Starting phenix.real_space_refine on Tue Jul 7 05:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snh_40625/07_2026/8snh_40625_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snh_40625/07_2026/8snh_40625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8snh_40625/07_2026/8snh_40625_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snh_40625/07_2026/8snh_40625_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8snh_40625/07_2026/8snh_40625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snh_40625/07_2026/8snh_40625.map" } resolution = 2.7 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= 0.002 sd= 0.182 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 19 7.16 5 Cu 1 5.60 5 S 140 5.16 5 C 15892 2.51 5 N 3937 2.21 5 O 4174 1.98 5 H 19392 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43557 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 452} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2827 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 20, 'TRANS': 169} Chain: "I" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6556 Classifications: {'peptide': 403} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "J" Number of atoms: 3663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3663 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain: "K" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2585 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "L" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 244 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "Z" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2883 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 20, 'TRANS': 173} Chain: "D" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6556 Classifications: {'peptide': 403} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "M" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3250 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2585 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 244 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 2917 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 188} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 4655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4655 Classifications: {'peptide': 304} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 289} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Ad-hoc single atom residues: {' CU': 1, ' CA': 2} Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'HEM': 2, 'I7Y': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 11 Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'FES': 1, 'I7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'HEM': 2, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5498 SG CYS C 124 85.925 89.842 78.269 1.00 73.85 S ATOM 5565 SG CYS C 129 82.145 90.282 77.754 1.00 84.77 S ATOM 5902 SG CYS C 152 83.432 92.560 79.326 1.00 77.21 S ATOM 21406 SG CYS Z 124 43.257 59.253 40.939 1.00 43.68 S ATOM 21811 SG CYS Z 152 46.202 59.766 39.023 1.00 46.64 S Time building chain proxies: 6.84, per 1000 atoms: 0.16 Number of scatterers: 43557 At special positions: 0 Unit cell: (115.36, 141.11, 161.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cu 1 28.99 Fe 19 26.01 Ca 2 19.99 S 140 16.00 O 4174 8.00 N 3937 7.00 C 15892 6.00 H 19392 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 165 " - pdb=" SG CYS J 191 " distance=2.03 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 155 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 126 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 152 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 124 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 129 " pdb=" FES Z 201 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 155 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 126 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 152 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 124 " Number of angles added : 9 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 20 sheets defined 60.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'E' and resid 11 through 42 removed outlier: 4.040A pdb=" N VAL E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'E' and resid 53 through 68 Proline residue: E 59 - end of helix removed outlier: 3.778A pdb=" N ILE E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 87 removed outlier: 4.165A pdb=" N GLN E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 Processing helix chain 'E' and resid 133 through 152 Processing helix chain 'E' and resid 159 through 180 removed outlier: 5.108A pdb=" N HIS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 211 removed outlier: 4.083A pdb=" N ASN E 209 " --> pdb=" O TRP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 232 Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 237 through 253 removed outlier: 4.409A pdb=" N ILE E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.617A pdb=" N HIS E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS E 261 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 294 removed outlier: 4.386A pdb=" N ALA E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Proline residue: E 283 - end of helix Processing helix chain 'E' and resid 298 through 304 Processing helix chain 'E' and resid 305 through 329 Proline residue: E 326 - end of helix Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.919A pdb=" N LEU E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 removed outlier: 4.222A pdb=" N ILE E 344 " --> pdb=" O THR E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 371 Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 378 through 413 removed outlier: 3.861A pdb=" N GLY E 392 " --> pdb=" O LEU E 388 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 461 Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.871A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 36 Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.582A pdb=" N LEU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.621A pdb=" N GLU C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 removed outlier: 3.612A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 32 through 35 Processing helix chain 'I' and resid 36 through 57 Processing helix chain 'I' and resid 65 through 76 Processing helix chain 'I' and resid 79 through 108 Processing helix chain 'I' and resid 115 through 139 removed outlier: 3.542A pdb=" N LEU I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 139 " --> pdb=" O MET I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 removed outlier: 4.007A pdb=" N PHE I 156 " --> pdb=" O ILE I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 177 through 190 Processing helix chain 'I' and resid 190 through 211 Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 236 through 262 removed outlier: 6.681A pdb=" N THR I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 293 through 303 Processing helix chain 'I' and resid 305 through 327 removed outlier: 3.633A pdb=" N ILE I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) Proline residue: I 324 - end of helix Processing helix chain 'I' and resid 338 through 360 Processing helix chain 'I' and resid 364 through 384 removed outlier: 3.925A pdb=" N PHE I 382 " --> pdb=" O TYR I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 392 removed outlier: 4.289A pdb=" N ARG I 390 " --> pdb=" O PRO I 386 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU I 392 " --> pdb=" O TYR I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 119 through 127 Processing helix chain 'J' and resid 154 through 159 Processing helix chain 'J' and resid 204 through 224 Processing helix chain 'J' and resid 226 through 254 Processing helix chain 'K' and resid 23 through 31 removed outlier: 3.977A pdb=" N ALA K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 56 through 69 Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 107 through 121 removed outlier: 4.573A pdb=" N ALA K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 176 through 184 removed outlier: 3.879A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.541A pdb=" N GLY K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'Z' and resid 9 through 36 Proline residue: Z 32 - end of helix Processing helix chain 'Z' and resid 42 through 46 removed outlier: 3.539A pdb=" N ALA Z 45 " --> pdb=" O LYS Z 42 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA Z 46 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 46' Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 86 through 92 removed outlier: 4.813A pdb=" N GLY Z 90 " --> pdb=" O SER Z 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Z 92 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.629A pdb=" N ARG D 11 " --> pdb=" O TRP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 32 through 35 Processing helix chain 'D' and resid 36 through 57 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 79 through 109 Processing helix chain 'D' and resid 115 through 139 Processing helix chain 'D' and resid 142 through 156 removed outlier: 4.033A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 190 through 211 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 236 through 262 removed outlier: 6.734A pdb=" N THR D 241 " --> pdb=" O HIS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 303 Processing helix chain 'D' and resid 305 through 327 removed outlier: 4.527A pdb=" N LEU D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Proline residue: D 324 - end of helix Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.885A pdb=" N PHE D 382 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 392 removed outlier: 4.388A pdb=" N ARG D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 51 Processing helix chain 'M' and resid 62 through 70 Processing helix chain 'M' and resid 72 through 80 Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 119 through 128 removed outlier: 3.547A pdb=" N ARG M 128 " --> pdb=" O TYR M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 159 Processing helix chain 'M' and resid 204 through 224 Processing helix chain 'M' and resid 226 through 256 removed outlier: 3.606A pdb=" N TYR M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 3.837A pdb=" N ALA N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 56 through 69 Processing helix chain 'N' and resid 74 through 78 Processing helix chain 'N' and resid 85 through 99 removed outlier: 3.630A pdb=" N GLN N 99 " --> pdb=" O TYR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 121 removed outlier: 4.665A pdb=" N ALA N 112 " --> pdb=" O PRO N 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 166 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 186 through 199 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'F' and resid 3 through 10 removed outlier: 4.240A pdb=" N LEU F 7 " --> pdb=" O ASN F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 30 removed outlier: 4.056A pdb=" N GLY F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.658A pdb=" N GLY F 67 " --> pdb=" O GLY F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.562A pdb=" N VAL F 93 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 125 removed outlier: 4.442A pdb=" N ALA F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.098A pdb=" N VAL F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.727A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'G' and resid 2 through 28 removed outlier: 4.151A pdb=" N THR G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 94 through 110 Processing helix chain 'G' and resid 110 through 120 removed outlier: 3.776A pdb=" N PHE G 114 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 172 through 181 removed outlier: 4.561A pdb=" N ILE G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 200 Processing helix chain 'G' and resid 201 through 206 Processing helix chain 'G' and resid 221 through 233 removed outlier: 3.754A pdb=" N VAL G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 273 Processing helix chain 'G' and resid 289 through 298 removed outlier: 3.697A pdb=" N ILE G 293 " --> pdb=" O GLU G 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 296 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.828A pdb=" N LYS E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.719A pdb=" N VAL C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AA5, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AA6, first strand: chain 'J' and resid 57 through 61 removed outlier: 6.451A pdb=" N GLN J 60 " --> pdb=" O MET J 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 130 through 132 Processing sheet with id=AA8, first strand: chain 'J' and resid 161 through 169 removed outlier: 6.235A pdb=" N VAL J 162 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU J 194 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY J 164 " --> pdb=" O ASP J 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'K' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'Z' and resid 50 through 53 removed outlier: 6.757A pdb=" N THR Z 189 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE Z 182 " --> pdb=" O THR Z 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 61 through 67 removed outlier: 3.873A pdb=" N GLN Z 61 " --> pdb=" O HIS Z 76 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Z' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AB6, first strand: chain 'M' and resid 57 through 61 removed outlier: 3.896A pdb=" N MET M 91 " --> pdb=" O ALA M 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 130 through 132 Processing sheet with id=AB8, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AB9, first strand: chain 'N' and resid 200 through 201 Processing sheet with id=AC1, first strand: chain 'G' and resid 39 through 43 removed outlier: 6.743A pdb=" N GLU G 49 " --> pdb=" O MET G 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 182 through 183 1264 hydrogen bonds defined for protein. 3639 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: 9.76 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 19379 1.11 - 1.38: 9774 1.38 - 1.66: 14878 1.66 - 1.93: 242 1.93 - 2.21: 68 Bond restraints: 44341 Sorted by residual: bond pdb=" C07 I7Y Z 202 " pdb=" C08 I7Y Z 202 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 501 " pdb=" C08 I7Y I 501 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 501 " pdb=" C15 I7Y I 501 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C07 I7Y Z 202 " pdb=" C15 I7Y Z 202 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C02 I7Y I 501 " pdb=" C10 I7Y I 501 " ideal model delta sigma weight residual 1.526 1.295 0.231 2.00e-02 2.50e+03 1.33e+02 ... (remaining 44336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 78276 6.76 - 13.53: 51 13.53 - 20.29: 1 20.29 - 27.05: 0 27.05 - 33.82: 9 Bond angle restraints: 78337 Sorted by residual: angle pdb=" C74 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" C76 I7Y I 501 " ideal model delta sigma weight residual 114.35 148.17 -33.82 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C76 I7Y Z 202 " ideal model delta sigma weight residual 114.35 148.16 -33.81 3.00e+00 1.11e-01 1.27e+02 angle pdb=" CD ARG F 77 " pdb=" CG ARG F 77 " pdb=" HG3 ARG F 77 " ideal model delta sigma weight residual 108.00 78.09 29.91 3.00e+00 1.11e-01 9.94e+01 angle pdb=" CD ARG F 77 " pdb=" CG ARG F 77 " pdb=" HG2 ARG F 77 " ideal model delta sigma weight residual 108.00 78.34 29.66 3.00e+00 1.11e-01 9.77e+01 angle pdb=" C74 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" O80 I7Y I 501 " ideal model delta sigma weight residual 107.63 79.89 27.74 3.00e+00 1.11e-01 8.55e+01 ... (remaining 78332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 19502 24.23 - 48.47: 1365 48.47 - 72.70: 325 72.70 - 96.94: 65 96.94 - 121.17: 13 Dihedral angle restraints: 21270 sinusoidal: 11150 harmonic: 10120 Sorted by residual: dihedral pdb=" C2B HEC G 401 " pdb=" C3B HEC G 401 " pdb=" CAB HEC G 401 " pdb=" CBB HEC G 401 " ideal model delta sinusoidal sigma weight residual 60.00 133.66 -73.66 2 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" C2B HEC J 500 " pdb=" C3B HEC J 500 " pdb=" CAB HEC J 500 " pdb=" CBB HEC J 500 " ideal model delta sinusoidal sigma weight residual 60.00 129.52 -69.52 2 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" C2C HEC N 501 " pdb=" C3C HEC N 501 " pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sinusoidal sigma weight residual 60.00 117.18 -57.18 2 1.00e+01 1.00e-02 3.39e+01 ... (remaining 21267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3576 0.282 - 0.565: 5 0.565 - 0.847: 2 0.847 - 1.130: 0 1.130 - 1.412: 2 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C74 I7Y I 501 " pdb=" C03 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" C75 I7Y I 501 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" C74 I7Y Z 202 " pdb=" C03 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C75 I7Y Z 202 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" C02 I7Y I 501 " pdb=" C03 I7Y I 501 " pdb=" C06 I7Y I 501 " pdb=" C10 I7Y I 501 " both_signs ideal model delta sigma weight residual False 2.93 2.25 0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3582 not shown) Planarity restraints: 6605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 D 503 " 0.129 2.00e-02 2.50e+03 1.89e-01 1.07e+03 pdb=" C1M U10 D 503 " 0.272 2.00e-02 2.50e+03 pdb=" C2 U10 D 503 " 0.030 2.00e-02 2.50e+03 pdb=" C3 U10 D 503 " -0.097 2.00e-02 2.50e+03 pdb=" C4 U10 D 503 " -0.110 2.00e-02 2.50e+03 pdb=" C5 U10 D 503 " -0.016 2.00e-02 2.50e+03 pdb=" C6 U10 D 503 " 0.103 2.00e-02 2.50e+03 pdb=" C7 U10 D 503 " -0.191 2.00e-02 2.50e+03 pdb=" O2 U10 D 503 " -0.265 2.00e-02 2.50e+03 pdb=" O3 U10 D 503 " -0.066 2.00e-02 2.50e+03 pdb=" O4 U10 D 503 " 0.398 2.00e-02 2.50e+03 pdb=" O5 U10 D 503 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 U10 I 504 " 0.289 2.00e-02 2.50e+03 2.38e-01 7.07e+02 pdb=" C18 U10 I 504 " -0.397 2.00e-02 2.50e+03 pdb=" C19 U10 I 504 " -0.068 2.00e-02 2.50e+03 pdb=" C20 U10 I 504 " -0.017 2.00e-02 2.50e+03 pdb=" C21 U10 I 504 " 0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C52 U10 D 503 " -0.284 2.00e-02 2.50e+03 2.33e-01 6.77e+02 pdb=" C53 U10 D 503 " 0.385 2.00e-02 2.50e+03 pdb=" C54 U10 D 503 " 0.068 2.00e-02 2.50e+03 pdb=" C55 U10 D 503 " -0.192 2.00e-02 2.50e+03 pdb=" C56 U10 D 503 " 0.022 2.00e-02 2.50e+03 ... (remaining 6602 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 431 1.98 - 2.64: 51962 2.64 - 3.29: 130455 3.29 - 3.95: 173374 3.95 - 4.60: 267224 Nonbonded interactions: 623446 Sorted by model distance: nonbonded pdb=" OD2 ASP E 417 " pdb="HH21 ARG G 137 " model vdw 1.331 2.450 nonbonded pdb=" OE1 GLU Z 104 " pdb=" H GLU Z 104 " model vdw 1.400 2.450 nonbonded pdb=" H CYS Z 124 " pdb=" O CYS Z 129 " model vdw 1.490 2.450 nonbonded pdb=" HH TYR J 240 " pdb=" O VAL Z 21 " model vdw 1.519 2.450 nonbonded pdb=" O TRP D 291 " pdb=" HG1 THR D 294 " model vdw 1.535 2.450 ... (remaining 623441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 6 through 195) selection = (chain 'Z' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 128 or (resid 12 \ 9 and (name N or name CA or name C or name O or name CB or name SG or name H or \ name HA or name HB2 or name HB3)) or resid 130 through 195)) } ncs_group { reference = (chain 'D' and (resid 1 through 403 or resid 502)) selection = (chain 'I' and (resid 1 through 403 or resid 502)) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or \ resid 194 through 500)) selection = (chain 'M' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 27 through 500)) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } 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 individual isotropic 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 46.980 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.010 0.367 24992 Z= 0.463 Angle : 0.893 33.817 34163 Z= 0.386 Chirality : 0.057 1.412 3585 Planarity : 0.012 0.238 4245 Dihedral : 18.251 121.174 8912 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Rotamer: Outliers : 1.04 % Allowed : 19.96 % Favored : 79.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.01 % 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: 0.51 (0.16), residues: 2964 helix: 0.80 (0.13), residues: 1624 sheet: -2.00 (0.63), residues: 56 loop : -0.00 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 253 TYR 0.044 0.002 TYR G 264 PHE 0.025 0.001 PHE G 68 TRP 0.015 0.001 TRP I 54 HIS 0.006 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00866 / 0.43 (24949) covalent geometry : angle 0.86226 / 0.38 (34152) SS BOND : bond 0.00221 / 0.15 ( 1) SS BOND : angle 1.75570 / 0.92 ( 2) hydrogen bonds : bond 0.13986 / 9.21 ( 1264) hydrogen bonds : angle 6.65472 / 4.85 ( 3639) metal coordination : bond 0.01686 / 1.12 ( 9) metal coordination : angle 14.27911 / 10.23 ( 9) Misc. bond : bond 0.15578 / 10.75 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 414 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 261 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: E 410 MET cc_start: 0.8113 (mmm) cc_final: 0.7715 (mtm) REVERT: D 3 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7809 (mppt) outliers start: 25 outliers final: 15 residues processed: 434 average time/residue: 1.1310 time to fit residues: 573.5612 Evaluate side-chains 403 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 387 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 473 ARG Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 203 GLN ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN E 432 HIS J 90 HIS Z 3 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.102089 restraints weight = 69694.939| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.15 r_work: 0.2652 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.399 24992 Z= 0.161 Angle : 0.676 22.245 34163 Z= 0.303 Chirality : 0.041 0.225 3585 Planarity : 0.004 0.055 4245 Dihedral : 12.001 133.449 3694 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 2.08 % Allowed : 18.00 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.64 (0.15), residues: 2964 helix: 0.92 (0.13), residues: 1645 sheet: -2.56 (0.57), residues: 52 loop : 0.04 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 253 TYR 0.017 0.002 TYR J 240 PHE 0.021 0.001 PHE M 243 TRP 0.016 0.001 TRP E 204 HIS 0.008 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (24949) covalent geometry : angle 0.65045 / 0.30 (34152) SS BOND : bond 0.00159 / 0.11 ( 1) SS BOND : angle 0.72986 / 0.44 ( 2) hydrogen bonds : bond 0.05029 / 3.25 ( 1264) hydrogen bonds : angle 5.40959 / 3.92 ( 3639) metal coordination : bond 0.01943 / 1.31 ( 9) metal coordination : angle 11.37834 / 7.77 ( 9) Misc. bond : bond 0.16082 / 10.93 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 406 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6748 (t80) cc_final: 0.6449 (t80) REVERT: E 252 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.5956 (m-10) REVERT: E 279 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7408 (mp) REVERT: E 280 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7875 (tp) REVERT: E 410 MET cc_start: 0.8501 (mmm) cc_final: 0.8164 (mtt) REVERT: E 426 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7751 (mt-10) REVERT: E 469 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7802 (pp) REVERT: K 23 ASP cc_start: 0.8376 (t0) cc_final: 0.8027 (t70) REVERT: D 3 LYS cc_start: 0.8319 (mmtp) cc_final: 0.7848 (mppt) REVERT: D 64 GLU cc_start: 0.8722 (mp0) cc_final: 0.8488 (mp0) REVERT: D 308 MET cc_start: 0.8549 (tpp) cc_final: 0.8296 (tpt) REVERT: M 231 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: O 30 GLU cc_start: 0.8085 (tp30) cc_final: 0.7646 (tt0) REVERT: F 81 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: F 172 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8330 (mp) REVERT: F 185 MET cc_start: 0.8730 (tpp) cc_final: 0.8451 (tpp) REVERT: G 72 TYR cc_start: 0.4625 (OUTLIER) cc_final: 0.3341 (t80) REVERT: G 114 PHE cc_start: 0.7132 (m-80) cc_final: 0.6915 (m-80) REVERT: G 172 GLN cc_start: 0.7462 (tp-100) cc_final: 0.7242 (tp-100) REVERT: G 200 ASN cc_start: 0.8454 (m-40) cc_final: 0.8105 (t0) outliers start: 50 outliers final: 19 residues processed: 436 average time/residue: 1.1552 time to fit residues: 588.4814 Evaluate side-chains 416 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 389 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 132 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 chunk 30 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 253 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN I 280 GLN Z 3 ASN G 172 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101650 restraints weight = 69480.597| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.99 r_work: 0.2645 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.410 24992 Z= 0.166 Angle : 0.654 19.369 34163 Z= 0.293 Chirality : 0.041 0.174 3585 Planarity : 0.004 0.054 4245 Dihedral : 11.311 132.428 3681 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 2.33 % Allowed : 17.83 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.71 (0.15), residues: 2964 helix: 0.99 (0.13), residues: 1654 sheet: -2.56 (0.56), residues: 51 loop : 0.06 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 166 TYR 0.016 0.002 TYR D 388 PHE 0.017 0.001 PHE M 243 TRP 0.017 0.001 TRP E 204 HIS 0.008 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (24949) covalent geometry : angle 0.63257 / 0.29 (34152) SS BOND : bond 0.00310 / 0.21 ( 1) SS BOND : angle 0.20512 / 0.11 ( 2) hydrogen bonds : bond 0.04871 / 3.14 ( 1264) hydrogen bonds : angle 5.11533 / 3.69 ( 3639) metal coordination : bond 0.01481 / 0.94 ( 9) metal coordination : angle 10.29506 / 7.17 ( 9) Misc. bond : bond 0.16199 / 10.97 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 415 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7060 (t80) cc_final: 0.6725 (t80) REVERT: E 239 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7698 (mtp85) REVERT: E 261 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7897 (m-70) REVERT: E 279 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7622 (mp) REVERT: E 280 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7802 (tp) REVERT: E 410 MET cc_start: 0.8687 (mmm) cc_final: 0.8391 (mtt) REVERT: E 412 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.8025 (ttm170) REVERT: C 193 ASP cc_start: 0.7998 (m-30) cc_final: 0.7724 (m-30) REVERT: J 255 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6798 (t80) REVERT: D 3 LYS cc_start: 0.8286 (mmtp) cc_final: 0.7809 (mppt) REVERT: D 308 MET cc_start: 0.8517 (tpp) cc_final: 0.8264 (tpt) REVERT: M 231 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: O 30 GLU cc_start: 0.8011 (tp30) cc_final: 0.7541 (tt0) REVERT: F 8 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7334 (mt-10) REVERT: F 134 GLU cc_start: 0.8845 (mp0) cc_final: 0.8583 (mp0) REVERT: F 172 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8330 (mp) REVERT: F 184 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8022 (mt-10) REVERT: F 185 MET cc_start: 0.8702 (tpp) cc_final: 0.8414 (tpp) REVERT: G 8 TYR cc_start: 0.6939 (t80) cc_final: 0.6684 (t80) REVERT: G 28 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7512 (ppp-140) REVERT: G 73 LEU cc_start: 0.8110 (tp) cc_final: 0.7905 (tm) REVERT: G 166 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7210 (ptp90) REVERT: G 192 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7480 (mm) outliers start: 56 outliers final: 22 residues processed: 444 average time/residue: 1.2602 time to fit residues: 652.3788 Evaluate side-chains 419 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 387 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 22 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 142 optimal weight: 0.0170 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS Z 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100606 restraints weight = 69392.230| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.19 r_work: 0.2633 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.420 24992 Z= 0.162 Angle : 0.640 18.326 34163 Z= 0.288 Chirality : 0.040 0.176 3585 Planarity : 0.004 0.054 4245 Dihedral : 11.120 130.395 3677 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 2.38 % Allowed : 18.33 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.79 (0.15), residues: 2964 helix: 1.07 (0.13), residues: 1650 sheet: -2.71 (0.55), residues: 50 loop : 0.08 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 84 TYR 0.017 0.002 TYR D 388 PHE 0.017 0.001 PHE M 243 TRP 0.016 0.001 TRP D 54 HIS 0.007 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (24949) covalent geometry : angle 0.62043 / 0.29 (34152) SS BOND : bond 0.00101 / 0.07 ( 1) SS BOND : angle 0.37179 / 0.24 ( 2) hydrogen bonds : bond 0.04681 / 3.02 ( 1264) hydrogen bonds : angle 4.99982 / 3.60 ( 3639) metal coordination : bond 0.01370 / 0.84 ( 9) metal coordination : angle 9.69489 / 6.60 ( 9) Misc. bond : bond 0.16502 / 11.13 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 461 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 404 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7161 (t80) cc_final: 0.6792 (t80) REVERT: E 261 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.8049 (m-70) REVERT: E 279 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7691 (mp) REVERT: E 280 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7785 (tp) REVERT: E 371 TYR cc_start: 0.8147 (m-80) cc_final: 0.7739 (m-80) REVERT: E 375 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8167 (ptmt) REVERT: E 410 MET cc_start: 0.8792 (mmm) cc_final: 0.8537 (mtt) REVERT: E 412 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.8044 (ttm170) REVERT: E 426 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: J 255 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6779 (t80) REVERT: Z 12 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8105 (ttm-80) REVERT: Z 68 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7976 (mtt180) REVERT: D 3 LYS cc_start: 0.8276 (mmtp) cc_final: 0.7824 (mppt) REVERT: D 308 MET cc_start: 0.8561 (tpp) cc_final: 0.8322 (tpt) REVERT: M 231 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: O 30 GLU cc_start: 0.8047 (tp30) cc_final: 0.7549 (tt0) REVERT: F 81 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: F 172 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8294 (mp) REVERT: F 185 MET cc_start: 0.8726 (tpp) cc_final: 0.8428 (tpp) REVERT: G 8 TYR cc_start: 0.6996 (t80) cc_final: 0.6751 (t80) REVERT: G 28 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7505 (ppp-140) REVERT: G 73 LEU cc_start: 0.8157 (tp) cc_final: 0.7946 (tm) REVERT: G 166 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7290 (ptp90) outliers start: 57 outliers final: 21 residues processed: 437 average time/residue: 1.1236 time to fit residues: 573.7461 Evaluate side-chains 427 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 395 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 233 optimal weight: 3.9990 chunk 205 optimal weight: 0.5980 chunk 284 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS I 227 ASN I 280 GLN Z 3 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.100810 restraints weight = 69559.699| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.18 r_work: 0.2644 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.378 24992 Z= 0.143 Angle : 0.647 27.193 34163 Z= 0.281 Chirality : 0.040 0.175 3585 Planarity : 0.004 0.054 4245 Dihedral : 10.828 125.004 3677 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.00 % Allowed : 18.79 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.89 (0.16), residues: 2964 helix: 1.17 (0.13), residues: 1647 sheet: -2.74 (0.56), residues: 50 loop : 0.10 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 253 TYR 0.017 0.001 TYR D 388 PHE 0.016 0.001 PHE M 243 TRP 0.015 0.001 TRP D 54 HIS 0.006 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (24949) covalent geometry : angle 0.60624 / 0.28 (34152) SS BOND : bond 0.00111 / 0.07 ( 1) SS BOND : angle 0.20809 / 0.14 ( 2) hydrogen bonds : bond 0.04494 / 2.90 ( 1264) hydrogen bonds : angle 4.90936 / 3.53 ( 3639) metal coordination : bond 0.01504 / 0.86 ( 9) metal coordination : angle 13.94824 / 10.08 ( 9) Misc. bond : bond 0.15639 / 10.52 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 410 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7255 (t80) cc_final: 0.6892 (t80) REVERT: E 280 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7734 (tp) REVERT: E 371 TYR cc_start: 0.8209 (m-80) cc_final: 0.7819 (m-80) REVERT: E 410 MET cc_start: 0.8843 (mmm) cc_final: 0.8612 (mtt) REVERT: E 412 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8035 (ttm170) REVERT: E 426 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 193 ASP cc_start: 0.7971 (m-30) cc_final: 0.7660 (m-30) REVERT: J 255 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6876 (t80) REVERT: Z 12 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: D 308 MET cc_start: 0.8522 (tpp) cc_final: 0.8297 (tpt) REVERT: M 231 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: O 30 GLU cc_start: 0.8051 (tp30) cc_final: 0.7550 (tt0) REVERT: F 81 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: F 185 MET cc_start: 0.8725 (tpp) cc_final: 0.8401 (tpp) REVERT: F 199 ILE cc_start: 0.8135 (mt) cc_final: 0.7915 (mp) REVERT: G 8 TYR cc_start: 0.7054 (t80) cc_final: 0.6832 (t80) REVERT: G 28 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7503 (ppp-140) REVERT: G 120 MET cc_start: 0.6290 (mpp) cc_final: 0.5402 (mpp) REVERT: G 166 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7362 (ptp90) REVERT: G 282 GLN cc_start: 0.8195 (tp40) cc_final: 0.7861 (mm110) REVERT: G 288 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8331 (tmmm) outliers start: 48 outliers final: 18 residues processed: 442 average time/residue: 1.2117 time to fit residues: 624.6666 Evaluate side-chains 418 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 392 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 113 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099471 restraints weight = 69518.828| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.12 r_work: 0.2617 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.435 24992 Z= 0.193 Angle : 0.685 26.192 34163 Z= 0.300 Chirality : 0.041 0.153 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.758 117.090 3674 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.00 % Allowed : 19.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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 (0.15), residues: 2964 helix: 1.10 (0.13), residues: 1653 sheet: -2.64 (0.57), residues: 50 loop : 0.12 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 84 TYR 0.018 0.002 TYR J 221 PHE 0.018 0.002 PHE I 95 TRP 0.016 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (24949) covalent geometry : angle 0.64946 / 0.30 (34152) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 0.31639 / 0.17 ( 2) hydrogen bonds : bond 0.04819 / 3.11 ( 1264) hydrogen bonds : angle 4.92919 / 3.55 ( 3639) metal coordination : bond 0.01814 / 1.02 ( 9) metal coordination : angle 13.39407 / 9.75 ( 9) Misc. bond : bond 0.16879 / 11.30 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 393 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7472 (t80) cc_final: 0.7131 (t80) REVERT: E 371 TYR cc_start: 0.8360 (m-80) cc_final: 0.7899 (m-80) REVERT: E 412 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8082 (ttm170) REVERT: E 426 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: J 255 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7205 (t80) REVERT: Z 12 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8085 (ttm-80) REVERT: D 308 MET cc_start: 0.8550 (tpp) cc_final: 0.8316 (tpt) REVERT: M 231 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: N 91 ASP cc_start: 0.8768 (m-30) cc_final: 0.8477 (m-30) REVERT: O 30 GLU cc_start: 0.8042 (tp30) cc_final: 0.7535 (tt0) REVERT: F 185 MET cc_start: 0.8728 (tpp) cc_final: 0.8445 (tpp) REVERT: F 199 ILE cc_start: 0.8166 (mt) cc_final: 0.7950 (mp) REVERT: G 28 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7578 (ppp-140) REVERT: G 120 MET cc_start: 0.6165 (mpp) cc_final: 0.5866 (mpp) REVERT: G 124 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6982 (tm-30) REVERT: G 166 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7360 (ptp90) outliers start: 48 outliers final: 27 residues processed: 418 average time/residue: 1.1985 time to fit residues: 583.8265 Evaluate side-chains 413 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 380 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 96 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 293 optimal weight: 0.3980 chunk 245 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101343 restraints weight = 68895.088| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.19 r_work: 0.2634 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.398 24992 Z= 0.140 Angle : 0.641 24.483 34163 Z= 0.282 Chirality : 0.040 0.161 3585 Planarity : 0.004 0.054 4245 Dihedral : 10.129 123.417 3674 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.75 % Allowed : 19.04 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.94 (0.16), residues: 2964 helix: 1.20 (0.13), residues: 1656 sheet: -2.61 (0.58), residues: 50 loop : 0.13 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 253 TYR 0.029 0.001 TYR G 264 PHE 0.015 0.001 PHE I 255 TRP 0.013 0.001 TRP I 54 HIS 0.011 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (24949) covalent geometry : angle 0.60826 / 0.28 (34152) SS BOND : bond 0.00075 / 0.05 ( 1) SS BOND : angle 0.22561 / 0.16 ( 2) hydrogen bonds : bond 0.04435 / 2.87 ( 1264) hydrogen bonds : angle 4.83648 / 3.48 ( 3639) metal coordination : bond 0.01466 / 0.88 ( 9) metal coordination : angle 12.38851 / 8.72 ( 9) Misc. bond : bond 0.16270 / 10.91 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 405 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7362 (t80) cc_final: 0.7038 (t80) REVERT: E 371 TYR cc_start: 0.8297 (m-80) cc_final: 0.7799 (m-80) REVERT: E 412 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.8022 (ttm170) REVERT: E 436 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 193 ASP cc_start: 0.8011 (m-30) cc_final: 0.7713 (m-30) REVERT: J 255 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6850 (t80) REVERT: Z 12 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8111 (ttm-80) REVERT: D 308 MET cc_start: 0.8541 (tpp) cc_final: 0.8321 (tpt) REVERT: M 231 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: N 91 ASP cc_start: 0.8745 (m-30) cc_final: 0.8457 (m-30) REVERT: O 30 GLU cc_start: 0.8054 (tp30) cc_final: 0.7544 (tt0) REVERT: F 81 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: F 185 MET cc_start: 0.8708 (tpp) cc_final: 0.8419 (tpp) REVERT: G 28 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7627 (ppp-140) REVERT: G 120 MET cc_start: 0.6134 (mpp) cc_final: 0.5828 (mpp) REVERT: G 124 GLU cc_start: 0.7278 (tm-30) cc_final: 0.7035 (tm-30) REVERT: G 166 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7409 (ptp90) REVERT: G 240 GLU cc_start: 0.7687 (mp0) cc_final: 0.7433 (mp0) REVERT: G 282 GLN cc_start: 0.8224 (tp40) cc_final: 0.7933 (mm110) outliers start: 42 outliers final: 20 residues processed: 431 average time/residue: 1.1655 time to fit residues: 584.7020 Evaluate side-chains 421 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 394 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 285 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 278 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN Z 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.098835 restraints weight = 69443.119| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.19 r_work: 0.2590 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.448 24992 Z= 0.181 Angle : 0.668 24.336 34163 Z= 0.295 Chirality : 0.041 0.143 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.180 131.225 3673 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.79 % Allowed : 19.29 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.90 (0.15), residues: 2964 helix: 1.15 (0.13), residues: 1658 sheet: -2.59 (0.53), residues: 62 loop : 0.15 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 253 TYR 0.026 0.002 TYR G 264 PHE 0.018 0.002 PHE I 95 TRP 0.015 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (24949) covalent geometry : angle 0.63706 / 0.29 (34152) SS BOND : bond 0.00066 / 0.04 ( 1) SS BOND : angle 0.15939 / 0.11 ( 2) hydrogen bonds : bond 0.04692 / 3.03 ( 1264) hydrogen bonds : angle 4.85245 / 3.50 ( 3639) metal coordination : bond 0.01637 / 0.92 ( 9) metal coordination : angle 12.34958 / 8.83 ( 9) Misc. bond : bond 0.16876 / 11.37 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 444 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7488 (t80) cc_final: 0.7174 (t80) REVERT: E 371 TYR cc_start: 0.8405 (m-80) cc_final: 0.7923 (m-80) REVERT: E 412 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8014 (ttm170) REVERT: E 426 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8030 (mt-10) REVERT: E 436 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8330 (mt) REVERT: I 361 GLN cc_start: 0.8130 (mt0) cc_final: 0.7733 (pt0) REVERT: J 255 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7177 (t80) REVERT: Z 12 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (ttm-80) REVERT: Z 114 LYS cc_start: 0.8146 (mttt) cc_final: 0.7776 (ptpt) REVERT: D 308 MET cc_start: 0.8561 (tpp) cc_final: 0.8340 (tpt) REVERT: M 231 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: O 30 GLU cc_start: 0.8049 (tp30) cc_final: 0.7518 (tt0) REVERT: F 81 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: F 185 MET cc_start: 0.8686 (tpp) cc_final: 0.8391 (tpp) REVERT: G 28 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7775 (ppp-140) REVERT: G 120 MET cc_start: 0.6327 (mpp) cc_final: 0.6045 (mpp) REVERT: G 124 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7023 (tm-30) REVERT: G 166 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7488 (ptp90) REVERT: G 282 GLN cc_start: 0.8254 (tp40) cc_final: 0.7983 (mm110) outliers start: 43 outliers final: 24 residues processed: 424 average time/residue: 1.0271 time to fit residues: 506.5321 Evaluate side-chains 416 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 385 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 220 optimal weight: 0.0770 chunk 142 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Z 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101350 restraints weight = 69165.553| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.17 r_work: 0.2633 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.388 24992 Z= 0.140 Angle : 0.638 23.488 34163 Z= 0.283 Chirality : 0.040 0.143 3585 Planarity : 0.004 0.053 4245 Dihedral : 9.890 124.669 3673 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.50 % Allowed : 19.92 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.99 (0.16), residues: 2964 helix: 1.24 (0.13), residues: 1657 sheet: -2.64 (0.56), residues: 56 loop : 0.16 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 253 TYR 0.018 0.001 TYR D 388 PHE 0.016 0.001 PHE J 247 TRP 0.014 0.001 TRP I 54 HIS 0.008 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (24949) covalent geometry : angle 0.60874 / 0.28 (34152) SS BOND : bond 0.00095 / 0.06 ( 1) SS BOND : angle 0.25448 / 0.18 ( 2) hydrogen bonds : bond 0.04382 / 2.84 ( 1264) hydrogen bonds : angle 4.78415 / 3.45 ( 3639) metal coordination : bond 0.01414 / 0.84 ( 9) metal coordination : angle 11.84985 / 8.25 ( 9) Misc. bond : bond 0.16073 / 10.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 403 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7362 (t80) cc_final: 0.7058 (t80) REVERT: E 371 TYR cc_start: 0.8371 (m-80) cc_final: 0.7853 (m-80) REVERT: E 412 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7877 (ttm170) REVERT: E 426 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8052 (mt-10) REVERT: E 436 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8316 (mt) REVERT: C 193 ASP cc_start: 0.7992 (m-30) cc_final: 0.7713 (m-30) REVERT: I 361 GLN cc_start: 0.8067 (mt0) cc_final: 0.7777 (pt0) REVERT: J 255 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6996 (t80) REVERT: Z 12 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8091 (ttm-80) REVERT: Z 114 LYS cc_start: 0.8156 (mttt) cc_final: 0.7790 (ptpt) REVERT: D 308 MET cc_start: 0.8520 (tpp) cc_final: 0.8310 (tpt) REVERT: M 231 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: O 30 GLU cc_start: 0.8067 (tp30) cc_final: 0.7570 (tt0) REVERT: F 185 MET cc_start: 0.8649 (tpp) cc_final: 0.8345 (tpp) REVERT: G 28 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7781 (ppp-140) REVERT: G 120 MET cc_start: 0.6461 (mpp) cc_final: 0.6128 (mpp) REVERT: G 124 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7022 (tm-30) REVERT: G 240 GLU cc_start: 0.7619 (mp0) cc_final: 0.7321 (mp0) REVERT: G 282 GLN cc_start: 0.8196 (tp40) cc_final: 0.7950 (mm110) outliers start: 36 outliers final: 21 residues processed: 423 average time/residue: 1.1905 time to fit residues: 585.2410 Evaluate side-chains 413 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 387 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 81 optimal weight: 0.4980 chunk 272 optimal weight: 0.5980 chunk 288 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN Z 61 GLN G 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101044 restraints weight = 69057.283| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.19 r_work: 0.2635 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.375 24992 Z= 0.147 Angle : 0.645 23.110 34163 Z= 0.286 Chirality : 0.040 0.160 3585 Planarity : 0.004 0.053 4245 Dihedral : 9.798 122.457 3673 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.54 % Allowed : 20.00 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.02 (0.16), residues: 2964 helix: 1.27 (0.13), residues: 1660 sheet: -2.55 (0.55), residues: 62 loop : 0.18 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 253 TYR 0.017 0.001 TYR D 388 PHE 0.019 0.001 PHE J 247 TRP 0.014 0.001 TRP D 147 HIS 0.007 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (24949) covalent geometry : angle 0.61608 / 0.29 (34152) SS BOND : bond 0.00080 / 0.05 ( 1) SS BOND : angle 0.24117 / 0.17 ( 2) hydrogen bonds : bond 0.04404 / 2.85 ( 1264) hydrogen bonds : angle 4.74990 / 3.42 ( 3639) metal coordination : bond 0.01435 / 0.84 ( 9) metal coordination : angle 11.72489 / 8.14 ( 9) Misc. bond : bond 0.15368 / 10.24 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 437 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 400 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7429 (t80) cc_final: 0.7106 (t80) REVERT: E 371 TYR cc_start: 0.8444 (m-80) cc_final: 0.7977 (m-80) REVERT: E 412 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7935 (ttm170) REVERT: E 426 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8074 (mt-10) REVERT: E 436 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 66 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6417 (tm-30) REVERT: I 361 GLN cc_start: 0.8067 (mt0) cc_final: 0.7741 (pt0) REVERT: J 255 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.7038 (t80) REVERT: Z 114 LYS cc_start: 0.8164 (mttt) cc_final: 0.7858 (ptpt) REVERT: D 308 MET cc_start: 0.8540 (tpp) cc_final: 0.8332 (tpt) REVERT: M 231 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: N 91 ASP cc_start: 0.8767 (m-30) cc_final: 0.8476 (m-30) REVERT: O 30 GLU cc_start: 0.8065 (tp30) cc_final: 0.7541 (tt0) REVERT: F 185 MET cc_start: 0.8638 (tpp) cc_final: 0.8298 (tpp) REVERT: G 28 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7793 (ppp-140) REVERT: G 120 MET cc_start: 0.6522 (mpp) cc_final: 0.6229 (mpp) REVERT: G 124 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7100 (tm-30) REVERT: G 240 GLU cc_start: 0.7735 (mp0) cc_final: 0.7424 (mp0) REVERT: G 282 GLN cc_start: 0.8246 (tp40) cc_final: 0.8006 (mm110) outliers start: 37 outliers final: 23 residues processed: 421 average time/residue: 1.1007 time to fit residues: 538.2228 Evaluate side-chains 412 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 385 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 161 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 288 optimal weight: 0.0000 chunk 64 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Z 61 GLN G 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099159 restraints weight = 69011.185| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.09 r_work: 0.2594 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.465 24992 Z= 0.196 Angle : 0.684 23.640 34163 Z= 0.303 Chirality : 0.041 0.151 3585 Planarity : 0.004 0.054 4245 Dihedral : 9.967 120.148 3673 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 1.29 % Allowed : 20.08 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.93 (0.15), residues: 2964 helix: 1.17 (0.13), residues: 1656 sheet: -2.41 (0.56), residues: 62 loop : 0.17 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 169 TYR 0.018 0.002 TYR J 221 PHE 0.019 0.002 PHE I 95 TRP 0.015 0.001 TRP I 54 HIS 0.009 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (24949) covalent geometry : angle 0.65521 / 0.30 (34152) SS BOND : bond 0.00038 / 0.03 ( 1) SS BOND : angle 0.22433 / 0.13 ( 2) hydrogen bonds : bond 0.04747 / 3.07 ( 1264) hydrogen bonds : angle 4.82128 / 3.48 ( 3639) metal coordination : bond 0.01729 / 0.97 ( 9) metal coordination : angle 12.02516 / 8.50 ( 9) Misc. bond : bond 0.17150 / 11.49 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15619.09 seconds wall clock time: 264 minutes 40.73 seconds (15880.73 seconds total)