Starting phenix.real_space_refine on Tue May 20 01:53:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vat_43102/05_2025/8vat_43102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vat_43102/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vat_43102/05_2025/8vat_43102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vat_43102/05_2025/8vat_43102.map" model { file = "/net/cci-nas-00/data/ceres_data/8vat_43102/05_2025/8vat_43102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vat_43102/05_2025/8vat_43102.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.75, per 1000 atoms: 0.66 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: 4.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 7.46 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: 6.50 Time building geometry restraints manager: 5.71 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 53.210 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.090 ------------------------------------------------------------------------------- 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 : 12.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP C 10 HIS 0.006 0.001 HIS B 0 PHE 0.021 0.002 PHE G 267 TYR 0.032 0.002 TYR C 41 ARG 0.004 0.000 ARG E 146 Details of bonding type rmsd hydrogen bonds : bond 0.13818 ( 1047) hydrogen bonds : angle 5.72762 ( 2975) metal coordination : bond 0.00914 ( 15) metal coordination : angle 14.73275 ( 18) covalent geometry : bond 0.00480 (19831) covalent geometry : angle 0.72277 (27053) 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 : 1.945 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: 0.8084 (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: 0.6469 (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: 0.3497 time to fit residues: 187.1445 Evaluate side-chains 259 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.189446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156630 restraints weight = 24311.722| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.83 r_work: 0.3641 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19849 Z= 0.197 Angle : 0.774 38.095 27071 Z= 0.342 Chirality : 0.042 0.215 3126 Planarity : 0.005 0.053 3407 Dihedral : 13.925 103.681 3033 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.63 % Rotamer: Outliers : 1.70 % Allowed : 8.61 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2379 helix: 0.93 (0.15), residues: 1204 sheet: -0.09 (0.26), residues: 381 loop : -0.53 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 10 HIS 0.011 0.001 HIS C 360 PHE 0.015 0.002 PHE D 15 TYR 0.029 0.002 TYR C 41 ARG 0.006 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 1047) hydrogen bonds : angle 4.69109 ( 2975) metal coordination : bond 0.01646 ( 15) metal coordination : angle 13.63676 ( 18) covalent geometry : bond 0.00466 (19831) covalent geometry : angle 0.68928 (27053) Misc. bond : bond 0.00391 ( 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 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7813 (ptp) cc_final: 0.7343 (ptp) REVERT: A 163 ASP cc_start: 0.6025 (p0) cc_final: 0.5039 (m-30) REVERT: A 194 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: A 239 GLU cc_start: 0.7966 (tt0) cc_final: 0.7702 (tt0) REVERT: A 252 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7356 (mtm-85) REVERT: C 160 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7425 (pm20) REVERT: C 192 ASN cc_start: 0.7222 (m110) cc_final: 0.6875 (m110) REVERT: D 41 TYR cc_start: 0.8994 (m-80) cc_final: 0.8781 (m-80) REVERT: D 288 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8563 (mp) REVERT: D 306 MET cc_start: 0.6928 (ptm) cc_final: 0.6686 (ptm) REVERT: E 91 ASP cc_start: 0.7925 (m-30) cc_final: 0.7628 (m-30) REVERT: F 1 MET cc_start: 0.7594 (ptt) cc_final: 0.7277 (ptp) REVERT: F 73 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7372 (mmm160) REVERT: F 201 ILE cc_start: 0.8444 (mt) cc_final: 0.7938 (pt) REVERT: F 284 TYR cc_start: 0.7327 (t80) cc_final: 0.7066 (t80) REVERT: G 254 LYS cc_start: 0.7712 (mppt) cc_final: 0.7371 (mmtp) REVERT: G 344 VAL cc_start: 0.9041 (t) cc_final: 0.8827 (p) outliers start: 34 outliers final: 19 residues processed: 297 average time/residue: 0.3512 time to fit residues: 152.3709 Evaluate side-chains 278 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 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 B residue 164 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 77 ASP 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 72 THR 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 222 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 139 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4183 r_free = 0.4183 target = 0.192553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160406 restraints weight = 24083.790| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.73 r_work: 0.3692 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1551 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= 0.128 Angle : 0.674 31.402 27071 Z= 0.298 Chirality : 0.039 0.215 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.666 106.463 3033 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer: Outliers : 1.50 % Allowed : 11.66 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2379 helix: 1.25 (0.15), residues: 1211 sheet: -0.27 (0.26), residues: 403 loop : -0.36 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 10 HIS 0.005 0.001 HIS A 105 PHE 0.013 0.001 PHE F 128 TYR 0.028 0.001 TYR F 310 ARG 0.005 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 1047) hydrogen bonds : angle 4.36511 ( 2975) metal coordination : bond 0.01370 ( 15) metal coordination : angle 11.81313 ( 18) covalent geometry : bond 0.00282 (19831) covalent geometry : angle 0.60188 (27053) Misc. bond : bond 0.00028 ( 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 327 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.6039 (p0) cc_final: 0.5133 (m-30) REVERT: A 223 MET cc_start: 0.8139 (mpp) cc_final: 0.7736 (mpp) REVERT: A 239 GLU cc_start: 0.7873 (tt0) cc_final: 0.7600 (tt0) REVERT: A 252 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7308 (mtm-85) REVERT: C 65 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7227 (mt-10) REVERT: C 160 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7423 (pm20) REVERT: D 13 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7821 (mm-40) REVERT: D 41 TYR cc_start: 0.8970 (m-80) cc_final: 0.8763 (m-80) REVERT: D 269 ASN cc_start: 0.6727 (t0) cc_final: 0.6473 (t0) REVERT: D 288 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8629 (mp) REVERT: E 254 ASP cc_start: 0.7628 (m-30) cc_final: 0.7182 (m-30) REVERT: E 280 HIS cc_start: 0.6972 (t70) cc_final: 0.6430 (m-70) REVERT: E 307 ASN cc_start: 0.8646 (t160) cc_final: 0.8278 (t0) REVERT: F 1 MET cc_start: 0.7683 (ptt) cc_final: 0.7448 (ptp) REVERT: F 201 ILE cc_start: 0.8448 (mt) cc_final: 0.7962 (pt) REVERT: F 289 GLN cc_start: 0.6946 (mt0) cc_final: 0.6310 (tm-30) outliers start: 30 outliers final: 17 residues processed: 317 average time/residue: 0.3422 time to fit residues: 160.3720 Evaluate side-chains 288 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 46 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 288 LEU 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 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 19 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 234 GLN B 110 ASN C 235 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.192265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160158 restraints weight = 24243.570| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.79 r_work: 0.3682 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19849 Z= 0.128 Angle : 0.658 26.094 27071 Z= 0.294 Chirality : 0.039 0.200 3126 Planarity : 0.004 0.050 3407 Dihedral : 13.534 106.303 3033 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 2.00 % Allowed : 13.31 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2379 helix: 1.40 (0.15), residues: 1205 sheet: -0.11 (0.27), residues: 388 loop : -0.42 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 10 HIS 0.009 0.001 HIS E 259 PHE 0.011 0.001 PHE F 128 TYR 0.020 0.001 TYR F 310 ARG 0.005 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1047) hydrogen bonds : angle 4.26177 ( 2975) metal coordination : bond 0.00921 ( 15) metal coordination : angle 10.68985 ( 18) covalent geometry : bond 0.00293 (19831) covalent geometry : angle 0.59803 (27053) Misc. bond : bond 0.00023 ( 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 334 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6821 (mp10) REVERT: A 163 ASP cc_start: 0.6099 (p0) cc_final: 0.5222 (m-30) REVERT: A 252 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7316 (mtm-85) REVERT: C 41 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5264 (p90) REVERT: C 65 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7276 (mt-10) REVERT: C 160 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7433 (pm20) REVERT: C 344 ASP cc_start: 0.7563 (t70) cc_final: 0.7353 (t70) REVERT: D 13 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7845 (mm-40) REVERT: D 22 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: D 41 TYR cc_start: 0.8988 (m-80) cc_final: 0.8761 (m-80) REVERT: D 241 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7756 (tp) REVERT: E 1 MET cc_start: 0.2371 (ppp) cc_final: 0.2055 (mmt) REVERT: E 280 HIS cc_start: 0.6994 (t70) cc_final: 0.6418 (m-70) REVERT: F 201 ILE cc_start: 0.8450 (mt) cc_final: 0.7983 (pt) REVERT: F 289 GLN cc_start: 0.7008 (mt0) cc_final: 0.6339 (tm-30) REVERT: G 204 MET cc_start: 0.8436 (tpp) cc_final: 0.7461 (tpp) outliers start: 40 outliers final: 25 residues processed: 318 average time/residue: 0.3629 time to fit residues: 169.8560 Evaluate side-chains 293 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 158 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 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 71 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN F 222 ASN G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.190678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158394 restraints weight = 24385.043| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.81 r_work: 0.3660 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19849 Z= 0.147 Angle : 0.656 23.299 27071 Z= 0.297 Chirality : 0.040 0.201 3126 Planarity : 0.004 0.060 3407 Dihedral : 13.434 104.635 3033 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 2.60 % Allowed : 14.81 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2379 helix: 1.41 (0.15), residues: 1205 sheet: -0.21 (0.26), residues: 395 loop : -0.39 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 10 HIS 0.005 0.001 HIS C 290 PHE 0.013 0.001 PHE F 319 TYR 0.018 0.001 TYR F 284 ARG 0.007 0.000 ARG B 215 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 1047) hydrogen bonds : angle 4.24148 ( 2975) metal coordination : bond 0.00882 ( 15) metal coordination : angle 9.92492 ( 18) covalent geometry : bond 0.00343 (19831) covalent geometry : angle 0.60447 (27053) Misc. bond : bond 0.00038 ( 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 328 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: A 163 ASP cc_start: 0.6144 (p0) cc_final: 0.5303 (m-30) REVERT: A 194 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: A 252 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7327 (mtm-85) REVERT: C 41 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5402 (p90) REVERT: C 65 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7254 (mt-10) REVERT: C 160 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7466 (pm20) REVERT: D 13 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7872 (mm-40) REVERT: D 22 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: D 41 TYR cc_start: 0.9001 (m-80) cc_final: 0.8753 (m-80) REVERT: D 306 MET cc_start: 0.7221 (ppp) cc_final: 0.6459 (ptm) REVERT: E 1 MET cc_start: 0.2608 (ppp) cc_final: 0.2345 (mmt) REVERT: E 280 HIS cc_start: 0.6959 (t70) cc_final: 0.6410 (m-70) REVERT: F 88 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7542 (mt) REVERT: F 201 ILE cc_start: 0.8406 (mt) cc_final: 0.7931 (pt) REVERT: F 289 GLN cc_start: 0.7029 (mt0) cc_final: 0.6406 (tm-30) REVERT: G 204 MET cc_start: 0.8493 (tpp) cc_final: 0.7595 (tpp) outliers start: 52 outliers final: 31 residues processed: 310 average time/residue: 0.3397 time to fit residues: 159.7361 Evaluate side-chains 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 193 VAL 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 148 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN C 360 HIS ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.187651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.156059 restraints weight = 24209.660| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.76 r_work: 0.3621 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19849 Z= 0.195 Angle : 0.708 23.282 27071 Z= 0.320 Chirality : 0.041 0.208 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.446 100.552 3033 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 2.85 % Allowed : 15.37 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2379 helix: 1.24 (0.15), residues: 1205 sheet: -0.21 (0.27), residues: 364 loop : -0.52 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 10 HIS 0.007 0.001 HIS C 290 PHE 0.014 0.002 PHE D 15 TYR 0.022 0.002 TYR C 41 ARG 0.005 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1047) hydrogen bonds : angle 4.38551 ( 2975) metal coordination : bond 0.00978 ( 15) metal coordination : angle 10.24030 ( 18) covalent geometry : bond 0.00465 (19831) covalent geometry : angle 0.65708 (27053) Misc. bond : bond 0.00054 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6652 (mp10) REVERT: A 96 GLN cc_start: 0.7473 (pt0) cc_final: 0.7127 (pt0) REVERT: A 223 MET cc_start: 0.8156 (mpp) cc_final: 0.7802 (mpp) REVERT: A 252 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7368 (mtm-85) REVERT: C 41 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.5697 (p90) REVERT: C 65 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7318 (mt-10) REVERT: C 160 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7449 (pm20) REVERT: D 22 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: D 41 TYR cc_start: 0.9053 (m-80) cc_final: 0.8780 (m-80) REVERT: D 247 ASP cc_start: 0.7138 (p0) cc_final: 0.6890 (p0) REVERT: D 251 SER cc_start: 0.8662 (t) cc_final: 0.8296 (p) REVERT: D 288 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8620 (mp) REVERT: D 306 MET cc_start: 0.7441 (ppp) cc_final: 0.6681 (ptm) REVERT: E 88 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8436 (tt) REVERT: E 91 ASP cc_start: 0.7901 (m-30) cc_final: 0.7633 (m-30) REVERT: E 280 HIS cc_start: 0.6991 (t70) cc_final: 0.6460 (m-70) REVERT: F 88 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7701 (mt) REVERT: F 201 ILE cc_start: 0.8466 (mt) cc_final: 0.7970 (pt) REVERT: F 289 GLN cc_start: 0.7064 (mt0) cc_final: 0.6471 (tm-30) REVERT: G 175 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: G 204 MET cc_start: 0.8535 (tpp) cc_final: 0.7767 (tpp) REVERT: G 254 LYS cc_start: 0.7785 (mppt) cc_final: 0.7323 (mmtp) outliers start: 57 outliers final: 39 residues processed: 315 average time/residue: 0.3144 time to fit residues: 149.7323 Evaluate side-chains 307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 78 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain 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 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 88 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS G 186 GLN G 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157256 restraints weight = 24144.038| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.78 r_work: 0.3647 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19849 Z= 0.160 Angle : 0.677 22.590 27071 Z= 0.306 Chirality : 0.040 0.200 3126 Planarity : 0.004 0.052 3407 Dihedral : 13.334 99.221 3033 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.50 % Allowed : 16.22 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2379 helix: 1.30 (0.15), residues: 1210 sheet: -0.41 (0.26), residues: 400 loop : -0.35 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.009 0.001 HIS E 259 PHE 0.012 0.001 PHE F 128 TYR 0.019 0.001 TYR C 41 ARG 0.006 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1047) hydrogen bonds : angle 4.30301 ( 2975) metal coordination : bond 0.00855 ( 15) metal coordination : angle 9.86644 ( 18) covalent geometry : bond 0.00379 (19831) covalent geometry : angle 0.62730 (27053) Misc. bond : bond 0.00041 ( 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 319 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: A 96 GLN cc_start: 0.7542 (pt0) cc_final: 0.7150 (pt0) REVERT: A 163 ASP cc_start: 0.6015 (p0) cc_final: 0.5190 (m-30) REVERT: A 194 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: A 252 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7286 (mtm-85) REVERT: C 41 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5656 (p90) REVERT: C 160 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7456 (pm20) REVERT: D 22 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: D 41 TYR cc_start: 0.9030 (m-80) cc_final: 0.8774 (m-80) REVERT: D 247 ASP cc_start: 0.7127 (p0) cc_final: 0.6868 (p0) REVERT: D 251 SER cc_start: 0.8638 (t) cc_final: 0.8257 (p) REVERT: D 288 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8631 (mp) REVERT: D 306 MET cc_start: 0.7396 (ppp) cc_final: 0.6733 (ptm) REVERT: E 68 MET cc_start: 0.7684 (mmm) cc_final: 0.7441 (mmm) REVERT: E 280 HIS cc_start: 0.6972 (t70) cc_final: 0.6466 (m-70) REVERT: E 318 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7884 (ttp-170) REVERT: F 29 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7770 (mt) REVERT: F 201 ILE cc_start: 0.8405 (mt) cc_final: 0.7921 (pt) REVERT: F 289 GLN cc_start: 0.7118 (mt0) cc_final: 0.6527 (tm-30) REVERT: G 175 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.7240 (m-70) REVERT: G 204 MET cc_start: 0.8557 (tpp) cc_final: 0.8027 (tpp) REVERT: G 254 LYS cc_start: 0.7739 (mppt) cc_final: 0.7266 (mmtp) outliers start: 50 outliers final: 34 residues processed: 304 average time/residue: 0.3163 time to fit residues: 145.7586 Evaluate side-chains 297 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 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 69 THR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain 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 175 HIS Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 190 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN C 360 HIS ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155483 restraints weight = 24216.668| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.75 r_work: 0.3627 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19849 Z= 0.191 Angle : 0.707 22.997 27071 Z= 0.320 Chirality : 0.042 0.201 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.367 95.737 3033 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer: Outliers : 2.95 % Allowed : 16.02 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2379 helix: 1.19 (0.15), residues: 1213 sheet: -0.41 (0.26), residues: 386 loop : -0.47 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 10 HIS 0.010 0.001 HIS E 259 PHE 0.013 0.002 PHE F 128 TYR 0.021 0.002 TYR C 41 ARG 0.006 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1047) hydrogen bonds : angle 4.37946 ( 2975) metal coordination : bond 0.00939 ( 15) metal coordination : angle 10.16947 ( 18) covalent geometry : bond 0.00456 (19831) covalent geometry : angle 0.65729 (27053) Misc. bond : bond 0.00060 ( 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 319 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: A 96 GLN cc_start: 0.7521 (pt0) cc_final: 0.7119 (pt0) REVERT: A 163 ASP cc_start: 0.5990 (p0) cc_final: 0.5257 (m-30) REVERT: A 223 MET cc_start: 0.8173 (mpp) cc_final: 0.7852 (mpp) REVERT: A 252 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7320 (mtm-85) REVERT: C 41 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.5674 (p90) REVERT: C 160 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7450 (pm20) REVERT: C 260 ASN cc_start: 0.7952 (t0) cc_final: 0.7748 (t0) REVERT: D 22 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: D 41 TYR cc_start: 0.9043 (m-80) cc_final: 0.8754 (m-80) REVERT: D 251 SER cc_start: 0.8675 (t) cc_final: 0.8289 (p) REVERT: D 306 MET cc_start: 0.7328 (ppp) cc_final: 0.6782 (ptm) REVERT: E 68 MET cc_start: 0.7679 (mmm) cc_final: 0.7420 (mmm) REVERT: E 88 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8411 (tt) REVERT: E 91 ASP cc_start: 0.7960 (m-30) cc_final: 0.7646 (m-30) REVERT: E 280 HIS cc_start: 0.7011 (t70) cc_final: 0.6503 (m-70) REVERT: E 318 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7690 (ttp-110) REVERT: F 29 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7841 (mp) REVERT: F 201 ILE cc_start: 0.8400 (mt) cc_final: 0.7906 (pt) REVERT: F 289 GLN cc_start: 0.7179 (mt0) cc_final: 0.6593 (tm-30) REVERT: G 175 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.7310 (m-70) REVERT: G 204 MET cc_start: 0.8546 (tpp) cc_final: 0.8094 (tpp) REVERT: G 254 LYS cc_start: 0.7753 (mppt) cc_final: 0.7271 (mmtp) outliers start: 59 outliers final: 42 residues processed: 307 average time/residue: 0.3156 time to fit residues: 147.1728 Evaluate side-chains 303 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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 78 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 ILE 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 F residue 317 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 247 VAL 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 105 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 HIS ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN G 226 HIS G 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.191485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160532 restraints weight = 24234.922| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.78 r_work: 0.3684 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19849 Z= 0.120 Angle : 0.642 20.269 27071 Z= 0.292 Chirality : 0.039 0.192 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.166 96.749 3033 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 17.47 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2379 helix: 1.47 (0.15), residues: 1224 sheet: -0.29 (0.27), residues: 389 loop : -0.38 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 175 HIS 0.010 0.001 HIS E 259 PHE 0.014 0.001 PHE F 128 TYR 0.016 0.001 TYR F 284 ARG 0.005 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 1047) hydrogen bonds : angle 4.14987 ( 2975) metal coordination : bond 0.00662 ( 15) metal coordination : angle 9.00362 ( 18) covalent geometry : bond 0.00273 (19831) covalent geometry : angle 0.59896 (27053) Misc. bond : bond 0.00025 ( 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 316 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: A 96 GLN cc_start: 0.7461 (pt0) cc_final: 0.7059 (pt0) REVERT: A 163 ASP cc_start: 0.5993 (p0) cc_final: 0.5257 (m-30) REVERT: A 223 MET cc_start: 0.8008 (mpp) cc_final: 0.7756 (mpp) REVERT: A 252 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7245 (mtm-85) REVERT: C 41 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.5432 (p90) REVERT: C 160 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7444 (pm20) REVERT: D 41 TYR cc_start: 0.8985 (m-80) cc_final: 0.8746 (m-80) REVERT: D 194 GLU cc_start: 0.7880 (tt0) cc_final: 0.7625 (mt-10) REVERT: D 306 MET cc_start: 0.7245 (ppp) cc_final: 0.6709 (ptm) REVERT: E 88 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8285 (tt) REVERT: E 280 HIS cc_start: 0.6957 (t70) cc_final: 0.6476 (m-70) REVERT: F 29 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7809 (mt) REVERT: F 201 ILE cc_start: 0.8342 (mt) cc_final: 0.7890 (pt) REVERT: F 289 GLN cc_start: 0.7200 (mt0) cc_final: 0.6630 (tm-30) REVERT: G 204 MET cc_start: 0.8362 (tpp) cc_final: 0.8091 (tpp) REVERT: G 254 LYS cc_start: 0.7770 (mppt) cc_final: 0.7369 (mmtp) outliers start: 41 outliers final: 27 residues processed: 304 average time/residue: 0.3221 time to fit residues: 147.5963 Evaluate side-chains 286 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 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 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 227 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 171 LEU 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 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 130 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 219 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 78 ASN C 360 HIS ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS G 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.189469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157185 restraints weight = 24077.667| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.80 r_work: 0.3658 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19849 Z= 0.149 Angle : 0.671 20.515 27071 Z= 0.305 Chirality : 0.041 0.259 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.206 95.073 3033 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 1.80 % Allowed : 17.67 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2379 helix: 1.45 (0.15), residues: 1219 sheet: -0.31 (0.26), residues: 395 loop : -0.38 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 175 HIS 0.011 0.001 HIS E 259 PHE 0.012 0.001 PHE F 128 TYR 0.021 0.001 TYR E 222 ARG 0.005 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1047) hydrogen bonds : angle 4.20316 ( 2975) metal coordination : bond 0.00733 ( 15) metal coordination : angle 9.07555 ( 18) covalent geometry : bond 0.00354 (19831) covalent geometry : angle 0.62863 (27053) Misc. bond : bond 0.00052 ( 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 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: A 96 GLN cc_start: 0.7445 (pt0) cc_final: 0.7039 (pt0) REVERT: A 163 ASP cc_start: 0.6006 (p0) cc_final: 0.5281 (m-30) REVERT: A 223 MET cc_start: 0.8113 (mpp) cc_final: 0.7837 (mpp) REVERT: A 252 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7274 (mtm-85) REVERT: C 41 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5664 (p90) REVERT: C 160 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7441 (pm20) REVERT: C 260 ASN cc_start: 0.7975 (t0) cc_final: 0.7736 (t0) REVERT: D 41 TYR cc_start: 0.9035 (m-80) cc_final: 0.8777 (m-80) REVERT: D 194 GLU cc_start: 0.7921 (tt0) cc_final: 0.7714 (mt-10) REVERT: D 251 SER cc_start: 0.8619 (t) cc_final: 0.8240 (p) REVERT: D 306 MET cc_start: 0.7261 (ppp) cc_final: 0.6706 (ptm) REVERT: E 88 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8312 (tt) REVERT: E 280 HIS cc_start: 0.6959 (t70) cc_final: 0.6477 (m-70) REVERT: F 29 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7861 (mt) REVERT: F 201 ILE cc_start: 0.8360 (mt) cc_final: 0.7915 (pt) REVERT: F 289 GLN cc_start: 0.7303 (mt0) cc_final: 0.6741 (tm-30) REVERT: G 204 MET cc_start: 0.8377 (tpp) cc_final: 0.8096 (tpp) REVERT: G 254 LYS cc_start: 0.7741 (mppt) cc_final: 0.7303 (mmtp) outliers start: 36 outliers final: 30 residues processed: 291 average time/residue: 0.3084 time to fit residues: 135.4434 Evaluate side-chains 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 286 MET Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 69 THR 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 111 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 214 LEU 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 29 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 130 LEU 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 247 VAL 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 38 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 135 optimal weight: 0.5980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 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 = 0.4175 r_free = 0.4175 target = 0.191683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159664 restraints weight = 24189.317| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.82 r_work: 0.3687 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19849 Z= 0.122 Angle : 0.642 18.927 27071 Z= 0.293 Chirality : 0.039 0.240 3126 Planarity : 0.004 0.051 3407 Dihedral : 13.077 94.630 3033 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 2.10 % Allowed : 17.37 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2379 helix: 1.53 (0.15), residues: 1227 sheet: -0.22 (0.27), residues: 389 loop : -0.35 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 175 HIS 0.011 0.001 HIS E 259 PHE 0.014 0.001 PHE F 128 TYR 0.014 0.001 TYR F 284 ARG 0.005 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 1047) hydrogen bonds : angle 4.10175 ( 2975) metal coordination : bond 0.00606 ( 15) metal coordination : angle 8.47425 ( 18) covalent geometry : bond 0.00282 (19831) covalent geometry : angle 0.60349 (27053) Misc. bond : bond 0.00035 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10996.71 seconds wall clock time: 190 minutes 20.29 seconds (11420.29 seconds total)