Starting phenix.real_space_refine on Thu Aug 6 16:25:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbk_16543/08_2026/8cbk_16543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbk_16543/08_2026/8cbk_16543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2026/8cbk_16543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2026/8cbk_16543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2026/8cbk_16543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2026/8cbk_16543.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 9874 2.51 5 N 2832 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16221 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3814 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 452} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2832 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "T" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1971 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 38, 'rna3p_pyr': 37} Link IDs: {'rna2p': 18, 'rna3p': 74} Chain breaks: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9321 SG CYS E 348 62.040 43.374 15.436 1.00196.69 S ATOM 9337 SG CYS E 351 64.801 44.405 12.797 1.00214.65 S ATOM 11179 SG CYS E 578 63.196 47.045 14.911 1.00211.34 S Time building chain proxies: 3.56, per 1000 atoms: 0.22 Number of scatterers: 16221 At special positions: 0 Unit cell: (103.016, 112.144, 166.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 71 16.00 P 101 15.00 Mg 1 11.99 O 3341 8.00 N 2832 7.00 C 9874 6.00 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=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 816.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 557 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 578 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 351 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 348 " Number of angles added : 3 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 11 sheets defined 56.5% alpha, 8.7% beta 33 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.031A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.559A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.384A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.839A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.546A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.144A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 removed outlier: 3.595A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.792A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.362A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.841A pdb=" N THR B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.899A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.615A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.333A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.767A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.523A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.658A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.659A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.407A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.615A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.541A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 129 removed outlier: 3.988A pdb=" N TRP E 124 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.876A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 160 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 188 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 211 through 221 Processing helix chain 'E' and resid 225 through 240 removed outlier: 4.033A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 278 through 290 removed outlier: 3.679A pdb=" N LEU E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 312 Processing helix chain 'E' and resid 316 through 330 Processing helix chain 'E' and resid 361 through 377 Processing helix chain 'E' and resid 379 through 386 Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 445 through 450 removed outlier: 3.996A pdb=" N ARG E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 Processing helix chain 'E' and resid 477 through 490 removed outlier: 4.121A pdb=" N PHE E 481 " --> pdb=" O GLU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 510 through 523 Processing helix chain 'F' and resid 62 through 82 Processing helix chain 'F' and resid 89 through 105 removed outlier: 3.863A pdb=" N ALA F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 168 removed outlier: 3.865A pdb=" N GLU F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.620A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 236 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.565A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing helix chain 'F' and resid 388 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.442A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.350A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.398A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.455A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 336 through 341 Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 470 removed outlier: 8.742A pdb=" N PHE E 470 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 442 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 407 " --> pdb=" O ILE E 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.575A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2857 1.33 - 1.45: 4443 1.45 - 1.57: 9092 1.57 - 1.69: 197 1.69 - 1.81: 113 Bond restraints: 16702 Sorted by residual: bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.579 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O3 NAD C 301 " pdb=" PA NAD C 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O3 NAD D 301 " pdb=" PA NAD D 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2N NAD D 301 " pdb=" C3N NAD D 301 " ideal model delta sigma weight residual 1.381 1.311 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 22161 1.41 - 2.81: 726 2.81 - 4.22: 142 4.22 - 5.62: 24 5.62 - 7.03: 10 Bond angle restraints: 23063 Sorted by residual: angle pdb=" N HIS E 447 " pdb=" CA HIS E 447 " pdb=" C HIS E 447 " ideal model delta sigma weight residual 111.07 105.85 5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" C GLU E 280 " pdb=" N THR E 281 " pdb=" CA THR E 281 " ideal model delta sigma weight residual 120.65 114.47 6.18 1.32e+00 5.74e-01 2.19e+01 angle pdb=" C TYR F 135 " pdb=" CA TYR F 135 " pdb=" CB TYR F 135 " ideal model delta sigma weight residual 110.90 104.36 6.54 1.58e+00 4.01e-01 1.72e+01 angle pdb=" CA THR F 127 " pdb=" CB THR F 127 " pdb=" OG1 THR F 127 " ideal model delta sigma weight residual 109.60 103.86 5.74 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C PHE E 339 " pdb=" N THR E 340 " pdb=" CA THR E 340 " ideal model delta sigma weight residual 122.82 116.49 6.33 1.68e+00 3.54e-01 1.42e+01 ... (remaining 23058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 9593 26.50 - 52.99: 515 52.99 - 79.49: 150 79.49 - 105.98: 11 105.98 - 132.48: 4 Dihedral angle restraints: 10273 sinusoidal: 5057 harmonic: 5216 Sorted by residual: dihedral pdb=" CA LEU F 385 " pdb=" C LEU F 385 " pdb=" N GLU F 386 " pdb=" CA GLU F 386 " ideal model delta harmonic sigma weight residual 180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C4' G T 31 " pdb=" C3' G T 31 " pdb=" O3' G T 31 " pdb=" P U T 32 " ideal model delta sinusoidal sigma weight residual -110.00 22.48 -132.48 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" C TYR F 135 " pdb=" N TYR F 135 " pdb=" CA TYR F 135 " pdb=" CB TYR F 135 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 10270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2207 0.047 - 0.094: 296 0.094 - 0.141: 192 0.141 - 0.188: 10 0.188 - 0.235: 3 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CA TYR F 135 " pdb=" N TYR F 135 " pdb=" C TYR F 135 " pdb=" CB TYR F 135 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR E 281 " pdb=" N THR E 281 " pdb=" C THR E 281 " pdb=" CB THR E 281 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C2' SAH F 501 " pdb=" C1' SAH F 501 " pdb=" C3' SAH F 501 " pdb=" O2' SAH F 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 2705 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.044 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 211 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C ARG E 211 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG E 211 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY E 212 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 209 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO E 210 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " 0.034 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 119 2.51 - 3.10: 12851 3.10 - 3.70: 26962 3.70 - 4.30: 38438 4.30 - 4.90: 61122 Nonbonded interactions: 139492 Sorted by model distance: nonbonded pdb=" OP1 G T 1 " pdb="MG MG T 201 " model vdw 1.908 2.170 nonbonded pdb=" O2' A T 19 " pdb=" OP1 A T 20 " model vdw 2.035 3.040 nonbonded pdb=" OG SER E 361 " pdb=" OE1 GLU E 363 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN F 162 " pdb=" N ILE F 163 " model vdw 2.245 3.120 nonbonded pdb=" O ASP E 510 " pdb=" OG1 THR E 513 " model vdw 2.249 3.040 ... (remaining 139487 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 'A' selection = chain 'B' selection = chain 'C' 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 : 0.004 0.075 16706 Z= 0.199 Angle : 0.600 7.028 23066 Z= 0.376 Chirality : 0.043 0.235 2708 Planarity : 0.003 0.062 2618 Dihedral : 16.814 132.477 6921 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.21), residues: 1821 helix: 2.53 (0.18), residues: 911 sheet: -0.21 (0.40), residues: 186 loop : -0.28 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.019 0.001 TYR F 135 PHE 0.014 0.001 PHE E 288 TRP 0.034 0.001 TRP F 66 HIS 0.008 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.20 (16702) covalent geometry : angle 0.59831 / 0.38 (23063) hydrogen bonds : bond 0.11882 / 8.37 ( 844) hydrogen bonds : angle 5.88195 / 4.28 ( 2365) metal coordination : bond 0.00588 / 0.30 ( 4) metal coordination : angle 3.74120 / 1.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8989 (m-30) cc_final: 0.8659 (m-30) REVERT: A 160 GLU cc_start: 0.7944 (pt0) cc_final: 0.7705 (pt0) REVERT: B 48 GLU cc_start: 0.8300 (pm20) cc_final: 0.8068 (pm20) REVERT: B 68 GLU cc_start: 0.8707 (tt0) cc_final: 0.8460 (tt0) REVERT: B 70 ASP cc_start: 0.9200 (m-30) cc_final: 0.8960 (m-30) REVERT: C 211 GLU cc_start: 0.8720 (tp30) cc_final: 0.8006 (tp30) REVERT: D 48 GLU cc_start: 0.8842 (tp30) cc_final: 0.8586 (tp30) REVERT: D 70 ASP cc_start: 0.9080 (m-30) cc_final: 0.8804 (m-30) REVERT: E 148 MET cc_start: 0.8413 (mmp) cc_final: 0.8136 (mmp) REVERT: E 161 LEU cc_start: 0.9632 (mm) cc_final: 0.9391 (mm) REVERT: E 178 LEU cc_start: 0.9194 (tp) cc_final: 0.8925 (tp) REVERT: E 182 LEU cc_start: 0.9791 (mt) cc_final: 0.9577 (mt) REVERT: E 269 GLU cc_start: 0.9175 (tp30) cc_final: 0.8631 (tp30) REVERT: E 404 PHE cc_start: 0.8009 (m-10) cc_final: 0.7580 (m-10) REVERT: E 427 LEU cc_start: 0.9571 (tt) cc_final: 0.9355 (pp) REVERT: E 428 ASN cc_start: 0.9597 (m-40) cc_final: 0.9358 (m110) REVERT: E 455 TRP cc_start: 0.9342 (m100) cc_final: 0.9067 (m100) REVERT: E 505 LYS cc_start: 0.9333 (pptt) cc_final: 0.9083 (pptt) REVERT: E 556 TRP cc_start: 0.8839 (m100) cc_final: 0.8145 (m100) REVERT: F 209 MET cc_start: 0.9014 (mpp) cc_final: 0.8286 (mpt) REVERT: F 314 ASP cc_start: 0.8926 (p0) cc_final: 0.8427 (p0) REVERT: F 371 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8712 (mt-10) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 0.5613 time to fit residues: 197.4197 Evaluate side-chains 251 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0170 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 152 ASN E 273 HIS E 447 HIS F 147 GLN F 222 ASN F 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.065318 restraints weight = 34606.363| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.71 r_work: 0.2612 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16706 Z= 0.152 Angle : 0.689 14.436 23066 Z= 0.340 Chirality : 0.044 0.364 2708 Planarity : 0.005 0.044 2618 Dihedral : 16.260 131.174 3561 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.26 % Allowed : 10.99 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1821 helix: 2.28 (0.17), residues: 916 sheet: -0.34 (0.35), residues: 222 loop : -0.10 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 227 TYR 0.017 0.001 TYR E 365 PHE 0.028 0.002 PHE E 481 TRP 0.028 0.003 TRP E 124 HIS 0.009 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16702) covalent geometry : angle 0.68764 / 0.34 (23063) hydrogen bonds : bond 0.04507 / 3.10 ( 844) hydrogen bonds : angle 5.00069 / 3.69 ( 2365) metal coordination : bond 0.00683 / 0.35 ( 4) metal coordination : angle 4.10322 / 2.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 289 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8888 (m-30) cc_final: 0.8591 (m-30) REVERT: A 119 ASP cc_start: 0.8939 (m-30) cc_final: 0.8707 (m-30) REVERT: A 160 GLU cc_start: 0.7782 (pt0) cc_final: 0.7569 (pt0) REVERT: A 249 GLU cc_start: 0.8530 (tp30) cc_final: 0.8281 (tp30) REVERT: B 48 GLU cc_start: 0.8308 (pm20) cc_final: 0.8094 (pm20) REVERT: B 64 ASP cc_start: 0.8162 (t0) cc_final: 0.7955 (t0) REVERT: B 70 ASP cc_start: 0.9018 (m-30) cc_final: 0.8744 (m-30) REVERT: B 160 GLU cc_start: 0.8626 (mp0) cc_final: 0.8037 (pm20) REVERT: C 135 GLU cc_start: 0.9099 (tp30) cc_final: 0.8882 (tp30) REVERT: C 211 GLU cc_start: 0.8673 (tp30) cc_final: 0.7958 (tp30) REVERT: D 48 GLU cc_start: 0.8878 (tp30) cc_final: 0.8536 (tp30) REVERT: D 70 ASP cc_start: 0.8973 (m-30) cc_final: 0.8689 (m-30) REVERT: D 135 GLU cc_start: 0.9002 (tp30) cc_final: 0.8724 (mm-30) REVERT: E 148 MET cc_start: 0.8352 (mmp) cc_final: 0.8053 (mmp) REVERT: E 178 LEU cc_start: 0.9245 (tp) cc_final: 0.9012 (tp) REVERT: E 182 LEU cc_start: 0.9768 (mt) cc_final: 0.9552 (mt) REVERT: E 209 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8479 (tp30) REVERT: E 266 LEU cc_start: 0.9561 (tm) cc_final: 0.9265 (tm) REVERT: E 283 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9255 (pptt) REVERT: E 285 PHE cc_start: 0.8906 (t80) cc_final: 0.8150 (t80) REVERT: E 288 PHE cc_start: 0.8550 (t80) cc_final: 0.8179 (t80) REVERT: E 326 TRP cc_start: 0.9546 (t-100) cc_final: 0.9247 (t-100) REVERT: E 353 LYS cc_start: 0.9187 (mmpt) cc_final: 0.8909 (mmmm) REVERT: E 404 PHE cc_start: 0.8321 (m-80) cc_final: 0.7901 (m-10) REVERT: E 428 ASN cc_start: 0.9642 (m-40) cc_final: 0.9440 (m-40) REVERT: E 448 MET cc_start: 0.9522 (tmm) cc_final: 0.9115 (tpt) REVERT: E 455 TRP cc_start: 0.9345 (m100) cc_final: 0.8551 (m100) REVERT: E 526 LEU cc_start: 0.9051 (mm) cc_final: 0.8346 (mm) REVERT: E 564 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9135 (mm) REVERT: F 100 MET cc_start: 0.9567 (mmm) cc_final: 0.9254 (mmm) REVERT: F 101 TRP cc_start: 0.9507 (m100) cc_final: 0.9240 (m100) REVERT: F 116 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8795 (mp0) REVERT: F 184 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8636 (t70) REVERT: F 209 MET cc_start: 0.8995 (mpp) cc_final: 0.8071 (mpt) REVERT: F 314 ASP cc_start: 0.9146 (p0) cc_final: 0.8831 (p0) REVERT: F 371 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8777 (mt-10) outliers start: 19 outliers final: 8 residues processed: 292 average time/residue: 0.5503 time to fit residues: 179.4261 Evaluate side-chains 239 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 162 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN E 396 ASN E 514 GLN E 522 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.064951 restraints weight = 34869.560| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.76 r_work: 0.2611 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16706 Z= 0.139 Angle : 0.655 15.188 23066 Z= 0.325 Chirality : 0.043 0.454 2708 Planarity : 0.004 0.047 2618 Dihedral : 16.147 126.986 3559 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.73 % Allowed : 13.32 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1821 helix: 2.09 (0.17), residues: 917 sheet: -0.31 (0.34), residues: 230 loop : -0.10 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 541 TYR 0.019 0.001 TYR E 484 PHE 0.014 0.001 PHE F 97 TRP 0.050 0.003 TRP F 66 HIS 0.008 0.001 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16702) covalent geometry : angle 0.65306 / 0.32 (23063) hydrogen bonds : bond 0.04076 / 2.80 ( 844) hydrogen bonds : angle 4.81098 / 3.54 ( 2365) metal coordination : bond 0.00793 / 0.40 ( 4) metal coordination : angle 4.22293 / 2.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8878 (m-30) cc_final: 0.8572 (m-30) REVERT: A 115 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7993 (tp40) REVERT: A 119 ASP cc_start: 0.8978 (m-30) cc_final: 0.8727 (m-30) REVERT: A 142 ASP cc_start: 0.8822 (t0) cc_final: 0.8618 (t0) REVERT: A 160 GLU cc_start: 0.7863 (pt0) cc_final: 0.7596 (pt0) REVERT: B 64 ASP cc_start: 0.8156 (t0) cc_final: 0.7940 (t0) REVERT: B 70 ASP cc_start: 0.9014 (m-30) cc_final: 0.8713 (m-30) REVERT: B 160 GLU cc_start: 0.8670 (mp0) cc_final: 0.8084 (pm20) REVERT: C 211 GLU cc_start: 0.8628 (tp30) cc_final: 0.7978 (tp30) REVERT: C 260 GLN cc_start: 0.8356 (mt0) cc_final: 0.8155 (mt0) REVERT: D 48 GLU cc_start: 0.8872 (tp30) cc_final: 0.8478 (tp30) REVERT: D 70 ASP cc_start: 0.8971 (m-30) cc_final: 0.8688 (m-30) REVERT: E 148 MET cc_start: 0.8384 (mmp) cc_final: 0.8061 (mmp) REVERT: E 178 LEU cc_start: 0.9270 (tp) cc_final: 0.9039 (tp) REVERT: E 182 LEU cc_start: 0.9771 (mt) cc_final: 0.9555 (mt) REVERT: E 209 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8480 (tp30) REVERT: E 248 ASN cc_start: 0.9638 (OUTLIER) cc_final: 0.9386 (p0) REVERT: E 273 HIS cc_start: 0.8952 (m90) cc_final: 0.8740 (m90) REVERT: E 278 MET cc_start: 0.9494 (mpm) cc_final: 0.9067 (mpm) REVERT: E 288 PHE cc_start: 0.8652 (t80) cc_final: 0.8221 (t80) REVERT: E 312 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8836 (tm-30) REVERT: E 353 LYS cc_start: 0.9178 (mmpt) cc_final: 0.8886 (mmmm) REVERT: E 404 PHE cc_start: 0.8300 (m-80) cc_final: 0.7872 (m-10) REVERT: E 426 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9516 (pp) REVERT: E 427 LEU cc_start: 0.9326 (pp) cc_final: 0.8905 (pp) REVERT: F 100 MET cc_start: 0.9573 (mmm) cc_final: 0.9257 (mmm) REVERT: F 101 TRP cc_start: 0.9474 (m100) cc_final: 0.9179 (m100) REVERT: F 166 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8058 (pp) REVERT: F 209 MET cc_start: 0.9038 (mpp) cc_final: 0.8071 (mpt) REVERT: F 257 GLU cc_start: 0.9060 (tp30) cc_final: 0.8717 (mm-30) REVERT: F 314 ASP cc_start: 0.9211 (p0) cc_final: 0.8810 (p0) REVERT: F 371 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8782 (mt-10) outliers start: 26 outliers final: 7 residues processed: 254 average time/residue: 0.5654 time to fit residues: 159.6881 Evaluate side-chains 235 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 157 optimal weight: 0.0060 chunk 156 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 ASN ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN E 540 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.106350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.063550 restraints weight = 34444.412| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.76 r_work: 0.2593 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16706 Z= 0.168 Angle : 0.657 15.863 23066 Z= 0.324 Chirality : 0.043 0.415 2708 Planarity : 0.004 0.045 2618 Dihedral : 16.080 127.565 3559 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.06 % Allowed : 14.91 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1821 helix: 2.08 (0.17), residues: 911 sheet: -0.31 (0.33), residues: 230 loop : -0.11 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 146 TYR 0.015 0.001 TYR E 267 PHE 0.012 0.001 PHE E 481 TRP 0.063 0.003 TRP F 66 HIS 0.007 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16702) covalent geometry : angle 0.65544 / 0.32 (23063) hydrogen bonds : bond 0.03985 / 2.70 ( 844) hydrogen bonds : angle 4.76142 / 3.50 ( 2365) metal coordination : bond 0.01023 / 0.51 ( 4) metal coordination : angle 4.18092 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8936 (m-30) cc_final: 0.8617 (m-30) REVERT: A 115 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7933 (tp-100) REVERT: A 119 ASP cc_start: 0.9037 (m-30) cc_final: 0.8734 (m-30) REVERT: A 142 ASP cc_start: 0.8892 (t0) cc_final: 0.8686 (t0) REVERT: A 160 GLU cc_start: 0.8038 (pt0) cc_final: 0.7793 (pt0) REVERT: B 64 ASP cc_start: 0.8286 (t0) cc_final: 0.8071 (t0) REVERT: B 70 ASP cc_start: 0.9110 (m-30) cc_final: 0.8802 (m-30) REVERT: B 160 GLU cc_start: 0.8719 (mp0) cc_final: 0.8221 (pm20) REVERT: C 211 GLU cc_start: 0.8642 (tp30) cc_final: 0.7891 (tp30) REVERT: D 48 GLU cc_start: 0.8897 (tp30) cc_final: 0.8500 (tp30) REVERT: D 70 ASP cc_start: 0.9044 (m-30) cc_final: 0.8761 (m-30) REVERT: D 86 ASP cc_start: 0.9081 (m-30) cc_final: 0.8801 (m-30) REVERT: E 148 MET cc_start: 0.8443 (mmp) cc_final: 0.8067 (mmp) REVERT: E 178 LEU cc_start: 0.9296 (tp) cc_final: 0.9053 (tp) REVERT: E 182 LEU cc_start: 0.9778 (mt) cc_final: 0.9567 (mt) REVERT: E 273 HIS cc_start: 0.9028 (m90) cc_final: 0.8787 (m90) REVERT: E 353 LYS cc_start: 0.9214 (mmpt) cc_final: 0.8840 (mmmm) REVERT: E 404 PHE cc_start: 0.8239 (m-80) cc_final: 0.7840 (m-10) REVERT: E 415 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8880 (mtmm) REVERT: E 426 LEU cc_start: 0.9779 (OUTLIER) cc_final: 0.9511 (pp) REVERT: E 427 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8993 (pp) REVERT: E 455 TRP cc_start: 0.9309 (m100) cc_final: 0.8984 (m100) REVERT: E 521 GLN cc_start: 0.9726 (tm-30) cc_final: 0.9523 (tm-30) REVERT: F 100 MET cc_start: 0.9542 (mmm) cc_final: 0.9312 (mmm) REVERT: F 107 GLU cc_start: 0.8726 (mm-30) cc_final: 0.7984 (mm-30) REVERT: F 137 TYR cc_start: 0.8715 (t80) cc_final: 0.8272 (t80) REVERT: F 166 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8053 (pp) REVERT: F 209 MET cc_start: 0.9091 (mpp) cc_final: 0.8245 (mpt) REVERT: F 257 GLU cc_start: 0.9065 (tp30) cc_final: 0.8723 (mm-30) REVERT: F 314 ASP cc_start: 0.9199 (p0) cc_final: 0.8805 (p0) REVERT: F 371 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8826 (mt-10) outliers start: 31 outliers final: 11 residues processed: 256 average time/residue: 0.5032 time to fit residues: 144.0434 Evaluate side-chains 238 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 136 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 157 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 44 ASN E 258 GLN ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063987 restraints weight = 34204.918| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.76 r_work: 0.2617 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16706 Z= 0.138 Angle : 0.677 19.073 23066 Z= 0.330 Chirality : 0.044 0.426 2708 Planarity : 0.004 0.045 2618 Dihedral : 16.051 126.958 3559 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 16.25 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1821 helix: 2.00 (0.17), residues: 909 sheet: -0.23 (0.33), residues: 226 loop : -0.15 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 227 TYR 0.014 0.001 TYR E 267 PHE 0.035 0.001 PHE E 481 TRP 0.056 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16702) covalent geometry : angle 0.67502 / 0.33 (23063) hydrogen bonds : bond 0.03830 / 2.60 ( 844) hydrogen bonds : angle 4.71211 / 3.46 ( 2365) metal coordination : bond 0.01005 / 0.51 ( 4) metal coordination : angle 4.03085 / 2.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8916 (m-30) cc_final: 0.8567 (m-30) REVERT: A 115 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7930 (tp-100) REVERT: A 119 ASP cc_start: 0.9034 (m-30) cc_final: 0.8748 (m-30) REVERT: B 41 ASP cc_start: 0.8946 (t0) cc_final: 0.8711 (t70) REVERT: B 64 ASP cc_start: 0.8306 (t0) cc_final: 0.8101 (t0) REVERT: B 70 ASP cc_start: 0.9131 (m-30) cc_final: 0.8829 (m-30) REVERT: B 160 GLU cc_start: 0.8711 (mp0) cc_final: 0.8262 (pm20) REVERT: C 211 GLU cc_start: 0.8610 (tp30) cc_final: 0.7851 (tp30) REVERT: D 48 GLU cc_start: 0.8875 (tp30) cc_final: 0.8474 (tp30) REVERT: D 70 ASP cc_start: 0.9049 (m-30) cc_final: 0.8770 (m-30) REVERT: D 86 ASP cc_start: 0.9100 (m-30) cc_final: 0.8849 (m-30) REVERT: E 148 MET cc_start: 0.8408 (mmp) cc_final: 0.8052 (mmp) REVERT: E 178 LEU cc_start: 0.9288 (tp) cc_final: 0.9036 (tp) REVERT: E 182 LEU cc_start: 0.9788 (mt) cc_final: 0.9580 (mt) REVERT: E 269 GLU cc_start: 0.9314 (pm20) cc_final: 0.8948 (pm20) REVERT: E 273 HIS cc_start: 0.8994 (m90) cc_final: 0.8579 (m90) REVERT: E 288 PHE cc_start: 0.8611 (t80) cc_final: 0.8098 (t80) REVERT: E 312 GLN cc_start: 0.9344 (pp30) cc_final: 0.8966 (tm-30) REVERT: E 353 LYS cc_start: 0.9207 (mmpt) cc_final: 0.8830 (mmmm) REVERT: E 404 PHE cc_start: 0.8170 (m-80) cc_final: 0.7756 (m-10) REVERT: E 426 LEU cc_start: 0.9763 (tt) cc_final: 0.9497 (pp) REVERT: E 427 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8998 (pp) REVERT: E 448 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.8961 (tpt) REVERT: E 455 TRP cc_start: 0.9271 (m100) cc_final: 0.8615 (m100) REVERT: E 521 GLN cc_start: 0.9726 (tm-30) cc_final: 0.9442 (tm-30) REVERT: E 564 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9081 (mm) REVERT: F 66 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7513 (p90) REVERT: F 101 TRP cc_start: 0.9358 (m100) cc_final: 0.9103 (m100) REVERT: F 166 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8056 (pp) REVERT: F 209 MET cc_start: 0.9058 (mpp) cc_final: 0.8145 (mpt) REVERT: F 257 GLU cc_start: 0.9038 (tp30) cc_final: 0.8694 (mm-30) REVERT: F 314 ASP cc_start: 0.9166 (p0) cc_final: 0.8793 (p0) REVERT: F 371 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8839 (mt-10) outliers start: 31 outliers final: 15 residues processed: 251 average time/residue: 0.5155 time to fit residues: 144.1284 Evaluate side-chains 238 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 66 TRP Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 77 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 171 optimal weight: 2.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN F 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.063332 restraints weight = 34207.376| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.79 r_work: 0.2583 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16706 Z= 0.181 Angle : 0.676 16.962 23066 Z= 0.332 Chirality : 0.044 0.415 2708 Planarity : 0.004 0.045 2618 Dihedral : 16.042 127.981 3559 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.20 % Allowed : 17.18 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1821 helix: 1.99 (0.17), residues: 909 sheet: -0.21 (0.33), residues: 225 loop : -0.17 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 227 TYR 0.012 0.001 TYR E 484 PHE 0.021 0.001 PHE F 97 TRP 0.050 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (16702) covalent geometry : angle 0.67432 / 0.33 (23063) hydrogen bonds : bond 0.03862 / 2.62 ( 844) hydrogen bonds : angle 4.72495 / 3.48 ( 2365) metal coordination : bond 0.01282 / 0.64 ( 4) metal coordination : angle 4.15731 / 2.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8946 (m-30) cc_final: 0.8623 (m-30) REVERT: A 115 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7914 (tp-100) REVERT: A 119 ASP cc_start: 0.8999 (m-30) cc_final: 0.8718 (m-30) REVERT: B 64 ASP cc_start: 0.8335 (t0) cc_final: 0.8116 (t0) REVERT: B 70 ASP cc_start: 0.9154 (m-30) cc_final: 0.8847 (m-30) REVERT: B 160 GLU cc_start: 0.8741 (mp0) cc_final: 0.8227 (pm20) REVERT: C 211 GLU cc_start: 0.8609 (tp30) cc_final: 0.7841 (tp30) REVERT: D 48 GLU cc_start: 0.8888 (tp30) cc_final: 0.8498 (tp30) REVERT: D 70 ASP cc_start: 0.9068 (m-30) cc_final: 0.8792 (m-30) REVERT: D 86 ASP cc_start: 0.9083 (m-30) cc_final: 0.8788 (m-30) REVERT: D 135 GLU cc_start: 0.9077 (tp30) cc_final: 0.8823 (mm-30) REVERT: E 148 MET cc_start: 0.8385 (mmp) cc_final: 0.8044 (mmp) REVERT: E 178 LEU cc_start: 0.9315 (tp) cc_final: 0.9070 (tp) REVERT: E 182 LEU cc_start: 0.9810 (mt) cc_final: 0.9607 (mt) REVERT: E 273 HIS cc_start: 0.9052 (m90) cc_final: 0.8625 (m170) REVERT: E 288 PHE cc_start: 0.8675 (t80) cc_final: 0.8154 (t80) REVERT: E 404 PHE cc_start: 0.8227 (m-80) cc_final: 0.7829 (m-10) REVERT: E 415 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8841 (mtmm) REVERT: E 426 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9500 (pp) REVERT: E 427 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9011 (pp) REVERT: E 448 MET cc_start: 0.9496 (OUTLIER) cc_final: 0.9202 (tpt) REVERT: E 521 GLN cc_start: 0.9746 (tm-30) cc_final: 0.9450 (tm-30) REVERT: F 95 ARG cc_start: 0.8840 (mmt180) cc_final: 0.8572 (mmt180) REVERT: F 107 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7915 (mm-30) REVERT: F 166 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8083 (pp) REVERT: F 209 MET cc_start: 0.9092 (mpp) cc_final: 0.8084 (mpt) REVERT: F 257 GLU cc_start: 0.9093 (tp30) cc_final: 0.8740 (mm-30) REVERT: F 314 ASP cc_start: 0.9185 (p0) cc_final: 0.8783 (p0) REVERT: F 371 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8856 (mt-10) outliers start: 33 outliers final: 14 residues processed: 233 average time/residue: 0.4826 time to fit residues: 127.0170 Evaluate side-chains 224 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.0000 chunk 178 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN C 115 GLN C 260 GLN D 44 ASN E 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.063381 restraints weight = 34235.554| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.78 r_work: 0.2590 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16706 Z= 0.168 Angle : 0.684 16.515 23066 Z= 0.335 Chirality : 0.044 0.394 2708 Planarity : 0.004 0.043 2618 Dihedral : 16.043 128.076 3559 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 17.71 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1821 helix: 1.96 (0.17), residues: 910 sheet: -0.23 (0.33), residues: 225 loop : -0.22 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 146 TYR 0.016 0.001 TYR F 137 PHE 0.036 0.001 PHE E 481 TRP 0.055 0.004 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16702) covalent geometry : angle 0.68190 / 0.33 (23063) hydrogen bonds : bond 0.03767 / 2.56 ( 844) hydrogen bonds : angle 4.71792 / 3.47 ( 2365) metal coordination : bond 0.01606 / 0.81 ( 4) metal coordination : angle 4.44646 / 2.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8990 (m-30) cc_final: 0.8681 (m-30) REVERT: B 64 ASP cc_start: 0.8328 (t0) cc_final: 0.8114 (t0) REVERT: B 70 ASP cc_start: 0.9144 (m-30) cc_final: 0.8857 (m-30) REVERT: B 118 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9172 (mp) REVERT: B 160 GLU cc_start: 0.8740 (mp0) cc_final: 0.8227 (pm20) REVERT: C 211 GLU cc_start: 0.8587 (tp30) cc_final: 0.7809 (tp30) REVERT: C 229 ASP cc_start: 0.8971 (t0) cc_final: 0.8748 (t0) REVERT: D 48 GLU cc_start: 0.8869 (tp30) cc_final: 0.8486 (tp30) REVERT: D 70 ASP cc_start: 0.9074 (m-30) cc_final: 0.8802 (m-30) REVERT: D 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8803 (m-30) REVERT: D 135 GLU cc_start: 0.9081 (tp30) cc_final: 0.8842 (mm-30) REVERT: E 148 MET cc_start: 0.8382 (mmp) cc_final: 0.8032 (mmp) REVERT: E 178 LEU cc_start: 0.9323 (tp) cc_final: 0.9093 (tp) REVERT: E 182 LEU cc_start: 0.9810 (mt) cc_final: 0.9606 (mt) REVERT: E 266 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9257 (tm) REVERT: E 269 GLU cc_start: 0.9301 (pm20) cc_final: 0.8905 (pm20) REVERT: E 273 HIS cc_start: 0.9063 (m90) cc_final: 0.8386 (m170) REVERT: E 288 PHE cc_start: 0.8666 (t80) cc_final: 0.8112 (t80) REVERT: E 353 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8824 (mttt) REVERT: E 404 PHE cc_start: 0.8212 (m-80) cc_final: 0.7827 (m-10) REVERT: E 426 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9498 (pp) REVERT: E 427 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8989 (pp) REVERT: E 448 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9153 (tpt) REVERT: E 521 GLN cc_start: 0.9748 (tm-30) cc_final: 0.9463 (tm-30) REVERT: E 564 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9070 (mm) REVERT: F 95 ARG cc_start: 0.8853 (mmt180) cc_final: 0.8649 (mmt180) REVERT: F 166 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (pp) REVERT: F 209 MET cc_start: 0.9017 (mpp) cc_final: 0.8104 (mpt) REVERT: F 257 GLU cc_start: 0.9077 (tp30) cc_final: 0.8727 (mm-30) REVERT: F 314 ASP cc_start: 0.9169 (p0) cc_final: 0.8771 (p0) REVERT: F 371 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8847 (mt-10) outliers start: 30 outliers final: 17 residues processed: 231 average time/residue: 0.4809 time to fit residues: 124.9684 Evaluate side-chains 229 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 183 optimal weight: 10.0000 chunk 122 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 188 optimal weight: 50.0000 chunk 156 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.106462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063533 restraints weight = 34222.726| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.81 r_work: 0.2598 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16706 Z= 0.149 Angle : 0.683 15.612 23066 Z= 0.334 Chirality : 0.045 0.469 2708 Planarity : 0.004 0.054 2618 Dihedral : 15.998 127.988 3559 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.33 % Allowed : 18.24 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1821 helix: 1.93 (0.17), residues: 910 sheet: -0.18 (0.33), residues: 223 loop : -0.25 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 146 TYR 0.011 0.001 TYR E 484 PHE 0.010 0.001 PHE E 481 TRP 0.063 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16702) covalent geometry : angle 0.68160 / 0.33 (23063) hydrogen bonds : bond 0.03669 / 2.49 ( 844) hydrogen bonds : angle 4.67485 / 3.45 ( 2365) metal coordination : bond 0.01204 / 0.61 ( 4) metal coordination : angle 4.14251 / 2.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8850 (m-30) cc_final: 0.8586 (m-30) REVERT: A 119 ASP cc_start: 0.8997 (m-30) cc_final: 0.8690 (m-30) REVERT: B 64 ASP cc_start: 0.8336 (t0) cc_final: 0.8119 (t0) REVERT: B 70 ASP cc_start: 0.9129 (m-30) cc_final: 0.8837 (m-30) REVERT: B 160 GLU cc_start: 0.8734 (mp0) cc_final: 0.8233 (pm20) REVERT: C 86 ASP cc_start: 0.9018 (m-30) cc_final: 0.8781 (m-30) REVERT: C 211 GLU cc_start: 0.8577 (tp30) cc_final: 0.7803 (tp30) REVERT: C 229 ASP cc_start: 0.8992 (t0) cc_final: 0.8770 (t0) REVERT: D 48 GLU cc_start: 0.8857 (tp30) cc_final: 0.8479 (tp30) REVERT: D 70 ASP cc_start: 0.9076 (m-30) cc_final: 0.8814 (m-30) REVERT: D 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8806 (m-30) REVERT: D 135 GLU cc_start: 0.9086 (tp30) cc_final: 0.8866 (mm-30) REVERT: E 148 MET cc_start: 0.8390 (mmp) cc_final: 0.8040 (mmp) REVERT: E 178 LEU cc_start: 0.9367 (tp) cc_final: 0.9092 (tp) REVERT: E 182 LEU cc_start: 0.9814 (mt) cc_final: 0.9609 (mt) REVERT: E 266 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9224 (tm) REVERT: E 273 HIS cc_start: 0.9089 (m90) cc_final: 0.8647 (m170) REVERT: E 288 PHE cc_start: 0.8619 (t80) cc_final: 0.8066 (t80) REVERT: E 353 LYS cc_start: 0.9221 (mmpt) cc_final: 0.8821 (mttt) REVERT: E 404 PHE cc_start: 0.8208 (m-80) cc_final: 0.7814 (m-10) REVERT: E 426 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9502 (pp) REVERT: E 427 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9028 (pp) REVERT: E 448 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9176 (tpt) REVERT: E 521 GLN cc_start: 0.9742 (tm-30) cc_final: 0.9473 (tm-30) REVERT: E 564 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9086 (mm) REVERT: F 95 ARG cc_start: 0.8806 (mmt180) cc_final: 0.8587 (mmt180) REVERT: F 107 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: F 121 MET cc_start: 0.8751 (mmm) cc_final: 0.8377 (mtm) REVERT: F 166 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8077 (pp) REVERT: F 257 GLU cc_start: 0.9078 (tp30) cc_final: 0.8729 (mm-30) REVERT: F 314 ASP cc_start: 0.9160 (p0) cc_final: 0.8755 (p0) REVERT: F 371 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8851 (mt-10) outliers start: 35 outliers final: 18 residues processed: 231 average time/residue: 0.5187 time to fit residues: 134.9340 Evaluate side-chains 231 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN D 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.063769 restraints weight = 34003.588| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.75 r_work: 0.2600 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16706 Z= 0.165 Angle : 0.712 16.632 23066 Z= 0.349 Chirality : 0.045 0.365 2708 Planarity : 0.004 0.044 2618 Dihedral : 15.970 128.321 3559 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.86 % Allowed : 18.97 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1821 helix: 1.92 (0.17), residues: 910 sheet: -0.17 (0.33), residues: 223 loop : -0.28 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 146 TYR 0.012 0.001 TYR E 484 PHE 0.034 0.001 PHE E 481 TRP 0.073 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (16702) covalent geometry : angle 0.71022 / 0.35 (23063) hydrogen bonds : bond 0.03745 / 2.54 ( 844) hydrogen bonds : angle 4.71175 / 3.47 ( 2365) metal coordination : bond 0.01348 / 0.68 ( 4) metal coordination : angle 4.15741 / 2.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8843 (m-30) cc_final: 0.8576 (m-30) REVERT: A 119 ASP cc_start: 0.8989 (m-30) cc_final: 0.8675 (m-30) REVERT: B 64 ASP cc_start: 0.8335 (t0) cc_final: 0.8117 (t0) REVERT: B 70 ASP cc_start: 0.9108 (m-30) cc_final: 0.8814 (m-30) REVERT: B 160 GLU cc_start: 0.8728 (mp0) cc_final: 0.8224 (pm20) REVERT: C 86 ASP cc_start: 0.9029 (m-30) cc_final: 0.8775 (m-30) REVERT: C 211 GLU cc_start: 0.8549 (tp30) cc_final: 0.7772 (tp30) REVERT: C 229 ASP cc_start: 0.9005 (t0) cc_final: 0.8767 (t0) REVERT: D 48 GLU cc_start: 0.8854 (tp30) cc_final: 0.8473 (tp30) REVERT: D 70 ASP cc_start: 0.9080 (m-30) cc_final: 0.8805 (m-30) REVERT: D 86 ASP cc_start: 0.9070 (m-30) cc_final: 0.8810 (m-30) REVERT: D 135 GLU cc_start: 0.9087 (tp30) cc_final: 0.8846 (mm-30) REVERT: E 148 MET cc_start: 0.8377 (mmp) cc_final: 0.8031 (mmp) REVERT: E 178 LEU cc_start: 0.9369 (tp) cc_final: 0.9085 (tp) REVERT: E 182 LEU cc_start: 0.9817 (mt) cc_final: 0.9605 (mt) REVERT: E 273 HIS cc_start: 0.9067 (m90) cc_final: 0.8618 (m170) REVERT: E 288 PHE cc_start: 0.8641 (t80) cc_final: 0.8124 (t80) REVERT: E 353 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8836 (mttt) REVERT: E 404 PHE cc_start: 0.8213 (m-80) cc_final: 0.7819 (m-10) REVERT: E 426 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9487 (pp) REVERT: E 427 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8987 (pp) REVERT: E 448 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9169 (tpt) REVERT: E 514 GLN cc_start: 0.9410 (tt0) cc_final: 0.9106 (mt0) REVERT: E 521 GLN cc_start: 0.9751 (tm-30) cc_final: 0.9443 (tm-30) REVERT: E 564 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9089 (mm) REVERT: F 95 ARG cc_start: 0.8824 (mmt180) cc_final: 0.8593 (mmt180) REVERT: F 107 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: F 166 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8073 (pp) REVERT: F 257 GLU cc_start: 0.9081 (tp30) cc_final: 0.8731 (mm-30) REVERT: F 314 ASP cc_start: 0.9162 (p0) cc_final: 0.8750 (p0) REVERT: F 371 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8835 (mt-10) outliers start: 28 outliers final: 15 residues processed: 222 average time/residue: 0.4621 time to fit residues: 115.4659 Evaluate side-chains 223 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 171 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN D 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.064065 restraints weight = 34243.470| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.82 r_work: 0.2612 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16706 Z= 0.139 Angle : 0.722 17.021 23066 Z= 0.351 Chirality : 0.047 0.644 2708 Planarity : 0.004 0.059 2618 Dihedral : 15.942 127.913 3559 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 19.04 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1821 helix: 1.90 (0.17), residues: 909 sheet: -0.23 (0.33), residues: 223 loop : -0.24 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 146 TYR 0.012 0.001 TYR E 484 PHE 0.011 0.001 PHE B 114 TRP 0.076 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16702) covalent geometry : angle 0.72114 / 0.35 (23063) hydrogen bonds : bond 0.03649 / 2.48 ( 844) hydrogen bonds : angle 4.69223 / 3.47 ( 2365) metal coordination : bond 0.01132 / 0.57 ( 4) metal coordination : angle 3.85325 / 1.94 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8855 (m-30) cc_final: 0.8591 (m-30) REVERT: A 119 ASP cc_start: 0.8990 (m-30) cc_final: 0.8781 (m-30) REVERT: B 41 ASP cc_start: 0.8957 (t0) cc_final: 0.8685 (t70) REVERT: B 70 ASP cc_start: 0.9103 (m-30) cc_final: 0.8828 (m-30) REVERT: B 160 GLU cc_start: 0.8691 (mp0) cc_final: 0.8207 (pm20) REVERT: B 259 MET cc_start: 0.9505 (mmm) cc_final: 0.9262 (mmm) REVERT: C 86 ASP cc_start: 0.9034 (m-30) cc_final: 0.8772 (m-30) REVERT: C 211 GLU cc_start: 0.8553 (tp30) cc_final: 0.7785 (tp30) REVERT: C 229 ASP cc_start: 0.8990 (t0) cc_final: 0.8771 (t0) REVERT: D 48 GLU cc_start: 0.8845 (tp30) cc_final: 0.8471 (tp30) REVERT: D 70 ASP cc_start: 0.9076 (m-30) cc_final: 0.8813 (m-30) REVERT: D 86 ASP cc_start: 0.9069 (m-30) cc_final: 0.8768 (m-30) REVERT: D 135 GLU cc_start: 0.9082 (tp30) cc_final: 0.8867 (mm-30) REVERT: E 148 MET cc_start: 0.8383 (mmp) cc_final: 0.8042 (mmp) REVERT: E 178 LEU cc_start: 0.9352 (tp) cc_final: 0.9052 (tp) REVERT: E 182 LEU cc_start: 0.9816 (mt) cc_final: 0.9602 (mt) REVERT: E 273 HIS cc_start: 0.9078 (m90) cc_final: 0.8599 (m170) REVERT: E 288 PHE cc_start: 0.8624 (t80) cc_final: 0.8100 (t80) REVERT: E 353 LYS cc_start: 0.9218 (mmpt) cc_final: 0.8837 (mttt) REVERT: E 404 PHE cc_start: 0.8229 (m-80) cc_final: 0.7804 (m-10) REVERT: E 426 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9498 (pp) REVERT: E 427 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9101 (pp) REVERT: E 448 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9146 (tpt) REVERT: E 514 GLN cc_start: 0.9403 (tt0) cc_final: 0.9101 (mt0) REVERT: E 521 GLN cc_start: 0.9743 (tm-30) cc_final: 0.9463 (tm-30) REVERT: E 564 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9096 (mm) REVERT: F 95 ARG cc_start: 0.8822 (mmt180) cc_final: 0.8610 (mmt180) REVERT: F 107 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: F 121 MET cc_start: 0.8687 (mmm) cc_final: 0.8337 (mtm) REVERT: F 257 GLU cc_start: 0.9059 (tp30) cc_final: 0.8711 (mm-30) REVERT: F 314 ASP cc_start: 0.9158 (p0) cc_final: 0.8753 (p0) REVERT: F 371 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8833 (mt-10) outliers start: 28 outliers final: 15 residues processed: 228 average time/residue: 0.5003 time to fit residues: 128.4810 Evaluate side-chains 227 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 92 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 0.0020 chunk 172 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN D 44 ASN E 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.107630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.064921 restraints weight = 34118.582| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.82 r_work: 0.2618 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16706 Z= 0.133 Angle : 0.719 16.808 23066 Z= 0.353 Chirality : 0.046 0.539 2708 Planarity : 0.004 0.044 2618 Dihedral : 15.891 127.584 3559 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.40 % Allowed : 19.64 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1821 helix: 1.89 (0.17), residues: 910 sheet: -0.23 (0.33), residues: 223 loop : -0.25 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 146 TYR 0.017 0.001 TYR E 545 PHE 0.035 0.001 PHE E 481 TRP 0.091 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16702) covalent geometry : angle 0.71802 / 0.35 (23063) hydrogen bonds : bond 0.03613 / 2.46 ( 844) hydrogen bonds : angle 4.66290 / 3.45 ( 2365) metal coordination : bond 0.00956 / 0.48 ( 4) metal coordination : angle 3.62073 / 1.83 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5483.07 seconds wall clock time: 94 minutes 20.07 seconds (5660.07 seconds total)