Starting phenix.real_space_refine on Wed Aug 27 00:56:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snh_40625/08_2025/8snh_40625_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snh_40625/08_2025/8snh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8snh_40625/08_2025/8snh_40625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snh_40625/08_2025/8snh_40625.map" model { file = "/net/cci-nas-00/data/ceres_data/8snh_40625/08_2025/8snh_40625_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snh_40625/08_2025/8snh_40625_trim.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 89 Unusual residues: {' CA': 2, ' CU': 1, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 8.75, per 1000 atoms: 0.20 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: 5.45 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.33 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: 11.16 Time building geometry restraints manager: 7.14 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: 78291 6.76 - 13.53: 36 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: 19508 24.23 - 48.47: 1357 48.47 - 72.70: 321 72.70 - 96.94: 66 96.94 - 121.17: 14 Dihedral angle restraints: 21266 sinusoidal: 11146 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 21263 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=" C1C HEC N 501 " -0.025 2.00e-02 2.50e+03 6.25e-02 8.80e+01 pdb=" C2C HEC N 501 " 0.171 2.00e-02 2.50e+03 pdb=" C3C HEC N 501 " -0.015 2.00e-02 2.50e+03 pdb=" C4C HEC N 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC N 501 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEC N 501 " -0.030 2.00e-02 2.50e+03 pdb=" CHD HEC N 501 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC N 501 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC N 501 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 501 " -0.018 2.00e-02 2.50e+03 5.67e-02 7.23e+01 pdb=" C2C HEC K 501 " 0.155 2.00e-02 2.50e+03 pdb=" C3C HEC K 501 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC K 501 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC K 501 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 501 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC K 501 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC K 501 " -0.046 2.00e-02 2.50e+03 pdb=" NC HEC K 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 301 " -0.013 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC F 301 " 0.083 2.00e-02 2.50e+03 pdb=" C3C HEC F 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4C HEC F 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC F 301 " -0.027 2.00e-02 2.50e+03 pdb=" CHC HEC F 301 " -0.017 2.00e-02 2.50e+03 pdb=" CHD HEC F 301 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC F 301 " -0.024 2.00e-02 2.50e+03 pdb=" NC HEC F 301 " -0.006 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 56.590 Find NCS groups from input model: 0.640 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:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.009 0.367 24992 Z= 0.404 Angle : 0.856 33.817 34163 Z= 0.376 Chirality : 0.057 1.412 3585 Planarity : 0.004 0.063 4245 Dihedral : 18.277 121.174 8908 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 aren 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 covalent geometry : bond 0.00737 (24949) covalent geometry : angle 0.82414 (34152) SS BOND : bond 0.00221 ( 1) SS BOND : angle 1.75570 ( 2) hydrogen bonds : bond 0.13986 ( 1264) hydrogen bonds : angle 6.65472 ( 3639) metal coordination : bond 0.01686 ( 9) metal coordination : angle 14.27911 ( 9) Misc. bond : bond 0.15578 ( 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 : 1.240 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: 1.3716 time to fit residues: 688.0970 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 : 1.343 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9980 chunk 111 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3625 r_free = 0.3625 target = 0.144230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101450 restraints weight = 69367.689| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.03 r_work: 0.2658 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.396 24992 Z= 0.163 Angle : 0.679 22.765 34163 Z= 0.306 Chirality : 0.041 0.190 3585 Planarity : 0.004 0.054 4245 Dihedral : 11.964 133.669 3690 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 2.17 % Allowed : 17.96 % Favored : 79.88 % 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 aren not related in a simple way. whole: 0.62 (0.15), residues: 2964 helix: 0.91 (0.13), residues: 1645 sheet: -2.52 (0.58), residues: 52 loop : 0.03 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 covalent geometry : bond 0.00361 (24949) covalent geometry : angle 0.65236 (34152) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.60548 ( 2) hydrogen bonds : bond 0.05064 ( 1264) hydrogen bonds : angle 5.44324 ( 3639) metal coordination : bond 0.01969 ( 9) metal coordination : angle 11.60058 ( 9) Misc. bond : bond 0.16194 ( 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 457 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 405 time to evaluate : 1.379 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: E 238 TYR cc_start: 0.6824 (t80) cc_final: 0.6571 (t80) REVERT: E 252 TYR cc_start: 0.6235 (OUTLIER) cc_final: 0.5923 (m-10) REVERT: E 279 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7448 (mp) REVERT: E 280 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7886 (tp) REVERT: E 410 MET cc_start: 0.8480 (mmm) cc_final: 0.8178 (mtt) REVERT: E 469 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7805 (pp) REVERT: K 23 ASP cc_start: 0.8358 (t0) cc_final: 0.8022 (t70) REVERT: D 3 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7860 (mppt) REVERT: D 308 MET cc_start: 0.8541 (tpp) cc_final: 0.8294 (tpt) REVERT: M 231 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: O 30 GLU cc_start: 0.8055 (tp30) cc_final: 0.7654 (tt0) REVERT: F 81 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: F 158 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: F 172 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8343 (mp) REVERT: F 185 MET cc_start: 0.8728 (tpp) cc_final: 0.8453 (tpp) REVERT: G 72 TYR cc_start: 0.4676 (OUTLIER) cc_final: 0.3376 (t80) REVERT: G 172 GLN cc_start: 0.7419 (tp-100) cc_final: 0.7205 (tp-100) outliers start: 52 outliers final: 20 residues processed: 437 average time/residue: 1.3456 time to fit residues: 681.5174 Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 380 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 212 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 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU 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 230 SER 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: 0.0370 chunk 30 optimal weight: 6.9990 chunk 190 optimal weight: 0.0870 chunk 138 optimal weight: 0.0060 chunk 253 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3640 r_free = 0.3640 target = 0.145396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103794 restraints weight = 69466.205| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.99 r_work: 0.2701 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.400 24992 Z= 0.127 Angle : 0.619 18.897 34163 Z= 0.278 Chirality : 0.040 0.178 3585 Planarity : 0.004 0.053 4245 Dihedral : 10.910 133.078 3678 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.17 % Allowed : 17.88 % Favored : 79.96 % 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 aren not related in a simple way. whole: 0.81 (0.16), residues: 2964 helix: 1.10 (0.13), residues: 1650 sheet: -2.67 (0.56), residues: 50 loop : 0.07 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 166 TYR 0.018 0.001 TYR D 388 PHE 0.018 0.001 PHE M 243 TRP 0.014 0.001 TRP E 204 HIS 0.006 0.001 HIS E 300 Details of bonding type rmsd covalent geometry : bond 0.00284 (24949) covalent geometry : angle 0.59761 (34152) SS BOND : bond 0.00313 ( 1) SS BOND : angle 0.12762 ( 2) hydrogen bonds : bond 0.04473 ( 1264) hydrogen bonds : angle 5.06285 ( 3639) metal coordination : bond 0.01217 ( 9) metal coordination : angle 9.90673 ( 9) Misc. bond : bond 0.14595 ( 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 470 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 418 time to evaluate : 1.161 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 261 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7856 (m-70) REVERT: E 410 MET cc_start: 0.8530 (mmm) cc_final: 0.8250 (mtt) REVERT: D 3 LYS cc_start: 0.8274 (mmtp) cc_final: 0.7817 (mppt) REVERT: D 308 MET cc_start: 0.8499 (tpp) cc_final: 0.8247 (tpt) REVERT: M 231 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: O 30 GLU cc_start: 0.8037 (tp30) cc_final: 0.7585 (tt0) REVERT: F 158 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: F 172 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8324 (mp) REVERT: F 185 MET cc_start: 0.8687 (tpp) cc_final: 0.8418 (tpp) REVERT: G 8 TYR cc_start: 0.6795 (t80) cc_final: 0.6486 (t80) REVERT: G 28 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7492 (ppp-140) REVERT: G 166 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7179 (ptp90) outliers start: 52 outliers final: 18 residues processed: 445 average time/residue: 1.3672 time to fit residues: 702.0947 Evaluate side-chains 415 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 391 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 287 ILE 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 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 158 GLU 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 166 ARG 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: 1.9990 chunk 217 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 152 optimal weight: 0.0670 chunk 280 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100909 restraints weight = 69469.004| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.18 r_work: 0.2626 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.413 24992 Z= 0.163 Angle : 0.667 27.789 34163 Z= 0.289 Chirality : 0.040 0.178 3585 Planarity : 0.004 0.054 4245 Dihedral : 10.850 130.212 3673 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 18.04 % Favored : 79.79 % 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 aren not related in a simple way. whole: 0.86 (0.15), residues: 2964 helix: 1.14 (0.13), residues: 1649 sheet: -2.66 (0.55), residues: 50 loop : 0.08 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 84 TYR 0.017 0.002 TYR J 240 PHE 0.016 0.001 PHE M 243 TRP 0.014 0.001 TRP E 204 HIS 0.009 0.001 HIS I 87 Details of bonding type rmsd covalent geometry : bond 0.00375 (24949) covalent geometry : angle 0.62862 (34152) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.36296 ( 2) hydrogen bonds : bond 0.04651 ( 1264) hydrogen bonds : angle 4.96465 ( 3639) metal coordination : bond 0.01568 ( 9) metal coordination : angle 13.68268 ( 9) Misc. bond : bond 0.15464 ( 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 457 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 405 time to evaluate : 1.184 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: 0.7166 (t80) cc_final: 0.6850 (t80) REVERT: E 261 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7949 (m-70) REVERT: E 410 MET cc_start: 0.8722 (mmm) cc_final: 0.8441 (mtt) REVERT: E 412 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.8007 (ttm170) REVERT: J 255 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6794 (t80) REVERT: D 3 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7813 (mppt) REVERT: D 308 MET cc_start: 0.8550 (tpp) cc_final: 0.8306 (tpt) REVERT: M 231 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: O 30 GLU cc_start: 0.8052 (tp30) cc_final: 0.7563 (tt0) REVERT: F 158 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: F 172 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8310 (mp) REVERT: F 185 MET cc_start: 0.8711 (tpp) cc_final: 0.8402 (tpp) REVERT: G 8 TYR cc_start: 0.7025 (t80) cc_final: 0.6809 (t80) REVERT: G 28 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7510 (ppp-140) REVERT: G 282 GLN cc_start: 0.8183 (tp40) cc_final: 0.7832 (mm110) outliers start: 52 outliers final: 25 residues processed: 432 average time/residue: 1.2403 time to fit residues: 619.4825 Evaluate side-chains 421 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 390 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 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 J residue 255 TYR 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 158 GLU 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 207 THR 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: 0.9980 chunk 284 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 183 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3628 r_free = 0.3628 target = 0.144336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.102610 restraints weight = 69336.820| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.02 r_work: 0.2660 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.387 24992 Z= 0.146 Angle : 0.644 25.534 34163 Z= 0.282 Chirality : 0.040 0.173 3585 Planarity : 0.004 0.054 4245 Dihedral : 10.596 125.683 3673 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.25 % Allowed : 18.21 % Favored : 79.54 % 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 aren not related in a simple way. whole: 0.92 (0.16), residues: 2964 helix: 1.20 (0.13), residues: 1647 sheet: -2.69 (0.56), residues: 50 loop : 0.11 (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 0.015 0.001 PHE M 243 TRP 0.013 0.001 TRP I 54 HIS 0.007 0.001 HIS I 87 Details of bonding type rmsd covalent geometry : bond 0.00338 (24949) covalent geometry : angle 0.61026 (34152) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.17833 ( 2) hydrogen bonds : bond 0.04498 ( 1264) hydrogen bonds : angle 4.89829 ( 3639) metal coordination : bond 0.01398 ( 9) metal coordination : angle 12.68583 ( 9) Misc. bond : bond 0.15491 ( 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 465 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 411 time to evaluate : 1.277 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: 0.7182 (t80) cc_final: 0.6848 (t80) REVERT: E 375 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8266 (ptmm) REVERT: E 410 MET cc_start: 0.8757 (mmm) cc_final: 0.8505 (mtt) REVERT: E 412 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7996 (ttm170) REVERT: C 193 ASP cc_start: 0.8050 (m-30) cc_final: 0.7723 (m-30) REVERT: J 255 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6679 (t80) REVERT: Z 12 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8091 (ttm-80) REVERT: D 3 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7806 (mppt) REVERT: D 308 MET cc_start: 0.8524 (tpp) cc_final: 0.8299 (tpt) REVERT: M 231 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: O 30 GLU cc_start: 0.8025 (tp30) cc_final: 0.7548 (tt0) REVERT: F 8 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7420 (mt-10) REVERT: F 81 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: F 134 GLU cc_start: 0.8856 (mp0) cc_final: 0.8620 (mp0) REVERT: F 172 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8317 (mp) REVERT: F 185 MET cc_start: 0.8703 (tpp) cc_final: 0.8442 (tpp) REVERT: G 28 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7514 (ppp-140) REVERT: G 282 GLN cc_start: 0.8168 (tp40) cc_final: 0.7838 (mm110) REVERT: G 288 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8255 (tmmm) outliers start: 54 outliers final: 21 residues processed: 440 average time/residue: 1.1173 time to fit residues: 569.6393 Evaluate side-chains 414 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 386 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 207 THR 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: 0.2980 chunk 51 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3616 r_free = 0.3616 target = 0.143355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.100814 restraints weight = 69613.429| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.13 r_work: 0.2635 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.409 24992 Z= 0.167 Angle : 0.662 24.316 34163 Z= 0.291 Chirality : 0.040 0.151 3585 Planarity : 0.004 0.054 4245 Dihedral : 10.429 118.120 3670 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.88 % Allowed : 18.75 % Favored : 79.38 % 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 aren not related in a simple way. whole: 0.92 (0.16), residues: 2964 helix: 1.16 (0.13), residues: 1657 sheet: -2.69 (0.56), residues: 50 loop : 0.17 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 253 TYR 0.016 0.002 TYR J 240 PHE 0.016 0.001 PHE I 95 TRP 0.014 0.001 TRP I 54 HIS 0.008 0.001 HIS I 87 Details of bonding type rmsd covalent geometry : bond 0.00387 (24949) covalent geometry : angle 0.63247 (34152) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.18940 ( 2) hydrogen bonds : bond 0.04605 ( 1264) hydrogen bonds : angle 4.87132 ( 3639) metal coordination : bond 0.01516 ( 9) metal coordination : angle 12.10725 ( 9) Misc. bond : bond 0.15959 ( 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 438 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 393 time to evaluate : 1.274 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: 0.7371 (t80) cc_final: 0.6975 (t80) REVERT: E 400 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8045 (mm) REVERT: E 410 MET cc_start: 0.8883 (mmm) cc_final: 0.8672 (mtt) REVERT: E 412 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8052 (ttm170) REVERT: J 255 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6981 (t80) REVERT: Z 12 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8081 (ttm-80) REVERT: D 308 MET cc_start: 0.8547 (tpp) cc_final: 0.8326 (tpt) REVERT: M 231 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: N 91 ASP cc_start: 0.8715 (m-30) cc_final: 0.8433 (m-30) REVERT: O 30 GLU cc_start: 0.8046 (tp30) cc_final: 0.7558 (tt0) REVERT: F 81 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: F 172 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8294 (mp) REVERT: F 185 MET cc_start: 0.8706 (tpp) cc_final: 0.8429 (tpp) REVERT: G 28 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7573 (ppp-140) REVERT: G 72 TYR cc_start: 0.4457 (t80) cc_final: 0.3960 (t80) REVERT: G 166 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7276 (ptp90) REVERT: G 282 GLN cc_start: 0.8197 (tp40) cc_final: 0.7977 (mm-40) outliers start: 45 outliers final: 23 residues processed: 420 average time/residue: 1.1669 time to fit residues: 569.7137 Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 378 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 400 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 195 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 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 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 96 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 293 optimal weight: 0.4980 chunk 245 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3614 r_free = 0.3614 target = 0.143140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100678 restraints weight = 69101.012| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.16 r_work: 0.2652 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.380 24992 Z= 0.138 Angle : 0.632 23.061 34163 Z= 0.280 Chirality : 0.040 0.162 3585 Planarity : 0.004 0.054 4245 Dihedral : 9.846 122.251 3670 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.58 % Allowed : 19.29 % Favored : 79.12 % 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 aren not related in a simple way. whole: 1.02 (0.16), residues: 2964 helix: 1.25 (0.13), residues: 1656 sheet: -2.58 (0.59), residues: 50 loop : 0.18 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 253 TYR 0.028 0.001 TYR G 264 PHE 0.015 0.001 PHE J 243 TRP 0.013 0.001 TRP D 147 HIS 0.011 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00320 (24949) covalent geometry : angle 0.60471 (34152) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.18860 ( 2) hydrogen bonds : bond 0.04372 ( 1264) hydrogen bonds : angle 4.79439 ( 3639) metal coordination : bond 0.01339 ( 9) metal coordination : angle 11.42398 ( 9) Misc. bond : bond 0.15333 ( 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 437 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 399 time to evaluate : 1.211 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 203 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8824 (tp-100) REVERT: E 238 TYR cc_start: 0.7332 (t80) cc_final: 0.6995 (t80) REVERT: E 412 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7955 (ttm170) REVERT: C 193 ASP cc_start: 0.8075 (m-30) cc_final: 0.7778 (m-30) REVERT: J 255 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6853 (t80) REVERT: Z 12 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8079 (ttm-80) REVERT: D 74 MET cc_start: 0.8933 (mmm) cc_final: 0.8720 (mmm) REVERT: D 308 MET cc_start: 0.8543 (tpp) cc_final: 0.8323 (tpt) REVERT: M 231 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: O 30 GLU cc_start: 0.8060 (tp30) cc_final: 0.7567 (tt0) REVERT: F 81 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: F 158 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: F 185 MET cc_start: 0.8691 (tpp) cc_final: 0.8402 (tpp) REVERT: G 28 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7557 (ppp-140) REVERT: G 166 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7287 (ptp90) REVERT: G 240 GLU cc_start: 0.7692 (mp0) cc_final: 0.7425 (mp0) REVERT: G 282 GLN cc_start: 0.8201 (tp40) cc_final: 0.7924 (mm110) outliers start: 38 outliers final: 17 residues processed: 421 average time/residue: 1.2313 time to fit residues: 599.1246 Evaluate side-chains 406 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 381 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 203 GLN 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 195 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 158 GLU 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 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: 0.6980 chunk 293 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Z 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099118 restraints weight = 69557.660| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.17 r_work: 0.2620 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.451 24992 Z= 0.186 Angle : 0.668 22.915 34163 Z= 0.296 Chirality : 0.041 0.142 3585 Planarity : 0.004 0.055 4245 Dihedral : 9.926 129.884 3669 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.58 % Allowed : 19.46 % Favored : 78.96 % 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 aren not related in a simple way. whole: 0.95 (0.16), residues: 2964 helix: 1.19 (0.13), residues: 1658 sheet: -2.56 (0.54), residues: 62 loop : 0.19 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 84 TYR 0.024 0.002 TYR G 264 PHE 0.018 0.002 PHE J 247 TRP 0.015 0.001 TRP I 54 HIS 0.010 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00429 (24949) covalent geometry : angle 0.64128 (34152) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.17423 ( 2) hydrogen bonds : bond 0.04696 ( 1264) hydrogen bonds : angle 4.83880 ( 3639) metal coordination : bond 0.01666 ( 9) metal coordination : angle 11.44341 ( 9) Misc. bond : bond 0.16440 ( 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 422 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 384 time to evaluate : 0.741 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: 0.7527 (t80) cc_final: 0.7197 (t80) REVERT: E 412 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: E 436 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8280 (mt) REVERT: E 462 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6957 (pt0) REVERT: I 361 GLN cc_start: 0.8164 (mt0) cc_final: 0.7863 (pt0) REVERT: J 255 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7122 (t80) REVERT: Z 114 LYS cc_start: 0.8153 (mttt) cc_final: 0.7806 (ptpt) REVERT: D 1 MET cc_start: 0.6112 (tpt) cc_final: 0.5900 (tpt) REVERT: D 308 MET cc_start: 0.8559 (tpp) cc_final: 0.8335 (tpt) REVERT: M 231 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: O 30 GLU cc_start: 0.8040 (tp30) cc_final: 0.7525 (tt0) REVERT: F 81 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: F 185 MET cc_start: 0.8660 (tpp) cc_final: 0.8368 (tpp) REVERT: G 28 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7654 (ppp-140) REVERT: G 166 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7422 (ptp90) REVERT: G 282 GLN cc_start: 0.8196 (tp40) cc_final: 0.7937 (mm110) outliers start: 38 outliers final: 19 residues processed: 410 average time/residue: 0.9332 time to fit residues: 443.4350 Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 383 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 425 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN 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 195 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 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 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 220 optimal weight: 0.1980 chunk 142 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 287 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3609 r_free = 0.3609 target = 0.142723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100283 restraints weight = 69358.217| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.17 r_work: 0.2648 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.394 24992 Z= 0.136 Angle : 0.627 22.136 34163 Z= 0.280 Chirality : 0.040 0.142 3585 Planarity : 0.004 0.053 4245 Dihedral : 9.659 124.567 3669 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 1.38 % Allowed : 19.75 % Favored : 78.88 % 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 aren not related in a simple way. whole: 1.06 (0.16), residues: 2964 helix: 1.29 (0.13), residues: 1659 sheet: -2.61 (0.57), residues: 56 loop : 0.22 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 253 TYR 0.017 0.001 TYR D 388 PHE 0.017 0.001 PHE J 243 TRP 0.016 0.001 TRP E 204 HIS 0.009 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00316 (24949) covalent geometry : angle 0.60064 (34152) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.26970 ( 2) hydrogen bonds : bond 0.04321 ( 1264) hydrogen bonds : angle 4.75466 ( 3639) metal coordination : bond 0.01313 ( 9) metal coordination : angle 11.04014 ( 9) Misc. bond : bond 0.15548 ( 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: 33 poor density : 406 time to evaluate : 0.702 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: 0.7464 (t80) cc_final: 0.7148 (t80) REVERT: E 412 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7932 (ttm170) REVERT: E 436 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8303 (mt) REVERT: C 193 ASP cc_start: 0.8081 (m-30) cc_final: 0.7795 (m-30) REVERT: I 361 GLN cc_start: 0.8042 (mt0) cc_final: 0.7760 (pt0) REVERT: J 255 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6835 (t80) REVERT: Z 114 LYS cc_start: 0.8142 (mttt) cc_final: 0.7804 (ptpt) REVERT: D 308 MET cc_start: 0.8535 (tpp) cc_final: 0.8304 (tpt) REVERT: M 231 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: O 30 GLU cc_start: 0.8044 (tp30) cc_final: 0.7541 (tt0) REVERT: F 8 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7441 (mt-10) REVERT: F 81 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: F 134 GLU cc_start: 0.8895 (mp0) cc_final: 0.8633 (mp0) REVERT: F 185 MET cc_start: 0.8650 (tpp) cc_final: 0.8345 (tpp) REVERT: G 28 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7562 (ppp-140) REVERT: G 240 GLU cc_start: 0.7654 (mp0) cc_final: 0.7351 (mp0) outliers start: 33 outliers final: 18 residues processed: 424 average time/residue: 0.8574 time to fit residues: 422.6487 Evaluate side-chains 407 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 384 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 MET 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 400 LEU Chi-restraints excluded: chain E residue 436 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 195 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 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 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 81 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 288 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3594 r_free = 0.3594 target = 0.141521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.098994 restraints weight = 69389.567| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.16 r_work: 0.2586 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.442 24992 Z= 0.174 Angle : 0.665 22.350 34163 Z= 0.297 Chirality : 0.041 0.153 3585 Planarity : 0.004 0.055 4245 Dihedral : 9.784 121.869 3669 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 1.33 % Allowed : 19.92 % Favored : 78.75 % 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 aren not related in a simple way. whole: 1.02 (0.16), residues: 2964 helix: 1.25 (0.13), residues: 1660 sheet: -2.49 (0.56), residues: 62 loop : 0.22 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 253 TYR 0.017 0.002 TYR J 240 PHE 0.020 0.002 PHE J 247 TRP 0.014 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00406 (24949) covalent geometry : angle 0.63984 (34152) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.22377 ( 2) hydrogen bonds : bond 0.04587 ( 1264) hydrogen bonds : angle 4.78106 ( 3639) metal coordination : bond 0.01491 ( 9) metal coordination : angle 11.27164 ( 9) Misc. bond : bond 0.16293 ( 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 419 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 387 time to evaluate : 0.756 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: 0.7555 (t80) cc_final: 0.7216 (t80) REVERT: E 412 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7966 (ttm170) REVERT: E 436 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8309 (mt) REVERT: I 361 GLN cc_start: 0.8108 (mt0) cc_final: 0.7795 (pt0) REVERT: J 255 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7140 (t80) REVERT: Z 114 LYS cc_start: 0.8138 (mttt) cc_final: 0.7844 (ptpt) REVERT: D 308 MET cc_start: 0.8558 (tpp) cc_final: 0.8353 (tpt) REVERT: M 231 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: O 30 GLU cc_start: 0.8043 (tp30) cc_final: 0.7433 (tt0) REVERT: F 81 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: F 185 MET cc_start: 0.8651 (tpp) cc_final: 0.8314 (tpp) REVERT: G 28 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7798 (ppp-140) REVERT: G 240 GLU cc_start: 0.7798 (mp0) cc_final: 0.7481 (mp0) outliers start: 32 outliers final: 20 residues processed: 402 average time/residue: 0.7825 time to fit residues: 366.2008 Evaluate side-chains 402 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 377 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 195 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 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 207 THR Chi-restraints excluded: chain G residue 279 MET 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: 3.9990 chunk 170 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 181 optimal weight: 0.3980 chunk 251 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100329 restraints weight = 69265.581| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.04 r_work: 0.2633 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.460 24992 Z= 0.186 Angle : 0.670 22.529 34163 Z= 0.300 Chirality : 0.041 0.163 3585 Planarity : 0.004 0.055 4245 Dihedral : 9.851 118.867 3669 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 1.25 % Allowed : 19.96 % Favored : 78.79 % 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 aren not related in a simple way. whole: 0.97 (0.16), residues: 2964 helix: 1.19 (0.13), residues: 1662 sheet: -2.42 (0.56), residues: 62 loop : 0.21 (0.18), residues: 1240 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 0.018 0.002 PHE I 95 TRP 0.015 0.001 TRP I 54 HIS 0.008 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00430 (24949) covalent geometry : angle 0.64405 (34152) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.20098 ( 2) hydrogen bonds : bond 0.04668 ( 1264) hydrogen bonds : angle 4.79945 ( 3639) metal coordination : bond 0.01727 ( 9) metal coordination : angle 11.36527 ( 9) Misc. bond : bond 0.16924 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15264.12 seconds wall clock time: 258 minutes 49.92 seconds (15529.92 seconds total)