Starting phenix.real_space_refine on Sun Aug 24 10:58:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vat_43102/08_2025/8vat_43102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vat_43102/08_2025/8vat_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2025/8vat_43102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2025/8vat_43102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2025/8vat_43102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vat_43102/08_2025/8vat_43102.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.90, per 1000 atoms: 0.25 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: 2.12 Conformation dependent library (CDL) restraints added in 886.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.58 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: 4.07 Time building geometry restraints manager: 2.69 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: 2592 0.052 - 0.105: 463 0.105 - 0.157: 64 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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= 0.831 Angle : 0.816 37.496 27071 Z= 0.345 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00480 (19831) covalent geometry : angle 0.72277 (27053) hydrogen bonds : bond 0.13818 ( 1047) hydrogen bonds : angle 5.72762 ( 2975) metal coordination : bond 0.00914 ( 15) metal coordination : angle 14.73275 ( 18) Misc. bond : bond 0.65340 ( 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 : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7713 (tt0) cc_final: 0.7413 (tt0) REVERT: A 252 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6685 (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: 0.1623 time to fit residues: 87.2668 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 : 0.571 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 182 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN E 209 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.192346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160113 restraints weight = 24391.874| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.86 r_work: 0.3684 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19849 Z= 0.151 Angle : 0.733 37.123 27071 Z= 0.323 Chirality : 0.040 0.208 3126 Planarity : 0.005 0.052 3407 Dihedral : 13.865 104.175 3033 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 1.35 % Allowed : 7.91 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2379 helix: 1.09 (0.15), residues: 1205 sheet: -0.03 (0.27), residues: 379 loop : -0.45 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.025 0.001 TYR C 41 PHE 0.014 0.001 PHE D 359 TRP 0.016 0.001 TRP C 10 HIS 0.008 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00339 (19831) covalent geometry : angle 0.64778 (27053) hydrogen bonds : bond 0.04170 ( 1047) hydrogen bonds : angle 4.59755 ( 2975) metal coordination : bond 0.02056 ( 15) metal coordination : angle 13.33096 ( 18) Misc. bond : bond 0.00315 ( 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 311 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7682 (ptp) cc_final: 0.7197 (ptp) REVERT: A 163 ASP cc_start: 0.5763 (p0) cc_final: 0.4964 (m-30) REVERT: A 223 MET cc_start: 0.7985 (mpp) cc_final: 0.7770 (mpp) REVERT: A 239 GLU cc_start: 0.7694 (tt0) cc_final: 0.7466 (tt0) REVERT: A 252 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7091 (mtm-85) REVERT: C 160 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7381 (pm20) REVERT: C 192 ASN cc_start: 0.7173 (m110) cc_final: 0.6831 (m110) REVERT: D 41 TYR cc_start: 0.8928 (m-80) cc_final: 0.8723 (m-80) REVERT: D 306 MET cc_start: 0.6813 (ptm) cc_final: 0.6584 (ptm) REVERT: E 91 ASP cc_start: 0.7577 (m-30) cc_final: 0.7294 (m-30) REVERT: E 208 ASP cc_start: 0.7533 (p0) cc_final: 0.7279 (p0) REVERT: F 1 MET cc_start: 0.7417 (ptt) cc_final: 0.7169 (ptp) REVERT: F 201 ILE cc_start: 0.8379 (mt) cc_final: 0.7891 (pt) REVERT: F 284 TYR cc_start: 0.7227 (t80) cc_final: 0.7017 (t80) REVERT: G 254 LYS cc_start: 0.7581 (mppt) cc_final: 0.7265 (mmtp) REVERT: G 344 VAL cc_start: 0.8986 (t) cc_final: 0.8785 (p) outliers start: 27 outliers final: 13 residues processed: 301 average time/residue: 0.1515 time to fit residues: 66.7444 Evaluate side-chains 269 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 256 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 GLN 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 C residue 288 LEU Chi-restraints excluded: chain D residue 77 ASP 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 F residue 309 THR 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: 0.7980 chunk 134 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 200 optimal weight: 0.0770 chunk 174 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 110 ASN C 192 ASN D 39 HIS 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 = 0.4197 r_free = 0.4197 target = 0.194103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.162296 restraints weight = 24456.159| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.79 r_work: 0.3708 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19849 Z= 0.124 Angle : 0.655 29.877 27071 Z= 0.292 Chirality : 0.039 0.196 3126 Planarity : 0.004 0.049 3407 Dihedral : 13.611 106.607 3033 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 1.45 % Allowed : 11.11 % Favored : 87.44 % 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 aren not related in a simple way. whole: 0.76 (0.18), residues: 2379 helix: 1.35 (0.15), residues: 1211 sheet: -0.15 (0.26), residues: 387 loop : -0.36 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.030 0.001 TYR F 310 PHE 0.014 0.001 PHE D 359 TRP 0.015 0.001 TRP C 10 HIS 0.004 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00267 (19831) covalent geometry : angle 0.58686 (27053) hydrogen bonds : bond 0.03474 ( 1047) hydrogen bonds : angle 4.28155 ( 2975) metal coordination : bond 0.01365 ( 15) metal coordination : angle 11.25901 ( 18) Misc. bond : bond 0.00096 ( 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 336 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 307 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7957 (mp) cc_final: 0.7694 (mp) REVERT: A 39 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7554 (mmt180) REVERT: A 163 ASP cc_start: 0.6070 (p0) cc_final: 0.5081 (m-30) REVERT: A 234 GLN cc_start: 0.7875 (tm130) cc_final: 0.7600 (tm-30) REVERT: A 252 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7262 (mtm-85) REVERT: C 160 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7380 (pm20) REVERT: C 192 ASN cc_start: 0.6926 (m-40) cc_final: 0.6711 (m110) REVERT: D 13 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7805 (mm-40) REVERT: D 41 TYR cc_start: 0.8946 (m-80) cc_final: 0.8709 (m-80) REVERT: D 306 MET cc_start: 0.6927 (ptm) cc_final: 0.6720 (ptm) REVERT: E 254 ASP cc_start: 0.7617 (m-30) cc_final: 0.7183 (m-30) REVERT: E 280 HIS cc_start: 0.7002 (t70) cc_final: 0.6416 (m-70) REVERT: E 307 ASN cc_start: 0.8634 (t160) cc_final: 0.8274 (t0) REVERT: F 1 MET cc_start: 0.7705 (ptt) cc_final: 0.7469 (ptp) REVERT: F 201 ILE cc_start: 0.8440 (mt) cc_final: 0.7951 (pt) REVERT: F 289 GLN cc_start: 0.6963 (mt0) cc_final: 0.6322 (tm-30) REVERT: F 315 MET cc_start: 0.4164 (ppp) cc_final: 0.3964 (ppp) REVERT: F 319 PHE cc_start: 0.6598 (m-10) cc_final: 0.6356 (m-10) REVERT: G 182 MET cc_start: 0.7551 (mmt) cc_final: 0.7347 (mmt) outliers start: 29 outliers final: 17 residues processed: 325 average time/residue: 0.1550 time to fit residues: 74.6194 Evaluate side-chains 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 71 THR 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 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 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: 6.9990 chunk 192 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 78 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 235 GLN G 217 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 = 0.4142 r_free = 0.4142 target = 0.188320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155432 restraints weight = 24286.193| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.78 r_work: 0.3629 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19849 Z= 0.197 Angle : 0.723 26.489 27071 Z= 0.324 Chirality : 0.042 0.219 3126 Planarity : 0.005 0.051 3407 Dihedral : 13.655 103.931 3033 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 2.40 % Allowed : 14.01 % Favored : 83.58 % 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 aren not related in a simple way. whole: 0.60 (0.18), residues: 2379 helix: 1.21 (0.15), residues: 1204 sheet: -0.17 (0.27), residues: 386 loop : -0.43 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 80 TYR 0.021 0.002 TYR F 310 PHE 0.012 0.002 PHE G 128 TRP 0.015 0.002 TRP C 10 HIS 0.010 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00468 (19831) covalent geometry : angle 0.66399 (27053) hydrogen bonds : bond 0.03923 ( 1047) hydrogen bonds : angle 4.41190 ( 2975) metal coordination : bond 0.01079 ( 15) metal coordination : angle 11.08934 ( 18) Misc. bond : bond 0.00075 ( 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 332 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: A 194 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: A 223 MET cc_start: 0.8305 (mpp) cc_final: 0.7915 (mpp) REVERT: A 252 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7370 (mtm-85) REVERT: C 41 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5631 (p90) REVERT: C 65 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7282 (mt-10) REVERT: C 160 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7458 (pm20) REVERT: C 192 ASN cc_start: 0.6903 (m-40) cc_final: 0.6686 (m110) REVERT: D 22 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: D 41 TYR cc_start: 0.9039 (m-80) cc_final: 0.8782 (m-80) REVERT: D 204 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: E 91 ASP cc_start: 0.7884 (m-30) cc_final: 0.7602 (m-30) REVERT: E 292 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7582 (t0) REVERT: F 1 MET cc_start: 0.7820 (ptt) cc_final: 0.7579 (ptp) REVERT: F 88 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7631 (mt) REVERT: F 201 ILE cc_start: 0.8425 (mt) cc_final: 0.7951 (pt) REVERT: F 289 GLN cc_start: 0.6997 (mt0) cc_final: 0.6369 (tm-30) REVERT: F 315 MET cc_start: 0.4063 (ppp) cc_final: 0.3728 (ppp) REVERT: F 319 PHE cc_start: 0.6688 (m-10) cc_final: 0.6484 (m-10) outliers start: 48 outliers final: 28 residues processed: 317 average time/residue: 0.1449 time to fit residues: 68.1397 Evaluate side-chains 299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 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 227 SER 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 171 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 229 ASP 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 292 ASP Chi-restraints excluded: chain E residue 296 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 222 ASN Chi-restraints excluded: chain G residue 247 VAL 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: 1.9990 chunk 210 optimal weight: 0.0040 chunk 3 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 149 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 143 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 303 GLN B 110 ASN C 235 GLN C 360 HIS F 222 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 = 0.4190 r_free = 0.4190 target = 0.193442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.162498 restraints weight = 24199.077| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.81 r_work: 0.3705 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19849 Z= 0.112 Angle : 0.627 22.614 27071 Z= 0.286 Chirality : 0.038 0.194 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.369 105.226 3033 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 1.60 % Allowed : 15.67 % Favored : 82.73 % 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 aren not related in a simple way. whole: 0.88 (0.18), residues: 2379 helix: 1.49 (0.15), residues: 1209 sheet: -0.21 (0.26), residues: 394 loop : -0.30 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.018 0.001 TYR F 284 PHE 0.014 0.001 PHE F 128 TRP 0.013 0.001 TRP C 10 HIS 0.006 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00245 (19831) covalent geometry : angle 0.57790 (27053) hydrogen bonds : bond 0.03208 ( 1047) hydrogen bonds : angle 4.16182 ( 2975) metal coordination : bond 0.00788 ( 15) metal coordination : angle 9.45056 ( 18) Misc. bond : bond 0.00012 ( 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 310 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6736 (mp10) REVERT: A 163 ASP cc_start: 0.5754 (p0) cc_final: 0.4756 (m-30) REVERT: A 234 GLN cc_start: 0.7921 (tm130) cc_final: 0.7684 (tm-30) REVERT: A 252 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7303 (mtm-85) REVERT: C 41 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5146 (p90) REVERT: C 160 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7440 (pm20) REVERT: D 41 TYR cc_start: 0.8970 (m-80) cc_final: 0.8758 (m-80) REVERT: E 253 MET cc_start: 0.7695 (ttm) cc_final: 0.7341 (ttp) REVERT: E 280 HIS cc_start: 0.6976 (t70) cc_final: 0.6461 (m-70) REVERT: F 51 MET cc_start: 0.8492 (mtp) cc_final: 0.8244 (mtm) REVERT: F 201 ILE cc_start: 0.8421 (mt) cc_final: 0.7960 (pt) REVERT: F 289 GLN cc_start: 0.7031 (mt0) cc_final: 0.6414 (tm-30) REVERT: F 315 MET cc_start: 0.4002 (ppp) cc_final: 0.3610 (ppp) REVERT: G 182 MET cc_start: 0.7327 (mmm) cc_final: 0.7033 (mmm) outliers start: 32 outliers final: 21 residues processed: 298 average time/residue: 0.1438 time to fit residues: 63.5926 Evaluate side-chains 277 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 158 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 97 SER 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 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 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 29 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 222 ASN 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: 7.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 330 GLN 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 = 0.4174 r_free = 0.4174 target = 0.191625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160632 restraints weight = 24167.574| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.80 r_work: 0.3685 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19849 Z= 0.134 Angle : 0.644 21.128 27071 Z= 0.291 Chirality : 0.039 0.199 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.319 103.349 3033 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 1.75 % Allowed : 16.07 % Favored : 82.18 % 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 aren not related in a simple way. whole: 0.91 (0.18), residues: 2379 helix: 1.51 (0.15), residues: 1214 sheet: -0.22 (0.26), residues: 397 loop : -0.27 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 149 TYR 0.015 0.001 TYR F 310 PHE 0.012 0.001 PHE F 128 TRP 0.011 0.001 TRP C 10 HIS 0.010 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00313 (19831) covalent geometry : angle 0.59677 (27053) hydrogen bonds : bond 0.03277 ( 1047) hydrogen bonds : angle 4.15021 ( 2975) metal coordination : bond 0.00739 ( 15) metal coordination : angle 9.38449 ( 18) Misc. bond : bond 0.00033 ( 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 306 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6652 (mp10) REVERT: A 223 MET cc_start: 0.8228 (mpp) cc_final: 0.7846 (mpp) REVERT: A 252 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7302 (mtm-85) REVERT: C 41 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5333 (p90) REVERT: C 160 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7455 (pm20) REVERT: D 22 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: D 41 TYR cc_start: 0.9022 (m-80) cc_final: 0.8768 (m-80) REVERT: E 280 HIS cc_start: 0.6996 (t70) cc_final: 0.6457 (m-70) REVERT: E 318 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7715 (ttp-110) REVERT: F 88 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7423 (mt) REVERT: F 201 ILE cc_start: 0.8425 (mt) cc_final: 0.7968 (pt) REVERT: F 289 GLN cc_start: 0.7061 (mt0) cc_final: 0.6443 (tm-30) REVERT: F 315 MET cc_start: 0.4064 (ppp) cc_final: 0.3622 (ppp) REVERT: G 204 MET cc_start: 0.8475 (tpp) cc_final: 0.8259 (tpp) REVERT: G 254 LYS cc_start: 0.7772 (mppt) cc_final: 0.7325 (mmtp) outliers start: 35 outliers final: 21 residues processed: 294 average time/residue: 0.1388 time to fit residues: 60.8657 Evaluate side-chains 280 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN 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 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 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 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 222 ASN 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: 0.7980 chunk 57 optimal weight: 10.0000 chunk 128 optimal weight: 0.0970 chunk 236 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN C 235 GLN C 360 HIS F 348 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 = 0.4187 r_free = 0.4187 target = 0.192851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162034 restraints weight = 24242.129| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.80 r_work: 0.3701 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2237 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= 0.117 Angle : 0.627 19.771 27071 Z= 0.285 Chirality : 0.039 0.181 3126 Planarity : 0.004 0.055 3407 Dihedral : 13.223 102.483 3033 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 2.25 % Allowed : 16.12 % Favored : 81.63 % 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 aren not related in a simple way. whole: 1.00 (0.18), residues: 2379 helix: 1.58 (0.15), residues: 1213 sheet: -0.19 (0.27), residues: 395 loop : -0.23 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 215 TYR 0.016 0.001 TYR F 284 PHE 0.012 0.001 PHE F 128 TRP 0.009 0.001 TRP E 175 HIS 0.006 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00268 (19831) covalent geometry : angle 0.58413 (27053) hydrogen bonds : bond 0.03139 ( 1047) hydrogen bonds : angle 4.08782 ( 2975) metal coordination : bond 0.00649 ( 15) metal coordination : angle 8.84325 ( 18) Misc. bond : bond 0.00022 ( 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: 45 poor density : 271 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: A 194 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: A 234 GLN cc_start: 0.7956 (tm130) cc_final: 0.7700 (tm-30) REVERT: A 252 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7270 (mtm-85) REVERT: B 34 LEU cc_start: 0.8265 (mp) cc_final: 0.8032 (mt) REVERT: C 41 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5351 (p90) REVERT: C 160 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7456 (pm20) REVERT: C 169 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7731 (mpt180) REVERT: D 22 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: D 288 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8696 (mp) REVERT: D 306 MET cc_start: 0.7294 (ppp) cc_final: 0.6487 (ptm) REVERT: E 88 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8319 (tt) REVERT: E 280 HIS cc_start: 0.7019 (t70) cc_final: 0.6470 (m-70) REVERT: F 51 MET cc_start: 0.8463 (mtp) cc_final: 0.8245 (mtm) REVERT: F 201 ILE cc_start: 0.8421 (mt) cc_final: 0.7974 (pt) REVERT: F 289 GLN cc_start: 0.7020 (mt0) cc_final: 0.6461 (tm-30) REVERT: F 315 MET cc_start: 0.4085 (ppp) cc_final: 0.3608 (ppp) REVERT: G 204 MET cc_start: 0.8416 (tpp) cc_final: 0.8214 (tpp) REVERT: G 254 LYS cc_start: 0.7768 (mppt) cc_final: 0.7312 (mmtp) outliers start: 45 outliers final: 25 residues processed: 305 average time/residue: 0.1504 time to fit residues: 69.2957 Evaluate side-chains 288 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 194 ASP 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 97 SER 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 169 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE 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 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 288 LEU 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 F residue 1 MET Chi-restraints excluded: chain F residue 29 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 193 VAL 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: 2.9990 chunk 191 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 110 ASN C 360 HIS G 143 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 = 0.4144 r_free = 0.4144 target = 0.188451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157007 restraints weight = 24199.274| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.79 r_work: 0.3638 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19849 Z= 0.185 Angle : 0.696 21.009 27071 Z= 0.316 Chirality : 0.041 0.201 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.311 97.788 3033 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 2.15 % Allowed : 16.87 % Favored : 80.98 % 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 aren not related in a simple way. whole: 0.74 (0.18), residues: 2379 helix: 1.32 (0.15), residues: 1218 sheet: -0.21 (0.27), residues: 384 loop : -0.32 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 149 TYR 0.019 0.002 TYR C 41 PHE 0.013 0.002 PHE D 15 TRP 0.010 0.001 TRP E 229 HIS 0.009 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00442 (19831) covalent geometry : angle 0.65116 (27053) hydrogen bonds : bond 0.03661 ( 1047) hydrogen bonds : angle 4.27331 ( 2975) metal coordination : bond 0.00857 ( 15) metal coordination : angle 9.52227 ( 18) Misc. bond : bond 0.00051 ( 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 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: A 96 GLN cc_start: 0.7464 (pt0) cc_final: 0.7038 (pt0) REVERT: A 163 ASP cc_start: 0.5930 (p0) cc_final: 0.4810 (m-30) REVERT: A 223 MET cc_start: 0.8116 (mpp) cc_final: 0.7843 (mpp) REVERT: A 252 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7333 (mtm-85) REVERT: C 41 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.5693 (p90) REVERT: C 160 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7481 (pm20) REVERT: D 22 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: D 251 SER cc_start: 0.8682 (t) cc_final: 0.8261 (p) REVERT: D 306 MET cc_start: 0.7248 (ppp) cc_final: 0.6427 (ptm) REVERT: E 88 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8349 (tt) REVERT: E 91 ASP cc_start: 0.7881 (m-30) cc_final: 0.7618 (m-30) REVERT: E 280 HIS cc_start: 0.6995 (t70) cc_final: 0.6461 (m-70) REVERT: F 201 ILE cc_start: 0.8462 (mt) cc_final: 0.8001 (pt) REVERT: F 289 GLN cc_start: 0.7174 (mt0) cc_final: 0.6616 (tm-30) REVERT: F 315 MET cc_start: 0.4035 (ppp) cc_final: 0.3540 (ppp) REVERT: G 182 MET cc_start: 0.7829 (mmm) cc_final: 0.7621 (mmm) REVERT: G 204 MET cc_start: 0.8530 (tpp) cc_final: 0.8315 (tpp) REVERT: G 254 LYS cc_start: 0.7781 (mppt) cc_final: 0.7284 (mmtp) outliers start: 43 outliers final: 31 residues processed: 298 average time/residue: 0.1271 time to fit residues: 58.0217 Evaluate side-chains 289 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 194 ASP 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 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 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 F residue 1 MET Chi-restraints excluded: chain F residue 29 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 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: 4.9990 chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN C 360 HIS G 143 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 = 0.4175 r_free = 0.4175 target = 0.191613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160673 restraints weight = 24074.680| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.78 r_work: 0.3685 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19849 Z= 0.123 Angle : 0.642 19.672 27071 Z= 0.291 Chirality : 0.039 0.197 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.171 97.857 3033 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.47 % Rotamer: Outliers : 2.10 % Allowed : 17.07 % Favored : 80.83 % 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 aren not related in a simple way. whole: 0.96 (0.18), residues: 2379 helix: 1.52 (0.15), residues: 1218 sheet: -0.11 (0.27), residues: 389 loop : -0.27 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 149 TYR 0.015 0.001 TYR F 284 PHE 0.013 0.001 PHE F 128 TRP 0.011 0.001 TRP E 175 HIS 0.010 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00284 (19831) covalent geometry : angle 0.60019 (27053) hydrogen bonds : bond 0.03219 ( 1047) hydrogen bonds : angle 4.12467 ( 2975) metal coordination : bond 0.00682 ( 15) metal coordination : angle 8.81136 ( 18) Misc. bond : bond 0.00036 ( 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: 42 poor density : 265 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6856 (mp10) REVERT: A 96 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7071 (pt0) REVERT: A 104 LEU cc_start: 0.8788 (mt) cc_final: 0.8500 (mp) REVERT: A 163 ASP cc_start: 0.5862 (p0) cc_final: 0.4756 (m-30) REVERT: A 194 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: A 223 MET cc_start: 0.8064 (mpp) cc_final: 0.7802 (mpp) REVERT: A 252 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7292 (mtm-85) REVERT: B 1 MET cc_start: 0.5618 (tmm) cc_final: 0.5221 (tmm) REVERT: C 41 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5463 (p90) REVERT: C 160 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7485 (pm20) REVERT: C 190 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6850 (mt) REVERT: D 306 MET cc_start: 0.7294 (ppp) cc_final: 0.6491 (ptm) REVERT: E 88 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8307 (tt) REVERT: E 280 HIS cc_start: 0.6978 (t70) cc_final: 0.6459 (m-70) REVERT: F 29 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7939 (mt) REVERT: F 182 MET cc_start: 0.7500 (mtt) cc_final: 0.7241 (mtp) REVERT: F 201 ILE cc_start: 0.8447 (mt) cc_final: 0.7996 (pt) REVERT: F 289 GLN cc_start: 0.7197 (mt0) cc_final: 0.6659 (tm-30) REVERT: F 315 MET cc_start: 0.4026 (ppp) cc_final: 0.3530 (ppp) REVERT: G 254 LYS cc_start: 0.7789 (mppt) cc_final: 0.7376 (mmtp) outliers start: 42 outliers final: 24 residues processed: 298 average time/residue: 0.1418 time to fit residues: 64.0022 Evaluate side-chains 287 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 194 ASP 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 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 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 F residue 29 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 193 VAL 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: 0.9990 chunk 21 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 234 GLN B 110 ASN C 360 HIS G 226 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.186349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155408 restraints weight = 24168.400| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.72 r_work: 0.3622 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19849 Z= 0.223 Angle : 0.740 22.249 27071 Z= 0.337 Chirality : 0.043 0.259 3126 Planarity : 0.005 0.051 3407 Dihedral : 13.376 93.062 3033 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.38 % Rotamer: Outliers : 2.10 % Allowed : 16.97 % 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 aren not related in a simple way. whole: 0.58 (0.18), residues: 2379 helix: 1.20 (0.15), residues: 1213 sheet: -0.16 (0.27), residues: 370 loop : -0.48 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 169 TYR 0.022 0.002 TYR C 41 PHE 0.017 0.002 PHE D 15 TRP 0.014 0.002 TRP E 229 HIS 0.011 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00539 (19831) covalent geometry : angle 0.69471 (27053) hydrogen bonds : bond 0.03964 ( 1047) hydrogen bonds : angle 4.40093 ( 2975) metal coordination : bond 0.00984 ( 15) metal coordination : angle 9.89051 ( 18) Misc. bond : bond 0.00071 ( 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: 42 poor density : 269 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6819 (mp10) REVERT: A 96 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: A 104 LEU cc_start: 0.8808 (mt) cc_final: 0.8567 (mt) REVERT: A 163 ASP cc_start: 0.6116 (p0) cc_final: 0.4968 (m-30) REVERT: A 223 MET cc_start: 0.8147 (mpp) cc_final: 0.7865 (mpp) REVERT: A 252 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7346 (mtm-85) REVERT: B 144 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7243 (pt0) REVERT: C 41 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.5772 (p90) REVERT: C 160 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7461 (pm20) REVERT: C 190 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6915 (mt) REVERT: C 260 ASN cc_start: 0.8012 (t0) cc_final: 0.7802 (t0) REVERT: D 22 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: D 247 ASP cc_start: 0.7329 (p0) cc_final: 0.7046 (p0) REVERT: D 251 SER cc_start: 0.8725 (t) cc_final: 0.8262 (p) REVERT: D 306 MET cc_start: 0.7224 (ppp) cc_final: 0.6495 (ptm) REVERT: E 68 MET cc_start: 0.7688 (mmm) cc_final: 0.7373 (mmm) REVERT: E 88 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8392 (tt) REVERT: E 91 ASP cc_start: 0.7916 (m-30) cc_final: 0.7640 (m-30) REVERT: E 280 HIS cc_start: 0.7001 (t70) cc_final: 0.6496 (m-70) REVERT: E 318 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7511 (ttp-170) REVERT: F 29 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7999 (mp) REVERT: F 201 ILE cc_start: 0.8460 (mt) cc_final: 0.7994 (pt) REVERT: F 289 GLN cc_start: 0.7321 (mt0) cc_final: 0.6759 (tm-30) REVERT: F 315 MET cc_start: 0.4077 (ppp) cc_final: 0.3606 (ppp) REVERT: G 254 LYS cc_start: 0.7776 (mppt) cc_final: 0.7335 (mmtp) outliers start: 42 outliers final: 31 residues processed: 297 average time/residue: 0.1528 time to fit residues: 68.2661 Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU 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 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 71 THR 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 265 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 110 ASN C 360 HIS ** D 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 = 0.4162 r_free = 0.4162 target = 0.190277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159795 restraints weight = 24161.889| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.74 r_work: 0.3675 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2487 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= 0.132 Angle : 0.663 20.606 27071 Z= 0.301 Chirality : 0.040 0.234 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.195 93.364 3033 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 1.90 % Allowed : 17.27 % Favored : 80.83 % 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 aren not related in a simple way. whole: 0.84 (0.18), residues: 2379 helix: 1.43 (0.15), residues: 1216 sheet: -0.19 (0.27), residues: 389 loop : -0.31 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 149 TYR 0.016 0.001 TYR F 284 PHE 0.013 0.001 PHE F 128 TRP 0.011 0.001 TRP E 175 HIS 0.011 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00308 (19831) covalent geometry : angle 0.62090 (27053) hydrogen bonds : bond 0.03322 ( 1047) hydrogen bonds : angle 4.21907 ( 2975) metal coordination : bond 0.00689 ( 15) metal coordination : angle 9.03989 ( 18) Misc. bond : bond 0.00031 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5033.28 seconds wall clock time: 86 minutes 49.48 seconds (5209.48 seconds total)