Starting phenix.real_space_refine on Fri Feb 6 09:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eg1_47983/02_2026/9eg1_47983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eg1_47983/02_2026/9eg1_47983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eg1_47983/02_2026/9eg1_47983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eg1_47983/02_2026/9eg1_47983.map" model { file = "/net/cci-nas-00/data/ceres_data/9eg1_47983/02_2026/9eg1_47983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eg1_47983/02_2026/9eg1_47983.cif" } resolution = 3.52 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= 0.005 sd= 0.019 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 138 5.16 5 C 15036 2.51 5 N 4115 2.21 5 O 4460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23752 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3062 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 362} Chain breaks: 1 Chain: "D" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3241 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 9, 'TRANS': 395} Chain: "E" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2313 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 7, 'TRANS': 283} Chain breaks: 2 Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2229 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "J" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2101 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 981 Unresolved non-hydrogen angles: 1245 Unresolved non-hydrogen dihedrals: 824 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLU:plan': 27, 'ASN:plan1': 16, 'TYR:plan': 7, 'ASP:plan': 12, 'ARG:plan': 15, 'GLN:plan1': 11, 'PHE:plan': 13, 'HIS:plan': 7, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 518 Chain: "K" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3229 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 8, 'TRANS': 395} Chain breaks: 2 Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3216 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16430 SG CYS K 80 82.546 84.427 67.391 1.00 48.86 S ATOM 16589 SG CYS K 99 83.698 82.441 70.497 1.00 46.78 S ATOM 16610 SG CYS K 102 86.169 84.569 68.530 1.00 47.64 S ATOM 16199 SG CYS K 50 83.537 72.351 73.956 1.00 44.87 S ATOM 16218 SG CYS K 53 84.349 68.945 75.293 1.00 50.94 S ATOM 16495 SG CYS K 88 81.648 70.910 77.073 1.00 60.12 S ATOM 16279 SG CYS K 61 77.534 66.335 78.178 1.00 85.69 S ATOM 16304 SG CYS K 64 74.222 65.239 77.891 1.00101.73 S ATOM 16376 SG CYS K 73 76.077 66.155 74.605 1.00 75.75 S ATOM 16489 SG CYS K 87 75.130 68.952 77.175 1.00 68.93 S Time building chain proxies: 4.69, per 1000 atoms: 0.20 Number of scatterers: 23752 At special positions: 0 Unit cell: (133.6, 166.165, 201.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 138 16.00 O 4460 8.00 N 4115 7.00 C 15036 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 920.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 102 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 99 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 80 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 85 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 50 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 88 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 61 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 64 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 87 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 73 " Number of angles added : 12 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5890 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 12 sheets defined 65.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'B' and resid 64 through 81 Processing helix chain 'B' and resid 84 through 103 removed outlier: 4.366A pdb=" N MET B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 144 through 156 removed outlier: 4.070A pdb=" N LYS B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 190 through 208 Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 250 through 268 removed outlier: 3.818A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.323A pdb=" N ASN B 304 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 305 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.863A pdb=" N HIS B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.638A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 14 removed outlier: 3.669A pdb=" N ASP D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 35 removed outlier: 3.654A pdb=" N GLY D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 3.922A pdb=" N ASN D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.826A pdb=" N GLU D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.714A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 140 through 158 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.922A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA D 171 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.811A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 258 " --> pdb=" O CYS D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 258' Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.797A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.713A pdb=" N ALA D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 299 through 313 removed outlier: 4.964A pdb=" N ILE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 327 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.822A pdb=" N LYS D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.679A pdb=" N ALA D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 28 removed outlier: 3.530A pdb=" N ILE E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 44 through 47 removed outlier: 3.545A pdb=" N LYS E 47 " --> pdb=" O PRO E 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 44 through 47' Processing helix chain 'E' and resid 59 through 73 Processing helix chain 'E' and resid 110 through 128 removed outlier: 3.530A pdb=" N TYR E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 245 through 252 Processing helix chain 'E' and resid 258 through 281 Processing helix chain 'E' and resid 299 through 329 Processing helix chain 'F' and resid 46 through 63 Processing helix chain 'F' and resid 101 through 112 removed outlier: 4.196A pdb=" N TYR F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 146 removed outlier: 3.566A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 142 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 207 removed outlier: 4.392A pdb=" N MET F 206 " --> pdb=" O HIS F 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR F 207 " --> pdb=" O VAL F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 248 removed outlier: 4.319A pdb=" N ILE F 222 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.622A pdb=" N GLU F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 removed outlier: 4.333A pdb=" N GLY F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 297 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 17 removed outlier: 3.868A pdb=" N LEU G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 20 No H-bonds generated for 'chain 'G' and resid 18 through 20' Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 44 through 49 removed outlier: 3.600A pdb=" N LEU G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.559A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.891A pdb=" N ALA G 80 " --> pdb=" O PRO G 76 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 81' Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.728A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 139 Processing helix chain 'G' and resid 166 through 221 Processing helix chain 'H' and resid 12 through 26 removed outlier: 3.934A pdb=" N LEU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.739A pdb=" N ALA H 53 " --> pdb=" O ASP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.658A pdb=" N ASN H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.621A pdb=" N ILE H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.926A pdb=" N MET H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU H 107 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 142 through 151 removed outlier: 3.652A pdb=" N GLN H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 209 removed outlier: 3.559A pdb=" N LEU H 200 " --> pdb=" O GLN H 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'J' and resid 428 through 444 removed outlier: 3.736A pdb=" N ALA J 432 " --> pdb=" O GLU J 428 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 463 removed outlier: 4.273A pdb=" N PHE J 450 " --> pdb=" O ASN J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 484 removed outlier: 3.879A pdb=" N VAL J 477 " --> pdb=" O GLU J 473 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU J 478 " --> pdb=" O GLU J 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 486 through 514 removed outlier: 3.562A pdb=" N VAL J 490 " --> pdb=" O PRO J 486 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP J 505 " --> pdb=" O LYS J 501 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 537 removed outlier: 3.659A pdb=" N SER J 537 " --> pdb=" O ALA J 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 533 through 537' Processing helix chain 'J' and resid 550 through 553 removed outlier: 4.041A pdb=" N ASP J 553 " --> pdb=" O GLU J 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 550 through 553' Processing helix chain 'J' and resid 554 through 566 Processing helix chain 'J' and resid 597 through 606 removed outlier: 4.154A pdb=" N TRP J 606 " --> pdb=" O VAL J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 624 Processing helix chain 'J' and resid 627 through 639 removed outlier: 3.527A pdb=" N ARG J 631 " --> pdb=" O ASP J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 679 Processing helix chain 'J' and resid 707 through 726 removed outlier: 3.715A pdb=" N LEU J 713 " --> pdb=" O GLN J 709 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG J 714 " --> pdb=" O LEU J 710 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR J 715 " --> pdb=" O ARG J 711 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN J 716 " --> pdb=" O ILE J 712 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU J 717 " --> pdb=" O LEU J 713 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA J 718 " --> pdb=" O ARG J 714 " (cutoff:3.500A) Processing helix chain 'J' and resid 730 through 742 Processing helix chain 'J' and resid 749 through 763 removed outlier: 3.975A pdb=" N ILE J 753 " --> pdb=" O GLN J 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 68 removed outlier: 3.987A pdb=" N GLN K 65 " --> pdb=" O CYS K 61 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.050A pdb=" N LEU K 91 " --> pdb=" O CYS K 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP K 92 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 53 through 67 removed outlier: 4.055A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.979A pdb=" N GLU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 156 removed outlier: 3.742A pdb=" N ASN A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.721A pdb=" N LYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 194 through 213 removed outlier: 3.632A pdb=" N TYR A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.568A pdb=" N GLN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.628A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 3.692A pdb=" N CYS A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 430 through 462 removed outlier: 4.004A pdb=" N ASN A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.518A pdb=" N LEU C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 29 " --> pdb=" O CYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 4.120A pdb=" N SER C 40 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS C 41 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.698A pdb=" N GLY C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 removed outlier: 3.723A pdb=" N LEU C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.899A pdb=" N THR C 97 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 removed outlier: 3.873A pdb=" N GLY C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.964A pdb=" N GLN C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.584A pdb=" N LEU C 150 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.194A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 4.157A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 removed outlier: 3.930A pdb=" N LEU C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU C 222 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 293 through 311 removed outlier: 3.663A pdb=" N CYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 399 removed outlier: 3.557A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 397 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 34 Processing sheet with id=AA1, first strand: chain 'B' and resid 368 through 370 removed outlier: 7.561A pdb=" N VAL A 382 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 402 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA A 384 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AA3, first strand: chain 'E' and resid 184 through 186 removed outlier: 3.612A pdb=" N TRP E 136 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA E 133 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY E 83 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY E 135 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 81 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET E 78 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA E 97 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP E 94 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS E 55 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE E 229 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 181 through 185 removed outlier: 9.681A pdb=" N LEU F 150 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU F 122 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU F 152 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE F 121 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY F 74 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.948A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 526 through 532 removed outlier: 6.252A pdb=" N ASN J 527 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA K 39 " --> pdb=" O ASN J 527 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS J 529 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TRP K 41 " --> pdb=" O LYS J 529 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU J 531 " --> pdb=" O TRP K 41 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N TRP K 43 " --> pdb=" O LEU J 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 526 through 532 removed outlier: 6.252A pdb=" N ASN J 527 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA K 39 " --> pdb=" O ASN J 527 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS J 529 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TRP K 41 " --> pdb=" O LYS J 529 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU J 531 " --> pdb=" O TRP K 41 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N TRP K 43 " --> pdb=" O LEU J 531 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU K 32 " --> pdb=" O THR J 583 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR J 583 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN J 579 " --> pdb=" O ASN K 36 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP J 592 " --> pdb=" O ILE J 686 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 728 through 729 removed outlier: 3.601A pdb=" N ILE J 729 " --> pdb=" O PHE J 776 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AB2, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'I' and resid 41 through 44 1387 hydrogen bonds defined for protein. 4074 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: 3.88 Time building geometry restraints manager: 2.35 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: 7899 1.34 - 1.46: 4979 1.46 - 1.58: 11041 1.58 - 1.70: 0 1.70 - 1.82: 222 Bond restraints: 24141 Sorted by residual: bond pdb=" CA LEU I 69 " pdb=" C LEU I 69 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.25e-02 6.40e+03 6.13e+00 bond pdb=" CA ASN B 84 " pdb=" C ASN B 84 " ideal model delta sigma weight residual 1.531 1.509 0.022 1.08e-02 8.57e+03 4.33e+00 bond pdb=" CA HIS I 68 " pdb=" C HIS I 68 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.23e-02 6.61e+03 3.68e+00 bond pdb=" CA MET B 88 " pdb=" C MET B 88 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.24e-02 6.50e+03 3.11e+00 bond pdb=" CA MET A 356 " pdb=" C MET A 356 " ideal model delta sigma weight residual 1.528 1.505 0.022 1.33e-02 5.65e+03 2.84e+00 ... (remaining 24136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 32047 2.24 - 4.49: 444 4.49 - 6.73: 118 6.73 - 8.98: 31 8.98 - 11.22: 13 Bond angle restraints: 32653 Sorted by residual: angle pdb=" C GLN I 40 " pdb=" CA GLN I 40 " pdb=" CB GLN I 40 " ideal model delta sigma weight residual 111.18 119.40 -8.22 1.56e+00 4.11e-01 2.78e+01 angle pdb=" C SER F 38 " pdb=" CA SER F 38 " pdb=" CB SER F 38 " ideal model delta sigma weight residual 117.23 110.48 6.75 1.36e+00 5.41e-01 2.47e+01 angle pdb=" N LEU B 82 " pdb=" CA LEU B 82 " pdb=" C LEU B 82 " ideal model delta sigma weight residual 111.81 104.51 7.30 1.54e+00 4.22e-01 2.25e+01 angle pdb=" CA GLN I 40 " pdb=" CB GLN I 40 " pdb=" CG GLN I 40 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.14e+01 angle pdb=" N SER C 268 " pdb=" CA SER C 268 " pdb=" C SER C 268 " ideal model delta sigma weight residual 114.04 108.32 5.72 1.24e+00 6.50e-01 2.13e+01 ... (remaining 32648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12364 17.98 - 35.95: 1771 35.95 - 53.93: 472 53.93 - 71.90: 85 71.90 - 89.88: 44 Dihedral angle restraints: 14736 sinusoidal: 5680 harmonic: 9056 Sorted by residual: dihedral pdb=" CA TYR E 51 " pdb=" C TYR E 51 " pdb=" N PHE E 52 " pdb=" CA PHE E 52 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ALA D 332 " pdb=" C ALA D 332 " pdb=" N ALA D 333 " pdb=" CA ALA D 333 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASP D 301 " pdb=" C ASP D 301 " pdb=" N ARG D 302 " pdb=" CA ARG D 302 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 14733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2895 0.045 - 0.090: 675 0.090 - 0.135: 163 0.135 - 0.181: 12 0.181 - 0.226: 4 Chirality restraints: 3749 Sorted by residual: chirality pdb=" CB VAL C 71 " pdb=" CA VAL C 71 " pdb=" CG1 VAL C 71 " pdb=" CG2 VAL C 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A 231 " pdb=" CA ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CG2 ILE A 231 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLU J 758 " pdb=" N GLU J 758 " pdb=" C GLU J 758 " pdb=" CB GLU J 758 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3746 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 40 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN I 40 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN I 40 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN I 41 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO C 72 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 758 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" CD GLU J 758 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU J 758 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU J 758 " 0.015 2.00e-02 2.50e+03 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9082 2.89 - 3.39: 24483 3.39 - 3.90: 37684 3.90 - 4.40: 40648 4.40 - 4.90: 69026 Nonbonded interactions: 180923 Sorted by model distance: nonbonded pdb=" O GLN I 40 " pdb=" OE1 GLN I 40 " model vdw 2.390 3.040 nonbonded pdb=" O LYS J 754 " pdb=" OE1 GLU J 758 " model vdw 2.438 3.040 nonbonded pdb=" O ASP H 18 " pdb=" OD1 ASN H 22 " model vdw 2.446 3.040 nonbonded pdb=" N GLU H 107 " pdb=" OE1 GLU H 107 " model vdw 2.484 3.120 nonbonded pdb=" N GLU K 46 " pdb=" OE1 GLU K 46 " model vdw 2.497 3.120 ... (remaining 180918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.520 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.003 0.092 24154 Z= 0.156 Angle : 0.737 11.581 32665 Z= 0.382 Chirality : 0.041 0.226 3749 Planarity : 0.004 0.061 4200 Dihedral : 18.453 89.877 8846 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.57 % Favored : 93.81 % Rotamer: Outliers : 0.94 % Allowed : 31.64 % Favored : 67.42 % 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: 0.08 (0.16), residues: 3035 helix: 1.29 (0.13), residues: 1834 sheet: -0.54 (0.42), residues: 173 loop : -2.17 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 204 TYR 0.023 0.001 TYR C 244 PHE 0.019 0.001 PHE E 52 TRP 0.035 0.002 TRP E 45 HIS 0.003 0.000 HIS D 360 Details of bonding type rmsd covalent geometry : bond 0.00302 (24141) covalent geometry : angle 0.73188 (32653) hydrogen bonds : bond 0.13429 ( 1387) hydrogen bonds : angle 5.77823 ( 4074) metal coordination : bond 0.00577 ( 12) metal coordination : angle 4.50935 ( 12) Misc. bond : bond 0.09198 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8071 (ppp) REVERT: B 76 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 82 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8830 (mt) REVERT: B 152 ASN cc_start: 0.9055 (t0) cc_final: 0.8750 (m110) REVERT: B 158 LEU cc_start: 0.8903 (tp) cc_final: 0.8522 (tp) REVERT: B 311 MET cc_start: 0.8288 (tpp) cc_final: 0.8026 (tpt) REVERT: D 1 MET cc_start: 0.6004 (mtt) cc_final: 0.4381 (tpt) REVERT: D 134 THR cc_start: 0.9038 (m) cc_final: 0.8802 (p) REVERT: E 52 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.4876 (m-80) REVERT: E 67 MET cc_start: 0.7989 (mmm) cc_final: 0.7713 (mmt) REVERT: E 187 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7657 (mtp180) REVERT: F 157 MET cc_start: 0.6872 (mmm) cc_final: 0.6518 (mmm) REVERT: G 204 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8423 (ttp80) REVERT: J 737 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7937 (mm-30) REVERT: J 772 ASP cc_start: 0.7730 (t0) cc_final: 0.7389 (t0) REVERT: K 89 MET cc_start: 0.8670 (mtp) cc_final: 0.8238 (ttm) REVERT: A 67 CYS cc_start: 0.8232 (t) cc_final: 0.7926 (t) REVERT: A 356 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7406 (ptp) REVERT: I 27 LYS cc_start: 0.6457 (mttm) cc_final: 0.6145 (ptpt) REVERT: I 33 LYS cc_start: 0.5444 (mtpp) cc_final: 0.4952 (tptp) outliers start: 23 outliers final: 11 residues processed: 285 average time/residue: 0.1639 time to fit residues: 72.0786 Evaluate side-chains 275 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 51 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0000 chunk 298 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 721 GLN C 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.116168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.088930 restraints weight = 67075.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.087675 restraints weight = 44960.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.088343 restraints weight = 41173.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088718 restraints weight = 31315.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088913 restraints weight = 30021.652| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24154 Z= 0.129 Angle : 0.596 10.664 32665 Z= 0.299 Chirality : 0.040 0.221 3749 Planarity : 0.003 0.053 4200 Dihedral : 5.123 87.070 3322 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.83 % Favored : 93.61 % Rotamer: Outliers : 4.01 % Allowed : 26.73 % Favored : 69.26 % 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: 0.50 (0.16), residues: 3035 helix: 1.68 (0.13), residues: 1886 sheet: -0.44 (0.42), residues: 163 loop : -2.34 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.016 0.001 TYR E 51 PHE 0.036 0.001 PHE B 149 TRP 0.017 0.001 TRP B 148 HIS 0.003 0.001 HIS D 360 Details of bonding type rmsd covalent geometry : bond 0.00281 (24141) covalent geometry : angle 0.58984 (32653) hydrogen bonds : bond 0.04069 ( 1387) hydrogen bonds : angle 4.10950 ( 4074) metal coordination : bond 0.00774 ( 12) metal coordination : angle 4.42032 ( 12) Misc. bond : bond 0.00180 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 273 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: B 234 MET cc_start: 0.8217 (tpp) cc_final: 0.7988 (tpp) REVERT: D 1 MET cc_start: 0.5921 (mtt) cc_final: 0.4356 (tpt) REVERT: D 134 THR cc_start: 0.9028 (m) cc_final: 0.8786 (p) REVERT: E 52 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.6256 (m-80) REVERT: E 67 MET cc_start: 0.7909 (mmm) cc_final: 0.7513 (mmt) REVERT: E 187 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7887 (mtp180) REVERT: F 157 MET cc_start: 0.6983 (mmm) cc_final: 0.6716 (mmm) REVERT: F 255 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: G 204 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8361 (ttp80) REVERT: H 15 LYS cc_start: 0.8360 (mmtm) cc_final: 0.7891 (mppt) REVERT: H 21 GLU cc_start: 0.7973 (tp30) cc_final: 0.7743 (mm-30) REVERT: J 737 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7803 (mm-30) REVERT: J 766 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8361 (mt) REVERT: J 772 ASP cc_start: 0.7807 (t0) cc_final: 0.7477 (t0) REVERT: A 201 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7968 (ppp) REVERT: C 271 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7033 (t0) REVERT: I 33 LYS cc_start: 0.5817 (mtpp) cc_final: 0.5358 (tptm) outliers start: 98 outliers final: 55 residues processed: 348 average time/residue: 0.1499 time to fit residues: 82.0772 Evaluate side-chains 316 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 208 GLU Chi-restraints excluded: chain J residue 747 LEU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 290 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.112893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086265 restraints weight = 68679.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086631 restraints weight = 39536.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086677 restraints weight = 45419.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087448 restraints weight = 31385.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.087680 restraints weight = 27479.727| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24154 Z= 0.134 Angle : 0.583 10.962 32665 Z= 0.292 Chirality : 0.040 0.248 3749 Planarity : 0.003 0.067 4200 Dihedral : 4.526 84.277 3301 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.73 % Favored : 93.71 % Rotamer: Outliers : 3.60 % Allowed : 26.52 % Favored : 69.87 % 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: 0.69 (0.16), residues: 3035 helix: 1.86 (0.13), residues: 1880 sheet: -0.40 (0.42), residues: 167 loop : -2.30 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 25 TYR 0.015 0.001 TYR E 51 PHE 0.023 0.001 PHE C 78 TRP 0.020 0.001 TRP E 45 HIS 0.003 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00307 (24141) covalent geometry : angle 0.57794 (32653) hydrogen bonds : bond 0.03966 ( 1387) hydrogen bonds : angle 3.91129 ( 4074) metal coordination : bond 0.00900 ( 12) metal coordination : angle 4.20713 ( 12) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 265 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: B 234 MET cc_start: 0.8365 (tpp) cc_final: 0.7948 (tpp) REVERT: D 1 MET cc_start: 0.6047 (mtt) cc_final: 0.4385 (tpt) REVERT: D 134 THR cc_start: 0.9087 (m) cc_final: 0.8785 (p) REVERT: E 52 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.4848 (m-80) REVERT: E 67 MET cc_start: 0.7867 (mmm) cc_final: 0.7414 (mmt) REVERT: E 187 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7894 (mmm160) REVERT: F 173 ASP cc_start: 0.3077 (OUTLIER) cc_final: 0.2828 (p0) REVERT: G 204 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8388 (ttp80) REVERT: J 723 MET cc_start: 0.9199 (mmm) cc_final: 0.8952 (mmp) REVERT: J 754 LYS cc_start: 0.8570 (mptt) cc_final: 0.7948 (mmtp) REVERT: J 766 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (mt) REVERT: J 772 ASP cc_start: 0.7767 (t0) cc_final: 0.7515 (t0) REVERT: A 91 TYR cc_start: 0.8270 (t80) cc_final: 0.8065 (t80) REVERT: A 201 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7906 (ppp) REVERT: A 454 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8314 (mtm) REVERT: C 159 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8091 (mm) REVERT: I 33 LYS cc_start: 0.5724 (mtpp) cc_final: 0.5391 (tptm) outliers start: 88 outliers final: 59 residues processed: 331 average time/residue: 0.1507 time to fit residues: 78.2265 Evaluate side-chains 318 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 747 LEU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 182 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 178 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 216 optimal weight: 0.0570 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 162 GLN ** J 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.115275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.087675 restraints weight = 66791.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086964 restraints weight = 43160.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087555 restraints weight = 45495.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087759 restraints weight = 34075.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088360 restraints weight = 31448.921| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24154 Z= 0.134 Angle : 0.574 10.441 32665 Z= 0.288 Chirality : 0.040 0.222 3749 Planarity : 0.003 0.052 4200 Dihedral : 4.529 81.348 3300 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.80 % Favored : 93.64 % Rotamer: Outliers : 4.05 % Allowed : 26.03 % Favored : 69.91 % 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: 0.73 (0.16), residues: 3035 helix: 1.90 (0.13), residues: 1881 sheet: -0.36 (0.42), residues: 164 loop : -2.30 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 25 TYR 0.014 0.001 TYR A 357 PHE 0.013 0.001 PHE C 181 TRP 0.022 0.001 TRP E 45 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00308 (24141) covalent geometry : angle 0.56881 (32653) hydrogen bonds : bond 0.03825 ( 1387) hydrogen bonds : angle 3.84427 ( 4074) metal coordination : bond 0.00965 ( 12) metal coordination : angle 3.99988 ( 12) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 259 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 MET cc_start: 0.8391 (ptp) cc_final: 0.8163 (ptp) REVERT: B 234 MET cc_start: 0.8310 (tpp) cc_final: 0.7850 (tpp) REVERT: D 1 MET cc_start: 0.5947 (mtt) cc_final: 0.4418 (tpt) REVERT: D 134 THR cc_start: 0.9078 (m) cc_final: 0.8757 (p) REVERT: E 52 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: E 56 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8385 (mmmm) REVERT: E 158 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7988 (t0) REVERT: E 187 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8188 (mtp180) REVERT: F 173 ASP cc_start: 0.3321 (OUTLIER) cc_final: 0.2996 (p0) REVERT: G 204 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8389 (ttp80) REVERT: J 709 GLN cc_start: 0.7918 (mp10) cc_final: 0.7602 (pm20) REVERT: J 713 LEU cc_start: 0.8723 (tp) cc_final: 0.8506 (tt) REVERT: J 766 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8382 (mt) REVERT: J 772 ASP cc_start: 0.7857 (t0) cc_final: 0.7551 (t0) REVERT: A 201 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7958 (ppp) REVERT: A 454 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: C 166 MET cc_start: 0.8918 (mmp) cc_final: 0.8606 (mmp) REVERT: C 271 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7285 (t0) REVERT: I 11 LYS cc_start: 0.9144 (tppt) cc_final: 0.8926 (tppt) REVERT: I 33 LYS cc_start: 0.5835 (mtpp) cc_final: 0.5518 (tptm) outliers start: 99 outliers final: 72 residues processed: 337 average time/residue: 0.1482 time to fit residues: 78.8700 Evaluate side-chains 329 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 249 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 208 GLU Chi-restraints excluded: chain J residue 747 LEU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 179 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 271 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 141 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.113312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087436 restraints weight = 67711.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086401 restraints weight = 38454.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087156 restraints weight = 40179.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.087396 restraints weight = 30609.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089191 restraints weight = 27879.798| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24154 Z= 0.117 Angle : 0.565 10.610 32665 Z= 0.282 Chirality : 0.040 0.261 3749 Planarity : 0.003 0.054 4200 Dihedral : 4.511 79.773 3300 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.73 % Favored : 93.74 % Rotamer: Outliers : 4.18 % Allowed : 25.95 % Favored : 69.87 % 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: 0.78 (0.16), residues: 3035 helix: 1.94 (0.13), residues: 1882 sheet: -0.34 (0.43), residues: 164 loop : -2.30 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 42 TYR 0.013 0.001 TYR E 51 PHE 0.012 0.001 PHE B 69 TRP 0.021 0.001 TRP E 45 HIS 0.004 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00261 (24141) covalent geometry : angle 0.56000 (32653) hydrogen bonds : bond 0.03647 ( 1387) hydrogen bonds : angle 3.76568 ( 4074) metal coordination : bond 0.00800 ( 12) metal coordination : angle 3.79599 ( 12) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 264 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: B 234 MET cc_start: 0.8347 (tpp) cc_final: 0.7855 (tpp) REVERT: D 1 MET cc_start: 0.5971 (mtt) cc_final: 0.4426 (tpt) REVERT: D 134 THR cc_start: 0.9049 (m) cc_final: 0.8690 (p) REVERT: E 52 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: E 56 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8422 (mmmm) REVERT: E 67 MET cc_start: 0.8008 (mmm) cc_final: 0.7697 (mmt) REVERT: E 187 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7931 (mmm160) REVERT: F 173 ASP cc_start: 0.3589 (OUTLIER) cc_final: 0.3063 (p0) REVERT: G 204 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8336 (ttp80) REVERT: J 709 GLN cc_start: 0.7898 (mp10) cc_final: 0.7595 (pm20) REVERT: J 754 LYS cc_start: 0.8303 (mptt) cc_final: 0.8079 (mmtp) REVERT: J 766 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8389 (mt) REVERT: J 772 ASP cc_start: 0.7655 (t0) cc_final: 0.7438 (t0) REVERT: A 201 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8000 (ppp) REVERT: A 454 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: C 159 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8071 (mm) REVERT: C 167 MET cc_start: 0.8256 (mmm) cc_final: 0.7980 (mmt) REVERT: C 271 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7360 (t0) REVERT: I 33 LYS cc_start: 0.5891 (mtpp) cc_final: 0.5621 (tptm) outliers start: 102 outliers final: 68 residues processed: 340 average time/residue: 0.1566 time to fit residues: 83.5509 Evaluate side-chains 328 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 747 LEU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 187 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 HIS ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.112482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.086724 restraints weight = 67905.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.085786 restraints weight = 47531.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086300 restraints weight = 53203.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086882 restraints weight = 35612.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087263 restraints weight = 32102.334| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24154 Z= 0.167 Angle : 0.608 12.568 32665 Z= 0.302 Chirality : 0.041 0.302 3749 Planarity : 0.003 0.050 4200 Dihedral : 4.596 77.681 3300 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.13 % Favored : 93.34 % Rotamer: Outliers : 4.58 % Allowed : 25.71 % Favored : 69.71 % 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: 0.75 (0.16), residues: 3035 helix: 1.90 (0.13), residues: 1881 sheet: -0.40 (0.43), residues: 164 loop : -2.25 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 42 TYR 0.017 0.001 TYR C 267 PHE 0.015 0.001 PHE C 181 TRP 0.024 0.001 TRP E 45 HIS 0.004 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00391 (24141) covalent geometry : angle 0.60331 (32653) hydrogen bonds : bond 0.03996 ( 1387) hydrogen bonds : angle 3.83300 ( 4074) metal coordination : bond 0.01348 ( 12) metal coordination : angle 4.05009 ( 12) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 260 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: B 89 MET cc_start: 0.8296 (ptp) cc_final: 0.7960 (mpp) REVERT: D 1 MET cc_start: 0.6054 (mtt) cc_final: 0.4476 (tpt) REVERT: D 134 THR cc_start: 0.9086 (m) cc_final: 0.8735 (p) REVERT: E 52 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.5083 (m-80) REVERT: E 56 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8393 (mmmm) REVERT: E 187 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8273 (mtp180) REVERT: F 173 ASP cc_start: 0.3178 (OUTLIER) cc_final: 0.2906 (p0) REVERT: F 196 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: G 167 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7636 (mt) REVERT: J 709 GLN cc_start: 0.7805 (mp10) cc_final: 0.7527 (pm20) REVERT: J 766 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8341 (mt) REVERT: J 772 ASP cc_start: 0.7867 (t0) cc_final: 0.7609 (t0) REVERT: A 96 ARG cc_start: 0.9122 (ptp90) cc_final: 0.8887 (ptp90) REVERT: A 201 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7868 (ppp) REVERT: A 454 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8366 (mtm) REVERT: C 159 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 271 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7397 (t0) outliers start: 112 outliers final: 78 residues processed: 346 average time/residue: 0.1607 time to fit residues: 87.4644 Evaluate side-chains 339 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 251 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain J residue 775 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 243 LYS Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 61 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 278 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 291 optimal weight: 0.2980 chunk 267 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 304 GLN J 721 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.110581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.086142 restraints weight = 69569.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.084441 restraints weight = 39568.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085540 restraints weight = 37650.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086067 restraints weight = 28006.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.086296 restraints weight = 26426.626| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24154 Z= 0.113 Angle : 0.582 10.580 32665 Z= 0.288 Chirality : 0.040 0.244 3749 Planarity : 0.003 0.054 4200 Dihedral : 4.520 76.788 3300 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.57 % Favored : 93.90 % Rotamer: Outliers : 3.60 % Allowed : 27.18 % Favored : 69.22 % 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: 0.84 (0.16), residues: 3035 helix: 1.98 (0.13), residues: 1880 sheet: -0.48 (0.39), residues: 184 loop : -2.24 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 204 TYR 0.015 0.001 TYR C 244 PHE 0.012 0.001 PHE B 69 TRP 0.025 0.001 TRP E 45 HIS 0.004 0.000 HIS I 68 Details of bonding type rmsd covalent geometry : bond 0.00252 (24141) covalent geometry : angle 0.57840 (32653) hydrogen bonds : bond 0.03550 ( 1387) hydrogen bonds : angle 3.70936 ( 4074) metal coordination : bond 0.00752 ( 12) metal coordination : angle 3.60171 ( 12) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 261 time to evaluate : 0.967 Fit side-chains REVERT: B 234 MET cc_start: 0.8243 (tpp) cc_final: 0.7988 (tpp) REVERT: B 311 MET cc_start: 0.8180 (tpp) cc_final: 0.7958 (tpt) REVERT: D 1 MET cc_start: 0.6108 (mtt) cc_final: 0.4484 (tpt) REVERT: D 134 THR cc_start: 0.9112 (m) cc_final: 0.8753 (p) REVERT: E 52 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.5029 (m-80) REVERT: E 56 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8447 (mmmm) REVERT: E 158 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7806 (t0) REVERT: E 165 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: E 187 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8287 (mtp180) REVERT: F 173 ASP cc_start: 0.3371 (OUTLIER) cc_final: 0.2954 (p0) REVERT: G 167 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7606 (mt) REVERT: G 204 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8355 (ttp80) REVERT: G 220 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6957 (mm) REVERT: H 50 MET cc_start: 0.8068 (tpp) cc_final: 0.7731 (tpp) REVERT: J 709 GLN cc_start: 0.7840 (mp10) cc_final: 0.7571 (pm20) REVERT: J 755 GLU cc_start: 0.8436 (tp30) cc_final: 0.8213 (tp30) REVERT: J 766 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8312 (mt) REVERT: J 772 ASP cc_start: 0.7863 (t0) cc_final: 0.7590 (t0) REVERT: A 96 ARG cc_start: 0.9112 (ptp90) cc_final: 0.8898 (ptp90) REVERT: A 185 TYR cc_start: 0.7151 (m-80) cc_final: 0.6917 (m-80) REVERT: A 201 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7892 (ppp) REVERT: A 454 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: C 159 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8090 (mm) REVERT: C 271 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7350 (t0) REVERT: I 33 LYS cc_start: 0.5737 (mtpt) cc_final: 0.5182 (tptp) outliers start: 88 outliers final: 59 residues processed: 329 average time/residue: 0.1642 time to fit residues: 84.8477 Evaluate side-chains 326 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 758 GLU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 162 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS F 304 GLN J 721 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.108877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083953 restraints weight = 70046.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083929 restraints weight = 40153.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.084152 restraints weight = 45882.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.085155 restraints weight = 31108.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085299 restraints weight = 26779.023| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24154 Z= 0.148 Angle : 0.608 11.790 32665 Z= 0.301 Chirality : 0.041 0.240 3749 Planarity : 0.003 0.055 4200 Dihedral : 4.573 76.675 3300 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.03 % Favored : 93.48 % Rotamer: Outliers : 3.52 % Allowed : 27.26 % Favored : 69.22 % 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: 0.81 (0.16), residues: 3035 helix: 1.96 (0.13), residues: 1875 sheet: -0.48 (0.39), residues: 184 loop : -2.23 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 204 TYR 0.041 0.001 TYR C 244 PHE 0.024 0.001 PHE E 165 TRP 0.020 0.001 TRP E 45 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00346 (24141) covalent geometry : angle 0.60433 (32653) hydrogen bonds : bond 0.03784 ( 1387) hydrogen bonds : angle 3.75760 ( 4074) metal coordination : bond 0.01099 ( 12) metal coordination : angle 3.69516 ( 12) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 259 time to evaluate : 0.959 Fit side-chains REVERT: B 234 MET cc_start: 0.8312 (tpp) cc_final: 0.7950 (tpp) REVERT: D 1 MET cc_start: 0.6180 (mtt) cc_final: 0.4521 (tpt) REVERT: D 134 THR cc_start: 0.9087 (m) cc_final: 0.8726 (p) REVERT: E 52 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.5172 (m-80) REVERT: E 56 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8455 (mmmm) REVERT: E 67 MET cc_start: 0.7836 (mmm) cc_final: 0.7573 (mmm) REVERT: E 187 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8339 (mtp180) REVERT: F 173 ASP cc_start: 0.3288 (OUTLIER) cc_final: 0.2919 (p0) REVERT: G 167 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7601 (mt) REVERT: G 204 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8359 (ttp80) REVERT: G 220 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6936 (mm) REVERT: J 709 GLN cc_start: 0.7794 (mp10) cc_final: 0.7592 (pm20) REVERT: J 754 LYS cc_start: 0.8740 (mmtp) cc_final: 0.8404 (mptt) REVERT: J 755 GLU cc_start: 0.8554 (tp30) cc_final: 0.8340 (tp30) REVERT: J 766 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8331 (mt) REVERT: J 772 ASP cc_start: 0.7918 (t0) cc_final: 0.7623 (t0) REVERT: A 96 ARG cc_start: 0.9073 (ptp90) cc_final: 0.8821 (ptp90) REVERT: A 185 TYR cc_start: 0.7181 (m-80) cc_final: 0.6949 (m-80) REVERT: A 201 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7894 (ppp) REVERT: A 454 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8310 (mtm) REVERT: C 159 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (mm) REVERT: C 271 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7425 (t0) REVERT: I 33 LYS cc_start: 0.5736 (mtpt) cc_final: 0.5249 (tptp) outliers start: 86 outliers final: 64 residues processed: 326 average time/residue: 0.1613 time to fit residues: 82.1883 Evaluate side-chains 328 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 758 GLU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain I residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN J 721 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.107759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.078336 restraints weight = 71967.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.080016 restraints weight = 41964.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080427 restraints weight = 29248.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.080738 restraints weight = 28086.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080713 restraints weight = 24424.391| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24154 Z= 0.154 Angle : 0.619 11.697 32665 Z= 0.307 Chirality : 0.041 0.234 3749 Planarity : 0.003 0.054 4200 Dihedral : 4.653 80.285 3300 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.03 % Favored : 93.48 % Rotamer: Outliers : 3.68 % Allowed : 27.34 % Favored : 68.97 % 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: 0.78 (0.16), residues: 3035 helix: 1.93 (0.13), residues: 1876 sheet: -0.51 (0.39), residues: 185 loop : -2.23 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.040 0.001 TYR A 357 PHE 0.014 0.001 PHE E 96 TRP 0.022 0.001 TRP E 45 HIS 0.005 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00362 (24141) covalent geometry : angle 0.61442 (32653) hydrogen bonds : bond 0.03905 ( 1387) hydrogen bonds : angle 3.76733 ( 4074) metal coordination : bond 0.01190 ( 12) metal coordination : angle 3.85466 ( 12) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 258 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: B 151 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7733 (m) REVERT: B 234 MET cc_start: 0.8426 (tpp) cc_final: 0.8053 (tpp) REVERT: D 1 MET cc_start: 0.6239 (mtt) cc_final: 0.4586 (tpt) REVERT: D 134 THR cc_start: 0.9104 (m) cc_final: 0.8720 (p) REVERT: E 52 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.5238 (m-80) REVERT: E 56 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8506 (mmmm) REVERT: E 67 MET cc_start: 0.8124 (mmm) cc_final: 0.7896 (mmm) REVERT: E 187 ARG cc_start: 0.8770 (mtp85) cc_final: 0.8353 (mtp180) REVERT: F 173 ASP cc_start: 0.3705 (OUTLIER) cc_final: 0.2997 (p0) REVERT: G 167 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7627 (mt) REVERT: G 204 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8336 (ttp80) REVERT: G 220 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6996 (mm) REVERT: H 50 MET cc_start: 0.7927 (tpp) cc_final: 0.7626 (tpp) REVERT: J 737 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7923 (mp0) REVERT: J 754 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8447 (mptt) REVERT: J 755 GLU cc_start: 0.8757 (tp30) cc_final: 0.8537 (tp30) REVERT: J 766 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8410 (mt) REVERT: J 772 ASP cc_start: 0.7848 (t0) cc_final: 0.7479 (t0) REVERT: A 96 ARG cc_start: 0.9121 (ptp90) cc_final: 0.8871 (ptp90) REVERT: A 185 TYR cc_start: 0.7293 (m-80) cc_final: 0.7033 (m-80) REVERT: A 201 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8101 (ppp) REVERT: A 454 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: A 456 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8217 (tpt90) REVERT: C 159 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8042 (mm) REVERT: C 271 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7454 (t0) REVERT: I 12 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8046 (mm-30) REVERT: I 33 LYS cc_start: 0.5904 (mtpt) cc_final: 0.5450 (tptp) outliers start: 90 outliers final: 63 residues processed: 325 average time/residue: 0.1581 time to fit residues: 80.9838 Evaluate side-chains 330 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 758 GLU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain I residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 165 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 294 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN E 158 ASN F 304 GLN J 721 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.108282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.079150 restraints weight = 71905.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080258 restraints weight = 43336.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.081022 restraints weight = 30538.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.081394 restraints weight = 28296.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081378 restraints weight = 24771.433| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24154 Z= 0.130 Angle : 0.619 11.836 32665 Z= 0.306 Chirality : 0.040 0.213 3749 Planarity : 0.003 0.053 4200 Dihedral : 4.626 81.532 3300 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.77 % Favored : 93.74 % Rotamer: Outliers : 3.15 % Allowed : 27.83 % Favored : 69.01 % 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: 0.83 (0.16), residues: 3035 helix: 1.97 (0.13), residues: 1877 sheet: -0.46 (0.40), residues: 185 loop : -2.22 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 204 TYR 0.044 0.001 TYR A 357 PHE 0.013 0.001 PHE B 69 TRP 0.020 0.001 TRP E 13 HIS 0.004 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00300 (24141) covalent geometry : angle 0.61563 (32653) hydrogen bonds : bond 0.03662 ( 1387) hydrogen bonds : angle 3.70047 ( 4074) metal coordination : bond 0.00971 ( 12) metal coordination : angle 3.60006 ( 12) Misc. bond : bond 0.00041 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 259 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: B 89 MET cc_start: 0.8264 (ptp) cc_final: 0.7937 (mpp) REVERT: B 151 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7752 (m) REVERT: B 234 MET cc_start: 0.8335 (tpp) cc_final: 0.7971 (tpp) REVERT: D 1 MET cc_start: 0.6195 (mtt) cc_final: 0.4568 (tpt) REVERT: D 134 THR cc_start: 0.9109 (m) cc_final: 0.8729 (p) REVERT: E 52 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: E 56 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8507 (mmmm) REVERT: E 67 MET cc_start: 0.8048 (mmm) cc_final: 0.7724 (mmm) REVERT: E 158 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7760 (t0) REVERT: E 187 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8382 (mtp180) REVERT: F 173 ASP cc_start: 0.3578 (OUTLIER) cc_final: 0.2944 (p0) REVERT: G 30 LEU cc_start: 0.7316 (tt) cc_final: 0.7062 (tp) REVERT: G 167 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7591 (mt) REVERT: G 204 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8343 (ttp80) REVERT: G 220 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7035 (mm) REVERT: H 50 MET cc_start: 0.7933 (tpp) cc_final: 0.7632 (tpp) REVERT: J 737 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7920 (mp0) REVERT: J 754 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8484 (mptt) REVERT: J 755 GLU cc_start: 0.8755 (tp30) cc_final: 0.8541 (tp30) REVERT: J 766 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8370 (mt) REVERT: J 772 ASP cc_start: 0.7870 (t0) cc_final: 0.7491 (t0) REVERT: A 96 ARG cc_start: 0.9106 (ptp90) cc_final: 0.8846 (ptp90) REVERT: A 185 TYR cc_start: 0.7308 (m-80) cc_final: 0.7064 (m-80) REVERT: A 201 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8064 (ppp) REVERT: A 454 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8163 (mtm) REVERT: A 456 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8265 (tpt90) REVERT: C 159 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 271 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7453 (t0) REVERT: I 33 LYS cc_start: 0.5819 (mtpt) cc_final: 0.5376 (tptp) outliers start: 77 outliers final: 61 residues processed: 321 average time/residue: 0.1676 time to fit residues: 84.1331 Evaluate side-chains 332 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 258 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain J residue 758 GLU Chi-restraints excluded: chain J residue 766 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 73 CYS Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 155 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN E 138 HIS F 304 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.108848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079794 restraints weight = 71642.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.080941 restraints weight = 43365.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.082039 restraints weight = 30279.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.082135 restraints weight = 27280.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.082163 restraints weight = 24226.658| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24154 Z= 0.116 Angle : 0.607 11.473 32665 Z= 0.298 Chirality : 0.040 0.229 3749 Planarity : 0.003 0.066 4200 Dihedral : 4.589 82.834 3300 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.83 % Favored : 93.67 % Rotamer: Outliers : 2.91 % Allowed : 28.16 % Favored : 68.93 % 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: 0.87 (0.16), residues: 3035 helix: 2.00 (0.13), residues: 1880 sheet: -0.55 (0.39), residues: 194 loop : -2.19 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 135 TYR 0.039 0.001 TYR A 357 PHE 0.013 0.001 PHE B 69 TRP 0.020 0.001 TRP E 13 HIS 0.005 0.000 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00260 (24141) covalent geometry : angle 0.60331 (32653) hydrogen bonds : bond 0.03506 ( 1387) hydrogen bonds : angle 3.65156 ( 4074) metal coordination : bond 0.00832 ( 12) metal coordination : angle 3.52641 ( 12) Misc. bond : bond 0.00030 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.96 seconds wall clock time: 79 minutes 26.58 seconds (4766.58 seconds total)