cc_final: 0.7925 (t80) REVERT: A 224 ARG cc_start: 0.5087 (mmt-90) cc_final: 0.4505 (mtp85) REVERT: A 238 MET cc_start: 0.5808 (mtt) cc_final: 0.5592 (ttm) REVERT: A 240 PHE cc_start: 0.8763 (m-80) cc_final: 0.8026 (m-80) REVERT: A 295 PHE cc_start: 0.8219 (m-80) cc_final: 0.7772 (m-80) REVERT: A 299 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.7167 (mtm-85) REVERT: A 329 PHE cc_start: 0.8678 (t80) cc_final: 0.8279 (t80) REVERT: F 76 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7670 (tp-100) REVERT: F 77 ILE cc_start: 0.8033 (mm) cc_final: 0.7624 (mm) REVERT: F 80 GLN cc_start: 0.8378 (tt0) cc_final: 0.8063 (tt0) REVERT: F 84 HIS cc_start: 0.6236 (p-80) cc_final: 0.5496 (p-80) REVERT: F 107 LYS cc_start: 0.8091 (tttt) cc_final: 0.7542 (tttt) REVERT: F 110 ASP cc_start: 0.7631 (m-30) cc_final: 0.7328 (t0) REVERT: F 148 MET cc_start: 0.6742 (mmm) cc_final: 0.6494 (mmm) REVERT: F 172 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7336 (pmt-80) REVERT: F 186 LYS cc_start: 0.5755 (tptt) cc_final: 0.5494 (tptt) REVERT: F 200 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6161 (mp10) REVERT: F 207 ARG cc_start: 0.8539 (ptm160) cc_final: 0.8243 (tmm-80) REVERT: B 83 TYR cc_start: 0.8335 (m-80) cc_final: 0.8127 (m-80) REVERT: B 406 VAL cc_start: 0.8634 (p) cc_final: 0.8366 (t) REVERT: B 429 ARG cc_start: 0.7818 (mmp-170) cc_final: 0.6788 (ttm170) REVERT: B 437 LYS cc_start: 0.8523 (tppt) cc_final: 0.8139 (mmmm) outliers start: 75 outliers final: 42 residues processed: 479 average time/residue: 0.1645 time to fit residues: 119.7143 Evaluate side-chains 463 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 411 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 19 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 219 optimal weight: 0.0980 chunk 245 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.137079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110331 restraints weight = 51241.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108846 restraints weight = 43953.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109530 restraints weight = 40945.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109947 restraints weight = 31035.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110117 restraints weight = 26536.164| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21878 Z= 0.131 Angle : 0.645 11.081 29606 Z= 0.329 Chirality : 0.042 0.316 3296 Planarity : 0.004 0.039 3766 Dihedral : 4.164 19.317 2922 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 2.22 % Allowed : 22.30 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2606 helix: 0.80 (0.13), residues: 1736 sheet: -1.38 (1.30), residues: 20 loop : -1.52 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 100 TYR 0.024 0.001 TYR A 444 PHE 0.052 0.001 PHE B 187 TRP 0.045 0.002 TRP A 19 HIS 0.003 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00281 (21878) covalent geometry : angle 0.64450 (29606) hydrogen bonds : bond 0.03890 ( 1244) hydrogen bonds : angle 4.39558 ( 3648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 479 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: G 132 ASN cc_start: 0.7603 (m110) cc_final: 0.7165 (t0) REVERT: G 148 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7020 (tpp) REVERT: C 60 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: C 193 PHE cc_start: 0.8007 (t80) cc_final: 0.7792 (t80) REVERT: C 224 ARG cc_start: 0.4788 (mmt-90) cc_final: 0.4254 (mtp85) REVERT: C 238 MET cc_start: 0.5956 (mtt) cc_final: 0.5720 (ttm) REVERT: C 299 ARG cc_start: 0.7792 (mmt-90) cc_final: 0.7206 (mtm-85) REVERT: C 311 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7243 (mpp80) REVERT: C 318 LYS cc_start: 0.7507 (mmpt) cc_final: 0.7281 (tppt) REVERT: H 76 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7795 (tp-100) REVERT: H 84 HIS cc_start: 0.6106 (p-80) cc_final: 0.5513 (p-80) REVERT: H 107 LYS cc_start: 0.7966 (tttt) cc_final: 0.7435 (tttt) REVERT: H 110 ASP cc_start: 0.7578 (m-30) cc_final: 0.7290 (t0) REVERT: H 148 MET cc_start: 0.6817 (mmm) cc_final: 0.6501 (mmm) REVERT: H 172 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7425 (pmt-80) REVERT: H 181 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5994 (tptp) REVERT: H 206 MET cc_start: 0.7535 (mmm) cc_final: 0.6436 (mmm) REVERT: H 207 ARG cc_start: 0.8478 (ptm160) cc_final: 0.8213 (tmm-80) REVERT: D 194 PHE cc_start: 0.7387 (m-80) cc_final: 0.7114 (m-80) REVERT: D 406 VAL cc_start: 0.8588 (p) cc_final: 0.8294 (t) REVERT: D 429 ARG cc_start: 0.7734 (mmp-170) cc_final: 0.6757 (ttm170) REVERT: D 437 LYS cc_start: 0.8448 (tppt) cc_final: 0.8166 (mmmm) REVERT: E 76 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: E 132 ASN cc_start: 0.7592 (m110) cc_final: 0.7179 (t0) REVERT: E 148 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7036 (tpp) REVERT: E 193 ASP cc_start: 0.8708 (t0) cc_final: 0.8086 (p0) REVERT: A 60 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: A 193 PHE cc_start: 0.8104 (t80) cc_final: 0.7902 (t80) REVERT: A 224 ARG cc_start: 0.4794 (mmt-90) cc_final: 0.4263 (mtp85) REVERT: A 238 MET cc_start: 0.5724 (mtt) cc_final: 0.5509 (ttm) REVERT: A 240 PHE cc_start: 0.8724 (m-80) cc_final: 0.7971 (m-80) REVERT: A 295 PHE cc_start: 0.8056 (m-80) cc_final: 0.7615 (m-80) REVERT: A 299 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7090 (mtm-85) REVERT: A 400 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7035 (tp) REVERT: F 76 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7715 (tp-100) REVERT: F 77 ILE cc_start: 0.7966 (mm) cc_final: 0.7557 (mm) REVERT: F 80 GLN cc_start: 0.8284 (tt0) cc_final: 0.8078 (tt0) REVERT: F 84 HIS cc_start: 0.6149 (p-80) cc_final: 0.5537 (p-80) REVERT: F 107 LYS cc_start: 0.7978 (tttt) cc_final: 0.7449 (tttt) REVERT: F 110 ASP cc_start: 0.7610 (m-30) cc_final: 0.7323 (t0) REVERT: F 172 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6943 (pmt-80) REVERT: F 206 MET cc_start: 0.7543 (mmm) cc_final: 0.6413 (mmm) REVERT: F 207 ARG cc_start: 0.8468 (ptm160) cc_final: 0.8193 (tmm-80) REVERT: B 194 PHE cc_start: 0.7441 (m-80) cc_final: 0.7208 (m-80) REVERT: B 406 VAL cc_start: 0.8594 (p) cc_final: 0.8338 (t) REVERT: B 429 ARG cc_start: 0.7721 (mmp-170) cc_final: 0.6731 (ttm170) REVERT: B 437 LYS cc_start: 0.8451 (tppt) cc_final: 0.8153 (mmmm) outliers start: 51 outliers final: 27 residues processed: 508 average time/residue: 0.1563 time to fit residues: 122.6257 Evaluate side-chains 460 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 423 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 213 optimal weight: 0.0570 chunk 178 optimal weight: 0.7980 chunk 193 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 GLN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS H 80 GLN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109265 restraints weight = 51306.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108603 restraints weight = 36388.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108741 restraints weight = 38977.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109272 restraints weight = 26652.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109605 restraints weight = 22505.846| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21878 Z= 0.137 Angle : 0.674 12.364 29606 Z= 0.342 Chirality : 0.043 0.318 3296 Planarity : 0.004 0.036 3766 Dihedral : 4.151 19.466 2922 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 2.35 % Allowed : 23.22 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2606 helix: 0.83 (0.13), residues: 1714 sheet: -1.42 (1.28), residues: 20 loop : -1.49 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 247 TYR 0.047 0.001 TYR D 137 PHE 0.045 0.001 PHE D 187 TRP 0.046 0.002 TRP C 19 HIS 0.003 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00306 (21878) covalent geometry : angle 0.67369 (29606) hydrogen bonds : bond 0.03895 ( 1244) hydrogen bonds : angle 4.45332 ( 3648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 447 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: G 148 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7157 (tpp) REVERT: G 206 MET cc_start: 0.6893 (mmp) cc_final: 0.6495 (mmp) REVERT: C 60 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: C 193 PHE cc_start: 0.7976 (t80) cc_final: 0.7773 (t80) REVERT: C 224 ARG cc_start: 0.4808 (mmt-90) cc_final: 0.4288 (mtp85) REVERT: C 238 MET cc_start: 0.5928 (mtt) cc_final: 0.5682 (ttm) REVERT: C 299 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7221 (mtm-85) REVERT: C 311 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7250 (mpp80) REVERT: C 318 LYS cc_start: 0.7548 (mmpt) cc_final: 0.7281 (tppt) REVERT: C 329 PHE cc_start: 0.8661 (t80) cc_final: 0.8341 (t80) REVERT: C 400 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6986 (tp) REVERT: H 76 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7774 (tp-100) REVERT: H 80 GLN cc_start: 0.8268 (tt0) cc_final: 0.7914 (tt0) REVERT: H 84 HIS cc_start: 0.6103 (p-80) cc_final: 0.5562 (p-80) REVERT: H 107 LYS cc_start: 0.7956 (tttt) cc_final: 0.7419 (tttt) REVERT: H 110 ASP cc_start: 0.7565 (m-30) cc_final: 0.7284 (t0) REVERT: H 148 MET cc_start: 0.6716 (mmm) cc_final: 0.6500 (mmm) REVERT: H 172 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7321 (pmt-80) REVERT: H 181 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.6004 (tptp) REVERT: H 200 GLN cc_start: 0.6478 (mp10) cc_final: 0.6012 (mp10) REVERT: H 207 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8305 (tmm-80) REVERT: D 176 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7883 (tm-30) REVERT: D 406 VAL cc_start: 0.8624 (p) cc_final: 0.8356 (t) REVERT: D 429 ARG cc_start: 0.7657 (mmp-170) cc_final: 0.6714 (ttm170) REVERT: E 76 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: E 132 ASN cc_start: 0.7526 (m110) cc_final: 0.7145 (t0) REVERT: E 148 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7147 (tpp) REVERT: A 60 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: A 224 ARG cc_start: 0.4832 (mmt-90) cc_final: 0.4301 (mtp85) REVERT: A 238 MET cc_start: 0.5800 (mtt) cc_final: 0.5573 (ttm) REVERT: A 240 PHE cc_start: 0.8836 (m-80) cc_final: 0.8089 (m-80) REVERT: A 295 PHE cc_start: 0.8083 (m-80) cc_final: 0.7677 (m-80) REVERT: A 299 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.7081 (mtm-85) REVERT: A 329 PHE cc_start: 0.8657 (t80) cc_final: 0.8052 (t80) REVERT: A 400 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6990 (tp) REVERT: F 76 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7758 (tp-100) REVERT: F 77 ILE cc_start: 0.7899 (mm) cc_final: 0.7515 (mm) REVERT: F 84 HIS cc_start: 0.6182 (p-80) cc_final: 0.5617 (p-80) REVERT: F 107 LYS cc_start: 0.7971 (tttt) cc_final: 0.7436 (tttt) REVERT: F 110 ASP cc_start: 0.7598 (m-30) cc_final: 0.7308 (t0) REVERT: F 128 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8273 (mmm-85) REVERT: F 172 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7247 (pmt-80) REVERT: F 200 GLN cc_start: 0.6474 (mp10) cc_final: 0.5926 (mp10) REVERT: F 207 ARG cc_start: 0.8488 (ptm160) cc_final: 0.8276 (tmm-80) REVERT: B 406 VAL cc_start: 0.8642 (p) cc_final: 0.8364 (t) REVERT: B 429 ARG cc_start: 0.7633 (mmp-170) cc_final: 0.6716 (ttm170) outliers start: 54 outliers final: 28 residues processed: 483 average time/residue: 0.1562 time to fit residues: 117.6484 Evaluate side-chains 459 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 420 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 256 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 50 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 GLN G 62 ASN G 173 GLN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 80 GLN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.133844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106187 restraints weight = 51408.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104004 restraints weight = 39519.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.104566 restraints weight = 37094.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105076 restraints weight = 26867.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105664 restraints weight = 24237.473| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21878 Z= 0.184 Angle : 0.702 10.623 29606 Z= 0.362 Chirality : 0.045 0.336 3296 Planarity : 0.004 0.036 3766 Dihedral : 4.264 20.108 2922 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 2.61 % Allowed : 23.65 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2606 helix: 0.76 (0.13), residues: 1720 sheet: -1.48 (1.26), residues: 20 loop : -1.56 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 434 TYR 0.055 0.002 TYR B 137 PHE 0.038 0.002 PHE D 187 TRP 0.049 0.003 TRP A 19 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00428 (21878) covalent geometry : angle 0.70156 (29606) hydrogen bonds : bond 0.04209 ( 1244) hydrogen bonds : angle 4.57945 ( 3648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 422 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8229 (t0) REVERT: G 76 GLN cc_start: 0.8460 (pm20) cc_final: 0.7923 (pm20) REVERT: G 148 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7277 (tpp) REVERT: G 213 GLN cc_start: 0.6162 (OUTLIER) cc_final: 0.5923 (tp-100) REVERT: C 60 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: C 224 ARG cc_start: 0.5118 (mmt-90) cc_final: 0.4611 (mtp85) REVERT: C 238 MET cc_start: 0.6047 (mtt) cc_final: 0.5792 (ttm) REVERT: C 299 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.7246 (mtm-85) REVERT: C 311 ARG cc_start: 0.7461 (mtm180) cc_final: 0.7237 (mpp80) REVERT: C 318 LYS cc_start: 0.7654 (mmpt) cc_final: 0.7111 (tppt) REVERT: C 400 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7136 (tp) REVERT: H 76 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7814 (tp-100) REVERT: H 80 GLN cc_start: 0.8359 (tt0) cc_final: 0.8089 (tt0) REVERT: H 84 HIS cc_start: 0.6219 (p-80) cc_final: 0.5697 (p-80) REVERT: H 107 LYS cc_start: 0.8077 (tttt) cc_final: 0.7512 (tttt) REVERT: H 148 MET cc_start: 0.6735 (mmm) cc_final: 0.6522 (mmm) REVERT: H 172 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7044 (pmt-80) REVERT: H 181 LYS cc_start: 0.6318 (OUTLIER) cc_final: 0.6053 (tptp) REVERT: H 200 GLN cc_start: 0.6388 (mp10) cc_final: 0.6177 (mp10) REVERT: H 206 MET cc_start: 0.7606 (mmm) cc_final: 0.6487 (mmm) REVERT: H 207 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8377 (tmm-80) REVERT: D 83 TYR cc_start: 0.8235 (m-80) cc_final: 0.8024 (m-80) REVERT: D 194 PHE cc_start: 0.7670 (m-80) cc_final: 0.7452 (m-80) REVERT: D 406 VAL cc_start: 0.8604 (p) cc_final: 0.8358 (t) REVERT: D 429 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.6650 (ttm170) REVERT: E 76 GLN cc_start: 0.8478 (pm20) cc_final: 0.7827 (pm20) REVERT: E 148 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7290 (tpp) REVERT: E 206 MET cc_start: 0.7051 (mmp) cc_final: 0.6691 (mmp) REVERT: A 60 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: A 224 ARG cc_start: 0.5134 (mmt-90) cc_final: 0.4618 (mtp85) REVERT: A 238 MET cc_start: 0.5788 (mtt) cc_final: 0.5578 (ttm) REVERT: A 240 PHE cc_start: 0.8851 (m-80) cc_final: 0.8252 (m-80) REVERT: A 295 PHE cc_start: 0.8164 (m-80) cc_final: 0.7757 (m-80) REVERT: A 299 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7194 (mtm-85) REVERT: A 400 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7081 (tp) REVERT: F 76 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7778 (tp-100) REVERT: F 77 ILE cc_start: 0.7892 (mm) cc_final: 0.7493 (mm) REVERT: F 80 GLN cc_start: 0.8339 (tt0) cc_final: 0.8067 (tt0) REVERT: F 84 HIS cc_start: 0.6205 (p-80) cc_final: 0.5683 (p-80) REVERT: F 107 LYS cc_start: 0.8083 (tttt) cc_final: 0.7522 (tttt) REVERT: F 172 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7364 (pmt-80) REVERT: F 200 GLN cc_start: 0.6442 (mp10) cc_final: 0.6162 (mp10) REVERT: F 206 MET cc_start: 0.7517 (mmm) cc_final: 0.6338 (mmm) REVERT: F 207 ARG cc_start: 0.8593 (ptm160) cc_final: 0.8362 (tmm-80) REVERT: B 83 TYR cc_start: 0.8241 (m-80) cc_final: 0.7998 (m-80) REVERT: B 194 PHE cc_start: 0.7690 (m-80) cc_final: 0.7395 (m-80) REVERT: B 406 VAL cc_start: 0.8616 (p) cc_final: 0.8358 (t) REVERT: B 429 ARG cc_start: 0.7704 (mmp-170) cc_final: 0.6642 (ttm170) outliers start: 60 outliers final: 38 residues processed: 461 average time/residue: 0.1540 time to fit residues: 110.6978 Evaluate side-chains 448 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 0.0270 chunk 211 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 246 optimal weight: 0.0870 chunk 178 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 202 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108890 restraints weight = 51180.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107401 restraints weight = 36939.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108024 restraints weight = 36501.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108403 restraints weight = 27660.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108694 restraints weight = 23776.853| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21878 Z= 0.141 Angle : 0.708 13.486 29606 Z= 0.359 Chirality : 0.044 0.325 3296 Planarity : 0.004 0.077 3766 Dihedral : 4.263 19.098 2922 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 2.04 % Allowed : 24.70 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2606 helix: 0.76 (0.13), residues: 1728 sheet: -1.52 (1.24), residues: 20 loop : -1.49 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 422 TYR 0.042 0.001 TYR D 137 PHE 0.037 0.001 PHE D 187 TRP 0.055 0.003 TRP A 19 HIS 0.007 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00310 (21878) covalent geometry : angle 0.70760 (29606) hydrogen bonds : bond 0.03964 ( 1244) hydrogen bonds : angle 4.47945 ( 3648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 444 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 76 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: G 132 ASN cc_start: 0.7655 (m110) cc_final: 0.7222 (t0) REVERT: G 148 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: C 60 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: C 193 PHE cc_start: 0.7989 (t80) cc_final: 0.7721 (t80) REVERT: C 224 ARG cc_start: 0.4886 (mmt-90) cc_final: 0.4349 (mtp85) REVERT: C 238 MET cc_start: 0.5930 (mtt) cc_final: 0.5686 (ttm) REVERT: C 299 ARG cc_start: 0.7917 (mmt-90) cc_final: 0.7221 (mtm-85) REVERT: C 311 ARG cc_start: 0.7524 (mtm180) cc_final: 0.7298 (mpp80) REVERT: C 318 LYS cc_start: 0.7572 (mmpt) cc_final: 0.7059 (tppt) REVERT: C 329 PHE cc_start: 0.8595 (t80) cc_final: 0.8212 (t80) REVERT: C 400 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7023 (tp) REVERT: H 76 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7773 (tp-100) REVERT: H 80 GLN cc_start: 0.8302 (tt0) cc_final: 0.7957 (tt0) REVERT: H 84 HIS cc_start: 0.5901 (p-80) cc_final: 0.5667 (p-80) REVERT: H 107 LYS cc_start: 0.7968 (tttt) cc_final: 0.7436 (tttt) REVERT: H 110 ASP cc_start: 0.7903 (m-30) cc_final: 0.7514 (t70) REVERT: H 172 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7397 (pmt-80) REVERT: H 181 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.6092 (tptp) REVERT: H 182 MET cc_start: 0.3403 (mmm) cc_final: 0.3196 (mmm) REVERT: H 200 GLN cc_start: 0.6541 (mp10) cc_final: 0.6308 (mp10) REVERT: H 206 MET cc_start: 0.7566 (mmm) cc_final: 0.6461 (mmm) REVERT: D 83 TYR cc_start: 0.8294 (m-80) cc_final: 0.8052 (m-80) REVERT: D 176 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 194 PHE cc_start: 0.7574 (m-80) cc_final: 0.7304 (m-80) REVERT: D 406 VAL cc_start: 0.8589 (p) cc_final: 0.8344 (t) REVERT: D 429 ARG cc_start: 0.7666 (mmp-170) cc_final: 0.6743 (ttm170) REVERT: D 437 LYS cc_start: 0.8505 (tppt) cc_final: 0.8052 (tptp) REVERT: E 76 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: E 132 ASN cc_start: 0.7484 (m110) cc_final: 0.7108 (t0) REVERT: E 148 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6913 (tpp) REVERT: E 206 MET cc_start: 0.6927 (mmp) cc_final: 0.6595 (mmp) REVERT: A 60 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: A 224 ARG cc_start: 0.4898 (mmt-90) cc_final: 0.4361 (mtp85) REVERT: A 238 MET cc_start: 0.5743 (mtt) cc_final: 0.5533 (ttm) REVERT: A 240 PHE cc_start: 0.8804 (m-80) cc_final: 0.8112 (m-80) REVERT: A 295 PHE cc_start: 0.8116 (m-80) cc_final: 0.7677 (m-80) REVERT: A 299 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7102 (mtm-85) REVERT: A 311 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7200 (mpp80) REVERT: F 76 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7696 (tp-100) REVERT: F 80 GLN cc_start: 0.8301 (tt0) cc_final: 0.7966 (tt0) REVERT: F 84 HIS cc_start: 0.5893 (p-80) cc_final: 0.5664 (p-80) REVERT: F 107 LYS cc_start: 0.7969 (tttt) cc_final: 0.7440 (tttt) REVERT: F 110 ASP cc_start: 0.7906 (m-30) cc_final: 0.7519 (t70) REVERT: F 148 MET cc_start: 0.6311 (mmm) cc_final: 0.5776 (mmm) REVERT: F 172 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7322 (pmt-80) REVERT: F 200 GLN cc_start: 0.6576 (mp10) cc_final: 0.6255 (mp10) REVERT: F 206 MET cc_start: 0.7555 (mmm) cc_final: 0.6462 (mmm) REVERT: B 83 TYR cc_start: 0.8302 (m-80) cc_final: 0.8057 (m-80) REVERT: B 176 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 406 VAL cc_start: 0.8586 (p) cc_final: 0.8314 (t) REVERT: B 429 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.6745 (ttm170) REVERT: B 437 LYS cc_start: 0.8515 (tppt) cc_final: 0.8026 (tptp) outliers start: 47 outliers final: 30 residues processed: 471 average time/residue: 0.1562 time to fit residues: 114.4151 Evaluate side-chains 461 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 421 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 172 TRP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 243 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 41 GLN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107061 restraints weight = 51551.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105755 restraints weight = 42813.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106227 restraints weight = 43100.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106792 restraints weight = 30536.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107207 restraints weight = 26318.808| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21878 Z= 0.187 Angle : 0.730 12.152 29606 Z= 0.377 Chirality : 0.045 0.315 3296 Planarity : 0.005 0.094 3766 Dihedral : 4.334 21.035 2922 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 2.43 % Allowed : 24.87 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2606 helix: 0.70 (0.13), residues: 1720 sheet: -1.61 (1.22), residues: 20 loop : -1.58 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 247 TYR 0.022 0.002 TYR D 274 PHE 0.034 0.002 PHE D 187 TRP 0.059 0.004 TRP A 19 HIS 0.006 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00436 (21878) covalent geometry : angle 0.72988 (29606) hydrogen bonds : bond 0.04240 ( 1244) hydrogen bonds : angle 4.62443 ( 3648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.77 seconds wall clock time: 67 minutes 24.92 seconds (4044.92 seconds total)