Starting phenix.real_space_refine on Fri Aug 7 03:59:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vat_43102/08_2026/8vat_43102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vat_43102/08_2026/8vat_43102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2026/8vat_43102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2026/8vat_43102.map" model { file = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2026/8vat_43102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2026/8vat_43102.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 4 6.06 5 P 37 5.49 5 Mg 3 5.21 5 S 105 5.16 5 Be 3 3.05 5 C 12098 2.51 5 N 3467 2.21 5 O 3697 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19423 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2828 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2878 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 17, 'TRANS': 352} Chain: "D" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2828 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2865 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 347} Chain: "G" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain: "H" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 8, 'rna3p': 2} Chain: "I" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 402 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3238 SG CYS B 64 75.938 75.504 112.483 1.00 66.96 S ATOM 3298 SG CYS B 73 79.605 75.311 112.680 1.00 83.13 S ATOM 3315 SG CYS B 76 78.875 72.860 111.723 1.00 78.73 S ATOM 3337 SG CYS B 79 77.214 73.571 109.402 1.00 67.06 S ATOM 6066 SG CYS C 64 90.770 43.355 81.922 1.00 47.62 S ATOM 6143 SG CYS C 76 88.632 40.388 79.926 1.00 63.98 S ATOM 6165 SG CYS C 79 87.154 42.658 79.361 1.00 61.59 S ATOM 8944 SG CYS D 64 59.665 23.588 52.604 1.00 54.67 S ATOM 9004 SG CYS D 73 58.229 21.365 49.904 1.00 57.03 S ATOM 9021 SG CYS D 76 56.935 21.029 53.491 1.00 75.55 S ATOM 9043 SG CYS D 79 55.920 23.917 51.850 1.00 63.33 S ATOM 11667 SG CYS E 50 17.543 41.276 52.102 1.00 76.32 S ATOM 11736 SG CYS E 59 14.467 38.989 51.712 1.00 98.26 S ATOM 11756 SG CYS E 62 16.530 38.681 54.688 1.00 95.62 S ATOM 11777 SG CYS E 65 14.423 41.639 54.506 1.00 89.97 S Time building chain proxies: 3.90, per 1000 atoms: 0.20 Number of scatterers: 19423 At special positions: 0 Unit cell: (106.48, 122.32, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 4 29.99 S 105 16.00 P 37 15.00 Mg 3 11.99 F 9 9.00 O 3697 8.00 N 3467 7.00 C 12098 6.00 Be 3 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 764.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 79 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 76 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 64 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 73 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 18 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 13 sheets defined 55.3% alpha, 13.7% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.829A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.547A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.613A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 279 through 291 removed outlier: 3.646A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.954A pdb=" N VAL A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.850A pdb=" N ILE B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.738A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 removed outlier: 3.515A pdb=" N LEU B 131 " --> pdb=" O VAL B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.133A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.679A pdb=" N ARG B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.585A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.999A pdb=" N SER B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 3.678A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.976A pdb=" N MET B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'B' and resid 344 through 360 removed outlier: 4.124A pdb=" N HIS B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.804A pdb=" N ALA C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.580A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.345A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.522A pdb=" N LYS C 161 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 162 " --> pdb=" O PRO C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.538A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 3.851A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.577A pdb=" N MET C 306 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA C 308 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.514A pdb=" N ILE C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 51 through 63 Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.680A pdb=" N GLU D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 110 removed outlier: 4.010A pdb=" N ASN D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.527A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.509A pdb=" N VAL D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 306 through 320 removed outlier: 4.611A pdb=" N LEU D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.686A pdb=" N ALA D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.475A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E 12 " --> pdb=" O ARG E 8 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.859A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.716A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 207 Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 231 through 237 removed outlier: 4.109A pdb=" N ALA E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.603A pdb=" N VAL E 274 " --> pdb=" O VAL E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 324 removed outlier: 3.780A pdb=" N GLN E 324 " --> pdb=" O GLU E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.260A pdb=" N GLY F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 131 through 141 removed outlier: 3.501A pdb=" N MET F 135 " --> pdb=" O PRO F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 196 through 206 Processing helix chain 'F' and resid 243 through 248 removed outlier: 3.769A pdb=" N VAL F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 3.642A pdb=" N ILE F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 removed outlier: 3.560A pdb=" N VAL F 308 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 331 Processing helix chain 'G' and resid 131 through 141 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 260 through 273 removed outlier: 4.191A pdb=" N LEU G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 331 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 5.723A pdb=" N ILE A 2 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR A 138 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 20 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 137 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 22 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 5.784A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.526A pdb=" N ILE B 91 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP B 126 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 93 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.709A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.301A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.313A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.080A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 27 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 3 through 5 removed outlier: 4.757A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 111 through 112 removed outlier: 6.744A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN F 222 " --> pdb=" O GLY F 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 309 through 310 removed outlier: 3.608A pdb=" N GLN F 348 " --> pdb=" O MET F 339 " (cutoff:3.500A) removed outlier: 15.934A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 16.091A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.390A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.725A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 14.031A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 289 through 294 Processing sheet with id=AB3, first strand: chain 'G' and resid 126 through 130 Processing sheet with id=AB4, first strand: chain 'G' and resid 309 through 310 removed outlier: 4.518A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.067A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 13.981A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 13.074A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 12.874A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1019 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6397 1.34 - 1.46: 3216 1.46 - 1.58: 9968 1.58 - 1.70: 74 1.70 - 1.82: 176 Bond restraints: 19831 Sorted by residual: bond pdb=" F1 BEF D 403 " pdb="BE BEF D 403 " ideal model delta sigma weight residual 1.476 1.618 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" F1 BEF C 403 " pdb="BE BEF C 403 " ideal model delta sigma weight residual 1.476 1.589 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" O3B ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 1.510 1.611 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O3B ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sigma weight residual 1.510 1.597 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 19826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 26963 4.30 - 8.60: 79 8.60 - 12.89: 7 12.89 - 17.19: 1 17.19 - 21.49: 3 Bond angle restraints: 27053 Sorted by residual: angle pdb=" O2B ADP D 402 " pdb=" PB ADP D 402 " pdb=" O3B ADP D 402 " ideal model delta sigma weight residual 119.90 98.41 21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" O2B ADP B 402 " pdb=" PB ADP B 402 " pdb=" O3B ADP B 402 " ideal model delta sigma weight residual 119.90 99.59 20.31 3.00e+00 1.11e-01 4.58e+01 angle pdb=" O2B ADP C 402 " pdb=" PB ADP C 402 " pdb=" O3B ADP C 402 " ideal model delta sigma weight residual 119.90 101.81 18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " pdb=" F3 BEF C 403 " ideal model delta sigma weight residual 119.96 106.21 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N HIS G 175 " pdb=" CA HIS G 175 " pdb=" C HIS G 175 " ideal model delta sigma weight residual 114.56 109.26 5.30 1.27e+00 6.20e-01 1.74e+01 ... (remaining 27048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 10952 20.41 - 40.82: 827 40.82 - 61.23: 202 61.23 - 81.64: 59 81.64 - 102.05: 16 Dihedral angle restraints: 12056 sinusoidal: 5117 harmonic: 6939 Sorted by residual: dihedral pdb=" O1B ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " pdb=" PA ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 27.28 -87.28 1 2.00e+01 2.50e-03 2.29e+01 dihedral pdb=" O1B ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " pdb=" PA ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 26.96 -86.96 1 2.00e+01 2.50e-03 2.27e+01 dihedral pdb=" CA TYR C 41 " pdb=" C TYR C 41 " pdb=" N LEU C 42 " pdb=" CA LEU C 42 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 12053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2575 0.052 - 0.105: 465 0.105 - 0.157: 79 0.157 - 0.210: 5 0.210 - 0.262: 2 Chirality restraints: 3126 Sorted by residual: chirality pdb=" C2' ADP D 402 " pdb=" C1' ADP D 402 " pdb=" C3' ADP D 402 " pdb=" O2' ADP D 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' ADP B 402 " pdb=" C1' ADP B 402 " pdb=" C3' ADP B 402 " pdb=" O2' ADP B 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU F 42 " pdb=" CB LEU F 42 " pdb=" CD1 LEU F 42 " pdb=" CD2 LEU F 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3123 not shown) Planarity restraints: 3407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 360 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO D 361 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 361 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 361 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 41 " 0.032 2.00e-02 2.50e+03 1.71e-02 5.86e+00 pdb=" CG TYR C 41 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR C 41 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 41 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 41 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 41 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 41 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 41 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET G 182 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO G 183 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 183 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 183 " -0.032 5.00e-02 4.00e+02 ... (remaining 3404 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 37 2.35 - 2.99: 9821 2.99 - 3.62: 30142 3.62 - 4.26: 45434 4.26 - 4.90: 76095 Nonbonded interactions: 161529 Sorted by model distance: nonbonded pdb=" F1 BEF C 403 " pdb="MG MG C 404 " model vdw 1.709 2.120 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 404 " model vdw 1.818 2.170 nonbonded pdb=" O1B ADP C 402 " pdb="MG MG C 404 " model vdw 1.849 2.170 nonbonded pdb=" O1B ADP D 402 " pdb="MG MG D 404 " model vdw 1.955 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 404 " model vdw 1.992 2.170 ... (remaining 161524 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 'B' selection = (chain 'C' and (resid -2 through 361 or resid 401 through 404)) selection = chain 'D' } 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.720 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 0.659 19849 Z= 0.840 Angle : 0.827 37.496 27071 Z= 0.389 Chirality : 0.042 0.262 3126 Planarity : 0.004 0.065 3407 Dihedral : 16.280 102.046 7554 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2379 helix: 0.79 (0.15), residues: 1183 sheet: 0.03 (0.26), residues: 374 loop : -0.60 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 146 TYR 0.032 0.002 TYR C 41 PHE 0.021 0.002 PHE G 267 TRP 0.015 0.002 TRP C 10 HIS 0.006 0.001 HIS B 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.25 (19831) covalent geometry : angle 0.73494 / 0.38 (27053) hydrogen bonds : bond 0.13818 / 9.07 ( 1047) hydrogen bonds : angle 5.72762 / 4.05 ( 2975) metal coordination : bond 0.00914 / 0.57 ( 15) metal coordination : angle 14.73275 / 7.14 ( 18) Misc. bond : bond 0.65340 / 32.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7713 (tt0) cc_final: 0.7414 (tt0) REVERT: A 252 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6652 (mtm-85) REVERT: B 318 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7334 (ptt-90) REVERT: C 160 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7508 (pm20) REVERT: C 328 TYR cc_start: 0.8536 (m-80) cc_final: 0.8083 (m-80) REVERT: D 41 TYR cc_start: 0.8840 (m-80) cc_final: 0.8631 (m-80) REVERT: D 256 MET cc_start: 0.8336 (tmm) cc_final: 0.8092 (ttp) REVERT: D 285 MET cc_start: 0.7763 (mtt) cc_final: 0.7451 (mtt) REVERT: D 306 MET cc_start: 0.6824 (ptm) cc_final: 0.6571 (ptm) REVERT: E 91 ASP cc_start: 0.7715 (m-30) cc_final: 0.7429 (m-30) REVERT: E 175 TRP cc_start: 0.6366 (t-100) cc_final: 0.6135 (t-100) REVERT: E 280 HIS cc_start: 0.6874 (t70) cc_final: 0.6470 (m-70) REVERT: F 1 MET cc_start: 0.7231 (ptt) cc_final: 0.7023 (ptp) REVERT: F 73 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6984 (mmm160) REVERT: F 201 ILE cc_start: 0.8453 (mt) cc_final: 0.8047 (pt) REVERT: G 254 LYS cc_start: 0.7547 (mppt) cc_final: 0.7291 (mmtp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1439 time to fit residues: 78.4038 Evaluate side-chains 260 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN B 182 GLN C 360 HIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN E 287 GLN E 307 ASN F 186 GLN G 186 GLN G 226 HIS ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.191385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159410 restraints weight = 24097.419| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.75 r_work: 0.3684 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19849 Z= 0.153 Angle : 0.756 43.562 27071 Z= 0.332 Chirality : 0.042 0.212 3126 Planarity : 0.005 0.056 3407 Dihedral : 13.936 100.587 3033 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 1.05 % Allowed : 7.71 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2379 helix: 1.08 (0.15), residues: 1199 sheet: -0.05 (0.26), residues: 380 loop : -0.48 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.025 0.001 TYR C 41 PHE 0.013 0.001 PHE D 359 TRP 0.017 0.001 TRP C 10 HIS 0.009 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (19831) covalent geometry : angle 0.66305 / 0.33 (27053) hydrogen bonds : bond 0.04481 / 2.98 ( 1047) hydrogen bonds : angle 4.70369 / 3.36 ( 2975) metal coordination : bond 0.01999 / 1.07 ( 15) metal coordination : angle 14.08233 / 5.91 ( 18) Misc. bond : bond 0.00233 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 287 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TRP cc_start: 0.7094 (m100) cc_final: 0.6580 (m100) REVERT: A 71 MET cc_start: 0.7811 (ptp) cc_final: 0.7358 (ptp) REVERT: A 163 ASP cc_start: 0.5979 (p0) cc_final: 0.4959 (m-30) REVERT: A 194 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: A 239 GLU cc_start: 0.7904 (tt0) cc_final: 0.7678 (tt0) REVERT: A 252 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7261 (mtm-85) REVERT: C 160 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7409 (pm20) REVERT: C 192 ASN cc_start: 0.7201 (m110) cc_final: 0.6879 (m110) REVERT: D 41 TYR cc_start: 0.8941 (m-80) cc_final: 0.8695 (m-80) REVERT: D 204 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: E 91 ASP cc_start: 0.7821 (m-30) cc_final: 0.7550 (m-30) REVERT: E 208 ASP cc_start: 0.7541 (p0) cc_final: 0.7245 (p0) REVERT: F 1 MET cc_start: 0.7435 (ptt) cc_final: 0.7128 (ptp) REVERT: F 73 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7291 (mmm160) REVERT: F 201 ILE cc_start: 0.8470 (mt) cc_final: 0.7985 (pt) REVERT: G 254 LYS cc_start: 0.7680 (mppt) cc_final: 0.7355 (mmtp) REVERT: G 344 VAL cc_start: 0.9027 (t) cc_final: 0.8814 (p) outliers start: 21 outliers final: 11 residues processed: 301 average time/residue: 0.1374 time to fit residues: 61.3366 Evaluate side-chains 271 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 258 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 98 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN B 110 ASN C 192 ASN C 235 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 307 ASN G 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.192499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160464 restraints weight = 24428.166| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.79 r_work: 0.3692 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19849 Z= 0.138 Angle : 0.691 31.860 27071 Z= 0.308 Chirality : 0.040 0.209 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.751 102.693 3033 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 1.65 % Allowed : 10.66 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2379 helix: 1.20 (0.15), residues: 1208 sheet: -0.06 (0.27), residues: 374 loop : -0.42 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 215 TYR 0.021 0.001 TYR C 41 PHE 0.013 0.001 PHE D 359 TRP 0.016 0.001 TRP C 10 HIS 0.005 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19831) covalent geometry : angle 0.62063 / 0.30 (27053) hydrogen bonds : bond 0.03839 / 2.53 ( 1047) hydrogen bonds : angle 4.43036 / 3.17 ( 2975) metal coordination : bond 0.01498 / 0.77 ( 15) metal coordination : angle 11.80702 / 5.39 ( 18) Misc. bond : bond 0.00370 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7610 (mmt180) REVERT: A 163 ASP cc_start: 0.6032 (p0) cc_final: 0.5035 (m-30) REVERT: A 223 MET cc_start: 0.8214 (mpp) cc_final: 0.7829 (mpp) REVERT: A 239 GLU cc_start: 0.7881 (tt0) cc_final: 0.7605 (tt0) REVERT: A 252 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7336 (mtm-85) REVERT: C 160 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7382 (pm20) REVERT: C 192 ASN cc_start: 0.6946 (m-40) cc_final: 0.6719 (m110) REVERT: D 13 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7811 (mm-40) REVERT: D 41 TYR cc_start: 0.8945 (m-80) cc_final: 0.8728 (m-80) REVERT: D 86 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7777 (ttp-110) REVERT: E 91 ASP cc_start: 0.7819 (m-30) cc_final: 0.7551 (m-30) REVERT: E 307 ASN cc_start: 0.8658 (t160) cc_final: 0.8297 (t0) REVERT: F 1 MET cc_start: 0.7630 (ptt) cc_final: 0.7412 (ptp) REVERT: F 201 ILE cc_start: 0.8469 (mt) cc_final: 0.7976 (pt) REVERT: F 315 MET cc_start: 0.4114 (ppp) cc_final: 0.3907 (ppp) REVERT: F 319 PHE cc_start: 0.6663 (m-10) cc_final: 0.6426 (m-10) outliers start: 33 outliers final: 20 residues processed: 310 average time/residue: 0.1325 time to fit residues: 61.5404 Evaluate side-chains 285 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 4 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 152 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN B 110 ASN C 235 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 226 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156571 restraints weight = 24271.570| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.79 r_work: 0.3644 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19849 Z= 0.183 Angle : 0.712 27.254 27071 Z= 0.319 Chirality : 0.042 0.214 3126 Planarity : 0.004 0.052 3407 Dihedral : 13.740 102.012 3033 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 12.66 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2379 helix: 1.17 (0.15), residues: 1203 sheet: -0.31 (0.26), residues: 393 loop : -0.44 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.021 0.002 TYR C 41 PHE 0.012 0.001 PHE F 128 TRP 0.015 0.001 TRP C 10 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (19831) covalent geometry : angle 0.64915 / 0.31 (27053) hydrogen bonds : bond 0.03933 / 2.59 ( 1047) hydrogen bonds : angle 4.45159 / 3.19 ( 2975) metal coordination : bond 0.01048 / 0.61 ( 15) metal coordination : angle 11.33970 / 5.40 ( 18) Misc. bond : bond 0.00219 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6761 (mp10) REVERT: A 163 ASP cc_start: 0.6044 (p0) cc_final: 0.5098 (m-30) REVERT: A 194 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: A 223 MET cc_start: 0.8163 (mpp) cc_final: 0.7889 (mpp) REVERT: A 252 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7506 (ttm110) REVERT: C 65 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7276 (mt-10) REVERT: C 160 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7418 (pm20) REVERT: C 192 ASN cc_start: 0.6987 (m-40) cc_final: 0.6757 (m110) REVERT: D 22 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: D 41 TYR cc_start: 0.9008 (m-80) cc_final: 0.8774 (m-80) REVERT: D 241 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (tp) REVERT: E 91 ASP cc_start: 0.7896 (m-30) cc_final: 0.7630 (m-30) REVERT: F 1 MET cc_start: 0.7780 (ptt) cc_final: 0.7503 (ptp) REVERT: F 201 ILE cc_start: 0.8453 (mt) cc_final: 0.7955 (pt) REVERT: F 289 GLN cc_start: 0.7080 (mt0) cc_final: 0.6403 (tm-30) REVERT: F 315 MET cc_start: 0.4166 (ppp) cc_final: 0.3866 (ppp) REVERT: F 319 PHE cc_start: 0.6658 (m-10) cc_final: 0.6389 (m-10) REVERT: G 254 LYS cc_start: 0.7570 (mmtm) cc_final: 0.7217 (mmtp) outliers start: 48 outliers final: 31 residues processed: 305 average time/residue: 0.1484 time to fit residues: 68.2887 Evaluate side-chains 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 95 optimal weight: 0.8980 chunk 210 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 HIS A 78 GLN A 234 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.190759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158395 restraints weight = 24221.317| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.80 r_work: 0.3662 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19849 Z= 0.139 Angle : 0.661 24.519 27071 Z= 0.299 Chirality : 0.040 0.212 3126 Planarity : 0.004 0.052 3407 Dihedral : 13.617 102.123 3033 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 2.30 % Allowed : 13.96 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2379 helix: 1.28 (0.15), residues: 1211 sheet: -0.33 (0.26), residues: 391 loop : -0.41 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.017 0.001 TYR C 41 PHE 0.013 0.001 PHE F 128 TRP 0.016 0.001 TRP C 10 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (19831) covalent geometry : angle 0.60520 / 0.29 (27053) hydrogen bonds : bond 0.03551 / 2.33 ( 1047) hydrogen bonds : angle 4.32186 / 3.10 ( 2975) metal coordination : bond 0.00891 / 0.50 ( 15) metal coordination : angle 10.28282 / 4.95 ( 18) Misc. bond : bond 0.00113 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: A 194 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: A 252 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7378 (mtm-85) REVERT: C 41 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5389 (p90) REVERT: C 65 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7293 (mt-10) REVERT: C 160 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7413 (pm20) REVERT: C 192 ASN cc_start: 0.6911 (m-40) cc_final: 0.6681 (m110) REVERT: C 344 ASP cc_start: 0.7512 (t70) cc_final: 0.7250 (t70) REVERT: D 22 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: D 41 TYR cc_start: 0.8987 (m-80) cc_final: 0.8777 (m-80) REVERT: D 241 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7794 (tp) REVERT: E 280 HIS cc_start: 0.6963 (t70) cc_final: 0.6433 (m-70) REVERT: E 318 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7769 (ttp-110) REVERT: F 88 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7502 (mt) REVERT: F 201 ILE cc_start: 0.8423 (mt) cc_final: 0.7960 (pt) REVERT: F 289 GLN cc_start: 0.7177 (mt0) cc_final: 0.6434 (tm-30) REVERT: F 319 PHE cc_start: 0.6693 (m-10) cc_final: 0.6374 (m-10) REVERT: G 182 MET cc_start: 0.7573 (mmm) cc_final: 0.7231 (mmm) REVERT: G 254 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7252 (mmtm) outliers start: 46 outliers final: 29 residues processed: 314 average time/residue: 0.1488 time to fit residues: 69.8580 Evaluate side-chains 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 78 ASN C 235 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS F 222 ASN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.187459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155328 restraints weight = 24172.733| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.80 r_work: 0.3618 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19849 Z= 0.202 Angle : 0.721 24.011 27071 Z= 0.328 Chirality : 0.043 0.216 3126 Planarity : 0.005 0.052 3407 Dihedral : 13.648 99.437 3033 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 2.90 % Allowed : 14.71 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2379 helix: 1.15 (0.15), residues: 1200 sheet: -0.50 (0.26), residues: 401 loop : -0.42 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 146 TYR 0.022 0.002 TYR C 41 PHE 0.016 0.002 PHE D 15 TRP 0.016 0.002 TRP C 10 HIS 0.010 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (19831) covalent geometry : angle 0.66821 / 0.32 (27053) hydrogen bonds : bond 0.03963 / 2.60 ( 1047) hydrogen bonds : angle 4.41406 / 3.16 ( 2975) metal coordination : bond 0.00986 / 0.59 ( 15) metal coordination : angle 10.48325 / 5.12 ( 18) Misc. bond : bond 0.00085 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: A 163 ASP cc_start: 0.6073 (p0) cc_final: 0.4918 (m-30) REVERT: A 223 MET cc_start: 0.8331 (mpp) cc_final: 0.7993 (mpp) REVERT: A 252 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7380 (mtm-85) REVERT: C 41 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.5652 (p90) REVERT: C 65 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7318 (mt-10) REVERT: C 160 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7453 (pm20) REVERT: C 192 ASN cc_start: 0.6928 (m-40) cc_final: 0.6687 (m110) REVERT: D 22 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: D 41 TYR cc_start: 0.9038 (m-80) cc_final: 0.8806 (m-80) REVERT: D 241 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7841 (tp) REVERT: D 251 SER cc_start: 0.8708 (t) cc_final: 0.8308 (p) REVERT: E 91 ASP cc_start: 0.7917 (m-30) cc_final: 0.7657 (m-30) REVERT: E 280 HIS cc_start: 0.6992 (t70) cc_final: 0.6469 (m-70) REVERT: F 88 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (mt) REVERT: F 201 ILE cc_start: 0.8447 (mt) cc_final: 0.7968 (pt) REVERT: F 289 GLN cc_start: 0.7446 (mt0) cc_final: 0.6786 (tm-30) REVERT: G 182 MET cc_start: 0.7582 (mmm) cc_final: 0.7225 (mmm) REVERT: G 254 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7274 (mmtm) outliers start: 58 outliers final: 40 residues processed: 312 average time/residue: 0.1353 time to fit residues: 64.3499 Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 197 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 chunk 236 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 203 optimal weight: 30.0000 chunk 12 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 303 GLN B 110 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS G 143 GLN G 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159871 restraints weight = 24201.134| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.78 r_work: 0.3677 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19849 Z= 0.122 Angle : 0.652 22.867 27071 Z= 0.296 Chirality : 0.040 0.206 3126 Planarity : 0.004 0.052 3407 Dihedral : 13.484 100.151 3033 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 2.35 % Allowed : 15.37 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2379 helix: 1.38 (0.15), residues: 1212 sheet: -0.44 (0.26), residues: 401 loop : -0.33 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.015 0.001 TYR C 41 PHE 0.013 0.001 PHE F 128 TRP 0.017 0.001 TRP C 10 HIS 0.006 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19831) covalent geometry : angle 0.60189 / 0.29 (27053) hydrogen bonds : bond 0.03381 / 2.22 ( 1047) hydrogen bonds : angle 4.23752 / 3.03 ( 2975) metal coordination : bond 0.00784 / 0.44 ( 15) metal coordination : angle 9.70499 / 4.71 ( 18) Misc. bond : bond 0.00049 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: A 163 ASP cc_start: 0.5952 (p0) cc_final: 0.4832 (m-30) REVERT: A 223 MET cc_start: 0.8255 (mpp) cc_final: 0.7864 (mpp) REVERT: A 252 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7329 (mtm-85) REVERT: A 336 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6350 (mp) REVERT: C 41 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5410 (p90) REVERT: C 160 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7394 (pm20) REVERT: C 192 ASN cc_start: 0.6829 (m-40) cc_final: 0.6601 (m110) REVERT: D 41 TYR cc_start: 0.8996 (m-80) cc_final: 0.8795 (m-80) REVERT: E 280 HIS cc_start: 0.6950 (t70) cc_final: 0.6449 (m-70) REVERT: F 29 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7717 (mt) REVERT: F 88 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7509 (mt) REVERT: F 201 ILE cc_start: 0.8432 (mt) cc_final: 0.7964 (pt) REVERT: F 289 GLN cc_start: 0.7429 (mt0) cc_final: 0.6890 (tm-30) REVERT: G 182 MET cc_start: 0.7575 (mmm) cc_final: 0.7247 (mmm) REVERT: G 254 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7246 (mmtp) outliers start: 47 outliers final: 27 residues processed: 299 average time/residue: 0.1353 time to fit residues: 61.8586 Evaluate side-chains 290 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 221 optimal weight: 10.0000 chunk 191 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 212 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 188 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN C 235 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.190839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159490 restraints weight = 24157.323| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.78 r_work: 0.3668 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19849 Z= 0.133 Angle : 0.655 21.169 27071 Z= 0.298 Chirality : 0.040 0.193 3126 Planarity : 0.004 0.052 3407 Dihedral : 13.381 98.911 3033 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 2.25 % Allowed : 15.62 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2379 helix: 1.41 (0.15), residues: 1215 sheet: -0.39 (0.26), residues: 396 loop : -0.35 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.018 0.001 TYR E 163 PHE 0.013 0.001 PHE F 128 TRP 0.015 0.001 TRP C 10 HIS 0.009 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (19831) covalent geometry : angle 0.60768 / 0.29 (27053) hydrogen bonds : bond 0.03376 / 2.22 ( 1047) hydrogen bonds : angle 4.19658 / 3.00 ( 2975) metal coordination : bond 0.00748 / 0.44 ( 15) metal coordination : angle 9.44817 / 4.65 ( 18) Misc. bond : bond 0.00023 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 45 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6657 (mp10) REVERT: A 223 MET cc_start: 0.8237 (mpp) cc_final: 0.7849 (mpp) REVERT: A 252 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7502 (mtp85) REVERT: C 41 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5427 (p90) REVERT: C 160 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7415 (pm20) REVERT: C 192 ASN cc_start: 0.6783 (m-40) cc_final: 0.6581 (m110) REVERT: D 22 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: D 41 TYR cc_start: 0.8998 (m-80) cc_final: 0.8777 (m-80) REVERT: E 88 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (tt) REVERT: E 280 HIS cc_start: 0.6955 (t70) cc_final: 0.6482 (m-70) REVERT: F 51 MET cc_start: 0.8526 (mtp) cc_final: 0.8318 (mtm) REVERT: F 88 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7485 (mt) REVERT: F 201 ILE cc_start: 0.8455 (mt) cc_final: 0.7988 (pt) REVERT: F 289 GLN cc_start: 0.7494 (mt0) cc_final: 0.6986 (tm-30) REVERT: G 175 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.7228 (m-70) REVERT: G 182 MET cc_start: 0.7558 (mmm) cc_final: 0.7252 (mmm) REVERT: G 254 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7270 (mmtm) outliers start: 45 outliers final: 31 residues processed: 293 average time/residue: 0.1344 time to fit residues: 60.1047 Evaluate side-chains 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS F 348 GLN G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.190714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160093 restraints weight = 23842.210| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.71 r_work: 0.3681 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19849 Z= 0.129 Angle : 0.651 20.607 27071 Z= 0.296 Chirality : 0.040 0.190 3126 Planarity : 0.004 0.055 3407 Dihedral : 13.340 98.070 3033 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 2.15 % Allowed : 16.17 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2379 helix: 1.45 (0.15), residues: 1216 sheet: -0.37 (0.27), residues: 395 loop : -0.32 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 149 TYR 0.016 0.001 TYR C 41 PHE 0.013 0.001 PHE F 128 TRP 0.015 0.001 TRP C 10 HIS 0.011 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19831) covalent geometry : angle 0.60695 / 0.29 (27053) hydrogen bonds : bond 0.03307 / 2.17 ( 1047) hydrogen bonds : angle 4.16080 / 2.98 ( 2975) metal coordination : bond 0.00709 / 0.41 ( 15) metal coordination : angle 9.15393 / 4.52 ( 18) Misc. bond : bond 0.00030 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 45 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: A 96 GLN cc_start: 0.7449 (pt0) cc_final: 0.7062 (pt0) REVERT: A 223 MET cc_start: 0.8188 (mpp) cc_final: 0.7865 (mpp) REVERT: A 252 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7307 (mtm-85) REVERT: C 41 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5363 (p90) REVERT: C 160 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7417 (pm20) REVERT: D 41 TYR cc_start: 0.8962 (m-80) cc_final: 0.8744 (m-80) REVERT: E 88 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8360 (tt) REVERT: E 280 HIS cc_start: 0.6985 (t70) cc_final: 0.6476 (m-70) REVERT: F 29 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7827 (mt) REVERT: F 51 MET cc_start: 0.8522 (mtp) cc_final: 0.8311 (mtm) REVERT: F 88 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7432 (mt) REVERT: F 201 ILE cc_start: 0.8463 (mt) cc_final: 0.7995 (pt) REVERT: F 289 GLN cc_start: 0.7652 (mt0) cc_final: 0.7094 (tm-30) REVERT: G 182 MET cc_start: 0.7624 (mmm) cc_final: 0.7344 (mmm) REVERT: G 254 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7310 (mmtp) outliers start: 43 outliers final: 32 residues processed: 294 average time/residue: 0.1282 time to fit residues: 57.8405 Evaluate side-chains 291 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN C 235 GLN C 360 HIS ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159382 restraints weight = 23873.710| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.70 r_work: 0.3670 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19849 Z= 0.141 Angle : 0.667 20.444 27071 Z= 0.303 Chirality : 0.040 0.210 3126 Planarity : 0.004 0.052 3407 Dihedral : 13.333 96.632 3033 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 2.20 % Allowed : 16.57 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2379 helix: 1.41 (0.15), residues: 1216 sheet: -0.22 (0.27), residues: 381 loop : -0.40 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 149 TYR 0.018 0.001 TYR F 284 PHE 0.013 0.001 PHE F 128 TRP 0.015 0.001 TRP C 10 HIS 0.011 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (19831) covalent geometry : angle 0.62421 / 0.30 (27053) hydrogen bonds : bond 0.03403 / 2.23 ( 1047) hydrogen bonds : angle 4.18894 / 2.99 ( 2975) metal coordination : bond 0.00717 / 0.43 ( 15) metal coordination : angle 9.13173 / 4.51 ( 18) Misc. bond : bond 0.00036 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 45 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6676 (mp10) REVERT: A 96 GLN cc_start: 0.7446 (pt0) cc_final: 0.7073 (pt0) REVERT: A 163 ASP cc_start: 0.5943 (p0) cc_final: 0.4910 (m-30) REVERT: A 223 MET cc_start: 0.8182 (mpp) cc_final: 0.7870 (mpp) REVERT: A 252 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7444 (mtp85) REVERT: C 41 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5498 (p90) REVERT: C 160 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7425 (pm20) REVERT: D 41 TYR cc_start: 0.8997 (m-80) cc_final: 0.8766 (m-80) REVERT: E 88 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8371 (tt) REVERT: E 280 HIS cc_start: 0.6962 (t70) cc_final: 0.6463 (m-70) REVERT: F 29 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7873 (mp) REVERT: F 51 MET cc_start: 0.8501 (mtp) cc_final: 0.8290 (mtm) REVERT: F 88 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7466 (mt) REVERT: F 201 ILE cc_start: 0.8436 (mt) cc_final: 0.7970 (pt) REVERT: F 289 GLN cc_start: 0.7776 (mt0) cc_final: 0.7248 (tm-30) REVERT: G 182 MET cc_start: 0.7629 (mmm) cc_final: 0.7341 (mmm) REVERT: G 254 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7322 (mmtp) outliers start: 44 outliers final: 33 residues processed: 299 average time/residue: 0.1322 time to fit residues: 59.8775 Evaluate side-chains 295 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 132 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 143 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.191172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160641 restraints weight = 23917.850| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.72 r_work: 0.3688 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19849 Z= 0.125 Angle : 0.667 20.033 27071 Z= 0.304 Chirality : 0.040 0.210 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.278 96.055 3033 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer: Outliers : 2.05 % Allowed : 17.02 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 2379 helix: 1.47 (0.15), residues: 1217 sheet: -0.18 (0.27), residues: 381 loop : -0.34 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 149 TYR 0.015 0.001 TYR C 41 PHE 0.013 0.001 PHE F 128 TRP 0.012 0.001 TRP C 10 HIS 0.011 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (19831) covalent geometry : angle 0.62680 / 0.30 (27053) hydrogen bonds : bond 0.03298 / 2.16 ( 1047) hydrogen bonds : angle 4.14533 / 2.96 ( 2975) metal coordination : bond 0.00654 / 0.38 ( 15) metal coordination : angle 8.89315 / 4.39 ( 18) Misc. bond : bond 0.00029 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4918.48 seconds wall clock time: 84 minutes 48.05 seconds (5088.05 seconds total)