Starting phenix.real_space_refine on Sun Jul 5 23:48:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1w_15091/07_2026/8a1w_15091_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1w_15091/07_2026/8a1w_15091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a1w_15091/07_2026/8a1w_15091_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1w_15091/07_2026/8a1w_15091_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a1w_15091/07_2026/8a1w_15091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1w_15091/07_2026/8a1w_15091.map" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 8 5.49 5 S 90 5.16 5 Na 2 4.78 5 C 9803 2.51 5 N 2437 2.21 5 O 3052 1.98 5 H 14776 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30172 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6877 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 6346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6346 Classifications: {'peptide': 412} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 395} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3154 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3041 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "F" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6239 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 280 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3PE': 3, 'FMN': 1, 'LMT': 2, 'RBF': 1, 'UQ1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18661 SG CYS D 112 67.213 82.111 58.874 1.00 24.95 S ATOM 20553 SG CYS E 26 64.800 82.618 61.643 1.00 5.84 S ATOM 17328 SG CYS D 29 67.684 83.714 65.347 1.00 23.84 S ATOM 22058 SG CYS E 120 70.535 84.585 62.993 1.00 23.62 S ATOM 24222 SG CYS F 70 53.201 67.528 38.642 1.00 11.37 S ATOM 24271 SG CYS F 76 51.055 64.749 37.261 1.00 12.01 S ATOM 24305 SG CYS F 79 55.886 61.678 37.911 1.00 16.45 S ATOM 24789 SG CYS F 111 57.219 64.963 39.196 1.00 14.30 S Time building chain proxies: 4.86, per 1000 atoms: 0.16 Number of scatterers: 30172 At special positions: 0 Unit cell: (113.15, 135.05, 131.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 8 15.00 Na 2 11.00 O 3052 8.00 N 2437 7.00 C 9803 6.00 H 14776 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 693.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 26 " pdb="FE1 FES E1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES E1001 " - pdb=" SG CYS D 29 " pdb="FE2 FES E1001 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 14 sheets defined 54.4% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.545A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.502A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.678A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.567A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.633A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 4.538A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.672A pdb=" N ALA B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.537A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.661A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.704A pdb=" N ILE B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.766A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.706A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'C' and resid 8 through 54 removed outlier: 4.812A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.813A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 9 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.543A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.515A pdb=" N SER D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.534A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.532A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.342A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 30 through 33 removed outlier: 4.214A pdb=" N LYS E 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 79 through 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 132 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 3 through 30 Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.634A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.670A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.057A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.597A pdb=" N TYR F 248 " --> pdb=" O GLN F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 removed outlier: 4.344A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 8.005A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.643A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.151A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.175A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 126 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 14.212A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 49 removed outlier: 5.262A pdb=" N LYS F 45 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE F 39 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER F 85 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 223 through 229 Processing sheet with id=AB3, first strand: chain 'F' and resid 208 through 213 Processing sheet with id=AB4, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB5, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.420A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU F 402 " --> pdb=" O CYS F 373 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14763 1.11 - 1.38: 5837 1.38 - 1.66: 9469 1.66 - 1.93: 151 1.93 - 2.20: 8 Bond restraints: 30228 Sorted by residual: bond pdb=" N ASP A 212 " pdb=" H ASP A 212 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" N LEU A 219 " pdb=" H LEU A 219 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N HIS A 215 " pdb=" H HIS A 215 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N GLY A 213 " pdb=" H GLY A 213 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" N ALA A 217 " pdb=" H ALA A 217 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 54169 1.91 - 3.83: 314 3.83 - 5.74: 54 5.74 - 7.65: 16 7.65 - 9.56: 11 Bond angle restraints: 54564 Sorted by residual: angle pdb=" N PRO A 216 " pdb=" CA PRO A 216 " pdb=" CB PRO A 216 " ideal model delta sigma weight residual 102.60 96.86 5.74 1.10e+00 8.26e-01 2.73e+01 angle pdb=" C ASP A 212 " pdb=" CA ASP A 212 " pdb=" CB ASP A 212 " ideal model delta sigma weight residual 109.66 118.57 -8.91 1.94e+00 2.66e-01 2.11e+01 angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" CB PHE A 136 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" C PRO A 216 " pdb=" N ALA A 217 " pdb=" CA ALA A 217 " ideal model delta sigma weight residual 120.60 126.58 -5.98 1.60e+00 3.91e-01 1.40e+01 angle pdb=" C SER B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta sigma weight residual 121.70 127.65 -5.95 1.80e+00 3.09e-01 1.09e+01 ... (remaining 54559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 13491 24.56 - 49.11: 671 49.11 - 73.67: 220 73.67 - 98.22: 30 98.22 - 122.78: 6 Dihedral angle restraints: 14418 sinusoidal: 7964 harmonic: 6454 Sorted by residual: dihedral pdb=" CA PRO A 214 " pdb=" C PRO A 214 " pdb=" N HIS A 215 " pdb=" CA HIS A 215 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" C2B LMT B 503 " pdb=" C1B LMT B 503 " pdb=" O5B LMT B 503 " pdb=" C5B LMT B 503 " ideal model delta sinusoidal sigma weight residual -57.12 65.66 -122.78 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C5B LMT B 503 " pdb=" C1B LMT B 503 " pdb=" O5B LMT B 503 " pdb=" O1B LMT B 503 " ideal model delta sinusoidal sigma weight residual 295.61 173.43 122.18 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 14415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1923 0.047 - 0.094: 304 0.094 - 0.141: 112 0.141 - 0.188: 1 0.188 - 0.235: 9 Chirality restraints: 2349 Sorted by residual: chirality pdb=" C4' LMT B 504 " pdb=" C3' LMT B 504 " pdb=" C5' LMT B 504 " pdb=" O1B LMT B 504 " both_signs ideal model delta sigma weight residual False -2.55 -2.79 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C4' LMT B 503 " pdb=" C3' LMT B 503 " pdb=" C5' LMT B 503 " pdb=" O1B LMT B 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C5' LMT D 302 " pdb=" C4' LMT D 302 " pdb=" C6' LMT D 302 " pdb=" O5' LMT D 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2346 not shown) Planarity restraints: 4418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 506 " 0.016 2.00e-02 2.50e+03 4.40e-02 5.81e+01 pdb=" C2 UQ1 B 506 " 0.019 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 506 " -0.031 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 506 " 0.011 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 506 " 0.013 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 506 " -0.022 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 506 " -0.084 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 506 " 0.048 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 506 " 0.035 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 506 " 0.048 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 506 " -0.083 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 506 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 211 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C PHE A 211 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE A 211 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP A 212 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 212 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C ASP A 212 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 212 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 213 " -0.017 2.00e-02 2.50e+03 ... (remaining 4415 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1284 2.18 - 2.78: 60568 2.78 - 3.39: 88533 3.39 - 3.99: 117511 3.99 - 4.60: 180344 Nonbonded interactions: 448240 Sorted by model distance: nonbonded pdb=" O TRP C 238 " pdb=" H PHE C 244 " model vdw 1.572 2.450 nonbonded pdb=" O PRO E 114 " pdb=" HG1 THR E 117 " model vdw 1.593 2.450 nonbonded pdb=" O ASP C 77 " pdb=" H GLY C 81 " model vdw 1.615 2.450 nonbonded pdb=" OE1 GLU F 371 " pdb=" H GLU F 371 " model vdw 1.617 2.450 nonbonded pdb="HE22 GLN A 242 " pdb=" O VAL A 261 " model vdw 1.628 2.450 ... (remaining 448235 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.094 15462 Z= 0.219 Angle : 0.621 22.033 20935 Z= 0.273 Chirality : 0.041 0.235 2349 Planarity : 0.003 0.050 2601 Dihedral : 16.079 122.779 5817 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.32 % Allowed : 10.78 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % 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: 1.65 (0.20), residues: 1896 helix: 1.92 (0.18), residues: 871 sheet: 0.39 (0.40), residues: 181 loop : 0.51 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.007 0.001 TYR F 217 PHE 0.011 0.001 PHE B 213 TRP 0.014 0.001 TRP B 226 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (15452) covalent geometry : angle 0.58669 / 0.27 (20923) hydrogen bonds : bond 0.21094 / 14.20 ( 761) hydrogen bonds : angle 7.32029 / 5.15 ( 2151) metal coordination : bond 0.00917 / 0.41 ( 8) metal coordination : angle 8.58077 / 4.98 ( 12) Misc. bond : bond 0.04290 / 2.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 280 time to evaluate : 0.857 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 1 MET cc_start: 0.6738 (mtp) cc_final: 0.6493 (ttm) REVERT: A 39 MET cc_start: 0.8820 (tmm) cc_final: 0.8518 (tmm) REVERT: A 401 ASP cc_start: 0.7658 (t0) cc_final: 0.7437 (t0) REVERT: A 433 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7560 (tp40) REVERT: C 188 GLN cc_start: 0.7261 (tt0) cc_final: 0.7060 (tt0) REVERT: D 115 MET cc_start: 0.7468 (mmm) cc_final: 0.7181 (mmm) REVERT: E 10 LYS cc_start: 0.6734 (mtmm) cc_final: 0.6352 (mptt) REVERT: F 331 ASP cc_start: 0.3747 (p0) cc_final: 0.2892 (m-30) outliers start: 5 outliers final: 4 residues processed: 285 average time/residue: 1.1871 time to fit residues: 377.3536 Evaluate side-chains 189 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 244 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 249 GLN B 267 ASN C 79 ASN C 188 GLN D 64 ASN E 92 GLN F 112 GLN F 330 ASN F 336 HIS ** F 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110709 restraints weight = 49468.699| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.66 r_work: 0.3010 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15462 Z= 0.265 Angle : 0.658 11.924 20935 Z= 0.339 Chirality : 0.046 0.359 2349 Planarity : 0.005 0.068 2601 Dihedral : 12.156 94.866 2469 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 14.96 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 1896 helix: 1.26 (0.17), residues: 899 sheet: 0.22 (0.40), residues: 160 loop : 0.14 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 199 TYR 0.014 0.002 TYR A 315 PHE 0.020 0.002 PHE D 50 TRP 0.017 0.002 TRP B 70 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 (15452) covalent geometry : angle 0.64242 / 0.34 (20923) hydrogen bonds : bond 0.06703 / 4.49 ( 761) hydrogen bonds : angle 5.74286 / 4.05 ( 2151) metal coordination : bond 0.01037 / 0.46 ( 8) metal coordination : angle 6.06494 / 3.59 ( 12) Misc. bond : bond 0.00210 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.853 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 1 MET cc_start: 0.7273 (mtp) cc_final: 0.7014 (ttm) REVERT: A 39 MET cc_start: 0.8862 (tmm) cc_final: 0.8488 (tmm) REVERT: A 46 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7665 (mtp85) REVERT: C 20 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7414 (mp) REVERT: C 105 LYS cc_start: 0.7300 (tptt) cc_final: 0.6985 (ttmm) REVERT: C 156 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: D 115 MET cc_start: 0.7834 (mmm) cc_final: 0.7530 (mmm) REVERT: E 10 LYS cc_start: 0.6747 (mtmm) cc_final: 0.5757 (mptt) REVERT: E 99 ASP cc_start: 0.4938 (t0) cc_final: 0.4657 (t70) REVERT: F 375 TYR cc_start: 0.6186 (m-80) cc_final: 0.5855 (m-80) outliers start: 35 outliers final: 19 residues processed: 206 average time/residue: 1.0787 time to fit residues: 251.0924 Evaluate side-chains 186 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN B 243 GLN B 267 ASN D 64 ASN E 57 ASN F 356 HIS F 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112368 restraints weight = 49761.815| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.59 r_work: 0.3052 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15462 Z= 0.158 Angle : 0.559 11.730 20935 Z= 0.284 Chirality : 0.043 0.402 2349 Planarity : 0.004 0.055 2601 Dihedral : 11.046 89.943 2469 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.18 % Allowed : 15.73 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1896 helix: 1.22 (0.17), residues: 901 sheet: 0.02 (0.40), residues: 158 loop : 0.04 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 199 TYR 0.015 0.001 TYR D 141 PHE 0.017 0.001 PHE B 213 TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (15452) covalent geometry : angle 0.54506 / 0.28 (20923) hydrogen bonds : bond 0.05525 / 3.69 ( 761) hydrogen bonds : angle 5.33992 / 3.76 ( 2151) metal coordination : bond 0.00797 / 0.38 ( 8) metal coordination : angle 5.13784 / 2.97 ( 12) Misc. bond : bond 0.00116 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.851 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 1 MET cc_start: 0.7135 (mtp) cc_final: 0.6892 (ttm) REVERT: A 39 MET cc_start: 0.8871 (tmm) cc_final: 0.8384 (tmm) REVERT: A 46 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7715 (ptp90) REVERT: A 260 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8244 (mtp85) REVERT: C 20 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7415 (mp) REVERT: C 105 LYS cc_start: 0.7357 (tptt) cc_final: 0.6955 (ttmm) REVERT: C 156 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: D 115 MET cc_start: 0.7843 (mmm) cc_final: 0.7529 (mmm) REVERT: E 10 LYS cc_start: 0.6786 (mtmm) cc_final: 0.5816 (mptt) REVERT: F 160 VAL cc_start: 0.0885 (t) cc_final: 0.0631 (m) REVERT: F 258 CYS cc_start: 0.4182 (OUTLIER) cc_final: 0.2754 (p) REVERT: F 288 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5415 (tmt) REVERT: F 309 TYR cc_start: 0.2520 (t80) cc_final: 0.2243 (t80) REVERT: F 330 ASN cc_start: 0.3250 (OUTLIER) cc_final: 0.3007 (m-40) REVERT: F 375 TYR cc_start: 0.6203 (m-80) cc_final: 0.5951 (m-80) outliers start: 34 outliers final: 20 residues processed: 199 average time/residue: 1.0597 time to fit residues: 237.2233 Evaluate side-chains 186 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 149 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 171 optimal weight: 0.0030 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN D 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111982 restraints weight = 49469.312| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.54 r_work: 0.3048 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15462 Z= 0.165 Angle : 0.561 10.938 20935 Z= 0.284 Chirality : 0.043 0.446 2349 Planarity : 0.004 0.057 2601 Dihedral : 10.395 89.719 2468 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.37 % Allowed : 16.82 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1896 helix: 1.22 (0.17), residues: 899 sheet: -0.11 (0.39), residues: 157 loop : -0.02 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 199 TYR 0.013 0.001 TYR D 141 PHE 0.024 0.001 PHE D 50 TRP 0.017 0.002 TRP B 103 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (15452) covalent geometry : angle 0.54769 / 0.28 (20923) hydrogen bonds : bond 0.05114 / 3.41 ( 761) hydrogen bonds : angle 5.17379 / 3.65 ( 2151) metal coordination : bond 0.00970 / 0.46 ( 8) metal coordination : angle 5.13140 / 2.98 ( 12) Misc. bond : bond 0.00113 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7106 (mtp) cc_final: 0.6877 (ttm) REVERT: A 39 MET cc_start: 0.8847 (tmm) cc_final: 0.8339 (tmm) REVERT: A 46 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7749 (ptp90) REVERT: A 260 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (mtp85) REVERT: C 20 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7417 (mp) REVERT: C 105 LYS cc_start: 0.7227 (tptt) cc_final: 0.6939 (ttmm) REVERT: C 216 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7711 (m170) REVERT: D 115 MET cc_start: 0.7852 (mmm) cc_final: 0.7549 (mmm) REVERT: E 10 LYS cc_start: 0.6776 (mtmm) cc_final: 0.5770 (mptt) REVERT: F 160 VAL cc_start: 0.0763 (t) cc_final: 0.0516 (m) REVERT: F 258 CYS cc_start: 0.4185 (OUTLIER) cc_final: 0.2968 (p) REVERT: F 288 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5684 (tmt) REVERT: F 330 ASN cc_start: 0.3398 (OUTLIER) cc_final: 0.3118 (m-40) REVERT: F 375 TYR cc_start: 0.6246 (m-80) cc_final: 0.6013 (m-80) outliers start: 37 outliers final: 19 residues processed: 192 average time/residue: 1.0796 time to fit residues: 233.3639 Evaluate side-chains 181 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111599 restraints weight = 49924.630| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.69 r_work: 0.3025 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15462 Z= 0.168 Angle : 0.561 11.031 20935 Z= 0.284 Chirality : 0.043 0.447 2349 Planarity : 0.004 0.056 2601 Dihedral : 10.074 88.681 2465 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.37 % Allowed : 16.94 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1896 helix: 1.21 (0.17), residues: 900 sheet: -0.29 (0.38), residues: 163 loop : -0.04 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 85 TYR 0.011 0.001 TYR D 141 PHE 0.019 0.002 PHE F 267 TRP 0.017 0.002 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (15452) covalent geometry : angle 0.54704 / 0.28 (20923) hydrogen bonds : bond 0.05040 / 3.37 ( 761) hydrogen bonds : angle 5.10590 / 3.59 ( 2151) metal coordination : bond 0.00906 / 0.43 ( 8) metal coordination : angle 5.13608 / 2.98 ( 12) Misc. bond : bond 0.00110 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7122 (mtp) cc_final: 0.6900 (ttm) REVERT: A 39 MET cc_start: 0.8833 (tmm) cc_final: 0.8325 (tmm) REVERT: A 46 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7787 (ptp90) REVERT: A 260 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (mtp85) REVERT: B 149 MET cc_start: 0.8337 (mtm) cc_final: 0.8053 (mtp) REVERT: C 20 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7372 (mp) REVERT: C 105 LYS cc_start: 0.7129 (tptt) cc_final: 0.6877 (ttmm) REVERT: D 115 MET cc_start: 0.7949 (mmm) cc_final: 0.7684 (mmm) REVERT: D 133 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8103 (t70) REVERT: E 10 LYS cc_start: 0.6802 (mtmm) cc_final: 0.5786 (mptt) REVERT: E 64 LEU cc_start: 0.8318 (mt) cc_final: 0.7961 (mm) REVERT: F 54 LYS cc_start: 0.3010 (mmtt) cc_final: 0.2762 (mppt) REVERT: F 258 CYS cc_start: 0.4346 (OUTLIER) cc_final: 0.3164 (p) REVERT: F 275 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5900 (tt0) REVERT: F 288 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5779 (tmt) REVERT: F 375 TYR cc_start: 0.6216 (m-80) cc_final: 0.6006 (m-80) outliers start: 37 outliers final: 23 residues processed: 189 average time/residue: 1.0936 time to fit residues: 233.3605 Evaluate side-chains 186 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN B 267 ASN F 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110965 restraints weight = 49774.001| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.64 r_work: 0.3028 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15462 Z= 0.179 Angle : 0.568 11.106 20935 Z= 0.289 Chirality : 0.043 0.423 2349 Planarity : 0.004 0.057 2601 Dihedral : 10.112 87.969 2465 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.02 % Allowed : 16.82 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1896 helix: 1.13 (0.17), residues: 905 sheet: -0.44 (0.37), residues: 166 loop : -0.07 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 71 TYR 0.011 0.002 TYR F 217 PHE 0.021 0.002 PHE F 267 TRP 0.017 0.002 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (15452) covalent geometry : angle 0.55387 / 0.29 (20923) hydrogen bonds : bond 0.05027 / 3.37 ( 761) hydrogen bonds : angle 5.08856 / 3.58 ( 2151) metal coordination : bond 0.00969 / 0.46 ( 8) metal coordination : angle 5.31841 / 3.11 ( 12) Misc. bond : bond 0.00101 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7152 (mtp) cc_final: 0.6928 (ttm) REVERT: A 27 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7871 (pttp) REVERT: A 39 MET cc_start: 0.8811 (tmm) cc_final: 0.8290 (tmm) REVERT: A 46 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7781 (ptp90) REVERT: A 260 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8289 (mtp85) REVERT: B 149 MET cc_start: 0.8355 (mtm) cc_final: 0.8073 (mtp) REVERT: C 20 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7437 (mp) REVERT: C 105 LYS cc_start: 0.7081 (tptt) cc_final: 0.6836 (ttmm) REVERT: C 200 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6739 (tttm) REVERT: D 115 MET cc_start: 0.7955 (mmm) cc_final: 0.7714 (mmm) REVERT: D 133 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8063 (t70) REVERT: E 10 LYS cc_start: 0.6841 (mtmm) cc_final: 0.5809 (mptt) REVERT: E 64 LEU cc_start: 0.8347 (mt) cc_final: 0.7990 (mm) REVERT: F 54 LYS cc_start: 0.3081 (mmtt) cc_final: 0.2770 (mppt) REVERT: F 258 CYS cc_start: 0.4165 (OUTLIER) cc_final: 0.3015 (p) REVERT: F 288 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5897 (tmt) outliers start: 47 outliers final: 26 residues processed: 195 average time/residue: 1.1602 time to fit residues: 255.0167 Evaluate side-chains 191 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN F 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111270 restraints weight = 49678.524| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.54 r_work: 0.3023 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15462 Z= 0.177 Angle : 0.563 10.857 20935 Z= 0.287 Chirality : 0.043 0.406 2349 Planarity : 0.004 0.057 2601 Dihedral : 10.147 89.305 2465 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.63 % Allowed : 16.94 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1896 helix: 1.13 (0.17), residues: 906 sheet: -0.47 (0.38), residues: 163 loop : -0.10 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.012 0.002 TYR F 217 PHE 0.020 0.002 PHE F 267 TRP 0.017 0.002 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (15452) covalent geometry : angle 0.54938 / 0.29 (20923) hydrogen bonds : bond 0.04973 / 3.32 ( 761) hydrogen bonds : angle 5.06346 / 3.56 ( 2151) metal coordination : bond 0.00978 / 0.47 ( 8) metal coordination : angle 5.25888 / 3.08 ( 12) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7146 (mtp) cc_final: 0.6916 (ttm) REVERT: A 27 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7866 (pttp) REVERT: A 39 MET cc_start: 0.8811 (tmm) cc_final: 0.8284 (tmm) REVERT: A 46 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7771 (ptp90) REVERT: A 260 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8283 (mtp85) REVERT: B 149 MET cc_start: 0.8355 (mtm) cc_final: 0.8068 (mtp) REVERT: C 20 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7435 (mp) REVERT: C 105 LYS cc_start: 0.7095 (tptt) cc_final: 0.6835 (ttmm) REVERT: C 200 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6435 (mtmt) REVERT: D 115 MET cc_start: 0.7932 (mmm) cc_final: 0.7679 (mmm) REVERT: D 133 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8077 (t70) REVERT: E 10 LYS cc_start: 0.6837 (mtmm) cc_final: 0.5800 (mptt) REVERT: E 64 LEU cc_start: 0.8342 (mt) cc_final: 0.7983 (mm) REVERT: F 54 LYS cc_start: 0.3121 (mmtt) cc_final: 0.2812 (mppt) REVERT: F 258 CYS cc_start: 0.4133 (OUTLIER) cc_final: 0.3004 (p) REVERT: F 288 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5913 (tmt) outliers start: 41 outliers final: 25 residues processed: 186 average time/residue: 1.1577 time to fit residues: 242.7949 Evaluate side-chains 185 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 7 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109786 restraints weight = 49737.003| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.69 r_work: 0.3003 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15462 Z= 0.250 Angle : 0.642 12.805 20935 Z= 0.326 Chirality : 0.046 0.408 2349 Planarity : 0.005 0.059 2601 Dihedral : 10.529 83.674 2465 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.70 % Allowed : 17.27 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1896 helix: 0.92 (0.17), residues: 908 sheet: -0.75 (0.37), residues: 166 loop : -0.23 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 85 TYR 0.014 0.002 TYR B 27 PHE 0.026 0.002 PHE D 50 TRP 0.019 0.002 TRP B 70 HIS 0.008 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (15452) covalent geometry : angle 0.62510 / 0.33 (20923) hydrogen bonds : bond 0.05512 / 3.69 ( 761) hydrogen bonds : angle 5.24620 / 3.68 ( 2151) metal coordination : bond 0.01233 / 0.59 ( 8) metal coordination : angle 6.09178 / 3.61 ( 12) Misc. bond : bond 0.00144 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7241 (mtp) cc_final: 0.7001 (ttm) REVERT: A 27 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7915 (pttp) REVERT: A 39 MET cc_start: 0.8789 (tmm) cc_final: 0.8241 (tmm) REVERT: A 46 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7815 (ptp90) REVERT: A 260 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8310 (mtp85) REVERT: C 20 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 99 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.4751 (mp0) REVERT: C 105 LYS cc_start: 0.7119 (tptt) cc_final: 0.6805 (ttmm) REVERT: D 115 MET cc_start: 0.7899 (mmm) cc_final: 0.7692 (mmm) REVERT: E 10 LYS cc_start: 0.6877 (mtmm) cc_final: 0.5821 (mptt) REVERT: E 64 LEU cc_start: 0.8319 (mt) cc_final: 0.7921 (mm) REVERT: F 258 CYS cc_start: 0.4347 (OUTLIER) cc_final: 0.3097 (p) REVERT: F 288 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6068 (tmt) outliers start: 42 outliers final: 26 residues processed: 186 average time/residue: 1.1496 time to fit residues: 240.7690 Evaluate side-chains 186 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 387 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.159232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111666 restraints weight = 49817.452| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.73 r_work: 0.3028 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15462 Z= 0.138 Angle : 0.544 10.147 20935 Z= 0.278 Chirality : 0.042 0.378 2349 Planarity : 0.004 0.056 2601 Dihedral : 10.196 81.997 2465 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 18.10 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1896 helix: 1.12 (0.17), residues: 908 sheet: -0.73 (0.37), residues: 166 loop : -0.13 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.013 0.001 TYR F 217 PHE 0.023 0.001 PHE F 267 TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15452) covalent geometry : angle 0.52998 / 0.28 (20923) hydrogen bonds : bond 0.04728 / 3.15 ( 761) hydrogen bonds : angle 5.02259 / 3.53 ( 2151) metal coordination : bond 0.00899 / 0.43 ( 8) metal coordination : angle 5.11630 / 2.96 ( 12) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7131 (mtp) cc_final: 0.6906 (ttm) REVERT: A 39 MET cc_start: 0.8800 (tmm) cc_final: 0.8278 (tmm) REVERT: A 46 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7781 (ptp90) REVERT: C 20 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7461 (mp) REVERT: C 105 LYS cc_start: 0.7121 (tptt) cc_final: 0.6791 (ttmm) REVERT: D 115 MET cc_start: 0.7846 (mmm) cc_final: 0.7627 (mmm) REVERT: E 10 LYS cc_start: 0.6852 (mtmm) cc_final: 0.5806 (mptt) REVERT: E 64 LEU cc_start: 0.8326 (mt) cc_final: 0.7961 (mm) REVERT: F 258 CYS cc_start: 0.4165 (OUTLIER) cc_final: 0.3079 (p) REVERT: F 288 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5922 (tmt) outliers start: 29 outliers final: 19 residues processed: 175 average time/residue: 1.1557 time to fit residues: 228.3562 Evaluate side-chains 175 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN B 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.159814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111897 restraints weight = 49688.297| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.64 r_work: 0.3045 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15462 Z= 0.121 Angle : 0.522 9.993 20935 Z= 0.265 Chirality : 0.041 0.352 2349 Planarity : 0.004 0.055 2601 Dihedral : 9.849 80.085 2465 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.67 % Allowed : 18.49 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1896 helix: 1.25 (0.17), residues: 909 sheet: -0.60 (0.37), residues: 164 loop : -0.04 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 200 TYR 0.013 0.001 TYR F 217 PHE 0.023 0.001 PHE F 267 TRP 0.017 0.001 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15452) covalent geometry : angle 0.50670 / 0.26 (20923) hydrogen bonds : bond 0.04433 / 2.95 ( 761) hydrogen bonds : angle 4.87065 / 3.41 ( 2151) metal coordination : bond 0.00920 / 0.45 ( 8) metal coordination : angle 5.19298 / 2.98 ( 12) Misc. bond : bond 0.00054 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8772 (tmm) cc_final: 0.8249 (tmm) REVERT: A 46 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7762 (ptp90) REVERT: C 20 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7417 (mp) REVERT: C 105 LYS cc_start: 0.7108 (tptt) cc_final: 0.6782 (ttmm) REVERT: E 10 LYS cc_start: 0.6816 (mtmm) cc_final: 0.5782 (mptt) REVERT: E 64 LEU cc_start: 0.8334 (mt) cc_final: 0.7962 (mm) REVERT: F 258 CYS cc_start: 0.4106 (OUTLIER) cc_final: 0.3063 (p) REVERT: F 288 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5916 (tmt) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 1.1725 time to fit residues: 227.9434 Evaluate side-chains 173 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 188 TYR Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 117 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 ASN C 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111635 restraints weight = 50141.580| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.72 r_work: 0.3026 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15462 Z= 0.158 Angle : 0.549 10.837 20935 Z= 0.278 Chirality : 0.042 0.347 2349 Planarity : 0.004 0.053 2601 Dihedral : 9.868 80.094 2465 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.60 % Allowed : 18.74 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1896 helix: 1.22 (0.17), residues: 908 sheet: -0.60 (0.38), residues: 161 loop : -0.08 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 200 TYR 0.014 0.001 TYR F 217 PHE 0.023 0.002 PHE F 267 TRP 0.017 0.002 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (15452) covalent geometry : angle 0.53436 / 0.28 (20923) hydrogen bonds : bond 0.04694 / 3.13 ( 761) hydrogen bonds : angle 4.93995 / 3.47 ( 2151) metal coordination : bond 0.01008 / 0.48 ( 8) metal coordination : angle 5.33855 / 3.11 ( 12) Misc. bond : bond 0.00091 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11071.39 seconds wall clock time: 188 minutes 2.53 seconds (11282.53 seconds total)