Starting phenix.real_space_refine on Fri Jul 3 14:18:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud4_64061/07_2026/9ud4_64061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud4_64061/07_2026/9ud4_64061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ud4_64061/07_2026/9ud4_64061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud4_64061/07_2026/9ud4_64061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ud4_64061/07_2026/9ud4_64061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud4_64061/07_2026/9ud4_64061.map" } resolution = 3.31 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 3 5.49 5 S 92 5.16 5 C 9520 2.51 5 N 2405 2.21 5 O 2695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 14720 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Chain: "B" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2969 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'LMT': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9093 SG CYS D 112 40.989 72.910 54.325 1.00 2.62 S ATOM 10059 SG CYS E 26 42.857 70.348 55.905 1.00 6.69 S ATOM 8454 SG CYS D 29 41.658 66.722 54.287 1.00 1.61 S ATOM 10781 SG CYS E 120 39.653 68.874 51.835 1.00 1.81 S ATOM 11907 SG CYS F 79 39.249 98.742 74.548 1.00156.77 S ATOM 12146 SG CYS F 111 39.738 96.410 71.825 1.00123.89 S ATOM 11907 SG CYS F 79 39.249 98.742 74.548 1.00156.77 S Time building chain proxies: 2.85, per 1000 atoms: 0.19 Number of scatterers: 14720 At special positions: 0 Unit cell: (90.64, 136.4, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 3 15.00 O 2695 8.00 N 2405 7.00 C 9520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 503.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 11 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 15 sheets defined 50.6% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.693A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.572A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.609A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.731A pdb=" N THR A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.891A pdb=" N HIS A 313 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.784A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.789A pdb=" N ARG A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 4.069A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 removed outlier: 4.366A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.938A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.808A pdb=" N GLY B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.695A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.057A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.706A pdb=" N LEU B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.837A pdb=" N GLY B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.871A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 4.001A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.871A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 333 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 374 removed outlier: 4.169A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 409 removed outlier: 3.709A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.794A pdb=" N PHE C 13 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.914A pdb=" N ALA C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.833A pdb=" N VAL C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 178 through 181 removed outlier: 3.851A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.706A pdb=" N ASP C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.619A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.643A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.822A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.146A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.784A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.735A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 184 through 202 Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 78 through 97 Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.695A pdb=" N ILE E 116 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 113 through 117' Processing helix chain 'E' and resid 119 through 133 removed outlier: 4.020A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) 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 190 Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.555A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 63 removed outlier: 4.331A pdb=" N GLY F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.617A pdb=" N GLU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 130 removed outlier: 4.365A pdb=" N PHE F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.138A pdb=" N GLY F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.550A pdb=" N PHE F 221 " --> pdb=" O PRO F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.876A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 380 through 395 removed outlier: 3.514A pdb=" N ALA F 385 " --> pdb=" O PRO F 381 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 386 " --> pdb=" O MET F 382 " (cutoff:3.500A) 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 removed outlier: 6.641A pdb=" N ILE A 149 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N CYS A 192 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 151 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.607A pdb=" N LEU A 274 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 325 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.446A 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: 7.124A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.066A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.629A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.914A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.388A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'F' and resid 136 through 139 removed outlier: 6.456A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.786A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB6, first strand: chain 'F' and resid 333 through 339 removed outlier: 3.550A pdb=" N GLY F 280 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY F 310 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 1974 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: 2.18 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6087 1.41 - 1.61: 8799 1.61 - 1.81: 150 1.81 - 2.01: 10 2.01 - 2.21: 8 Bond restraints: 15054 Sorted by residual: bond pdb=" C4 FMN C 302 " pdb=" C4A FMN C 302 " ideal model delta sigma weight residual 1.485 1.384 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C4A FMN C 302 " pdb=" N5 FMN C 302 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O5' FMN C 302 " pdb=" P FMN C 302 " ideal model delta sigma weight residual 1.676 1.607 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C10 FMN C 302 " pdb=" N1 FMN C 302 " ideal model delta sigma weight residual 1.317 1.377 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C10 FMN C 302 " pdb=" C4A FMN C 302 " ideal model delta sigma weight residual 1.443 1.387 0.056 2.00e-02 2.50e+03 7.79e+00 ... (remaining 15049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20104 2.01 - 4.03: 279 4.03 - 6.04: 31 6.04 - 8.05: 9 8.05 - 10.07: 3 Bond angle restraints: 20426 Sorted by residual: angle pdb=" C THR A 185 " pdb=" N THR A 186 " pdb=" CA THR A 186 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.74e+01 angle pdb=" C PHE F 195 " pdb=" N ASN F 196 " pdb=" CA ASN F 196 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 120.19 -6.59 1.90e+00 2.77e-01 1.20e+01 angle pdb=" N ALA E 108 " pdb=" CA ALA E 108 " pdb=" C ALA E 108 " ideal model delta sigma weight residual 112.90 108.44 4.46 1.31e+00 5.83e-01 1.16e+01 ... (remaining 20421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.02: 8536 29.02 - 58.04: 375 58.04 - 87.05: 33 87.05 - 116.07: 2 116.07 - 145.09: 1 Dihedral angle restraints: 8947 sinusoidal: 3584 harmonic: 5363 Sorted by residual: dihedral pdb=" O5' FAD F 502 " pdb=" O3P FAD F 502 " pdb=" P FAD F 502 " pdb=" PA FAD F 502 " ideal model delta sinusoidal sigma weight residual 298.23 153.14 145.09 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA VAL F 66 " pdb=" C VAL F 66 " pdb=" N SER F 67 " pdb=" CA SER F 67 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA D 33 " pdb=" C ALA D 33 " pdb=" N VAL D 34 " pdb=" CA VAL D 34 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1472 0.034 - 0.068: 576 0.068 - 0.102: 207 0.102 - 0.136: 57 0.136 - 0.170: 4 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CA TRP B 103 " pdb=" N TRP B 103 " pdb=" C TRP B 103 " pdb=" CB TRP B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB VAL A 268 " pdb=" CA VAL A 268 " pdb=" CG1 VAL A 268 " pdb=" CG2 VAL A 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CG LEU F 56 " pdb=" CB LEU F 56 " pdb=" CD1 LEU F 56 " pdb=" CD2 LEU F 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 2313 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 126 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.80e+00 pdb=" N PRO D 127 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 127 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 127 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 133 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASP E 133 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP E 133 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR E 134 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 91 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO F 92 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 92 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 92 " -0.026 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 456 2.72 - 3.26: 14649 3.26 - 3.81: 23147 3.81 - 4.35: 28755 4.35 - 4.90: 50703 Nonbonded interactions: 117710 Sorted by model distance: nonbonded pdb=" O2B LMT D 301 " pdb=" O6' LMT D 301 " model vdw 2.169 3.040 nonbonded pdb=" O GLN F 169 " pdb=" OG SER F 261 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR F 179 " pdb=" OG SER F 247 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP F 294 " pdb=" NE ARG F 298 " model vdw 2.213 3.120 nonbonded pdb=" OG1 THR C 225 " pdb=" O1P FMN C 302 " model vdw 2.221 3.040 ... (remaining 117705 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: 2.410 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.003 0.101 15060 Z= 0.163 Angle : 0.694 33.187 20437 Z= 0.329 Chirality : 0.042 0.170 2316 Planarity : 0.005 0.049 2566 Dihedral : 15.438 145.088 5527 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.36 % Allowed : 15.34 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1882 helix: 1.06 (0.19), residues: 828 sheet: -1.26 (0.42), residues: 163 loop : -0.94 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.019 0.001 TYR F 309 PHE 0.013 0.001 PHE B 34 TRP 0.025 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15054) covalent geometry : angle 0.60440 / 0.33 (20426) hydrogen bonds : bond 0.14311 / 9.76 ( 694) hydrogen bonds : angle 6.18716 / 4.17 ( 1974) metal coordination : bond 0.00950 / 0.61 ( 6) metal coordination : angle 14.67130 / 9.11 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: B 112 MET cc_start: 0.8399 (mmp) cc_final: 0.7482 (mmp) REVERT: B 152 LYS cc_start: 0.8568 (mttp) cc_final: 0.7438 (mmtt) REVERT: C 117 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6861 (mtp85) REVERT: C 216 HIS cc_start: 0.8368 (m170) cc_final: 0.8030 (m-70) REVERT: E 113 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7111 (tp) REVERT: F 268 PHE cc_start: 0.7044 (m-80) cc_final: 0.6144 (m-80) REVERT: F 288 MET cc_start: 0.6420 (mmt) cc_final: 0.5994 (mmt) REVERT: F 307 TYR cc_start: 0.7942 (t80) cc_final: 0.7466 (t80) REVERT: F 361 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6620 (mp0) REVERT: F 383 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4274 (tpp) outliers start: 21 outliers final: 16 residues processed: 193 average time/residue: 0.1088 time to fit residues: 32.1373 Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.176309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.129744 restraints weight = 15046.115| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.77 r_work: 0.3053 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15060 Z= 0.226 Angle : 0.686 25.432 20437 Z= 0.325 Chirality : 0.046 0.175 2316 Planarity : 0.005 0.046 2566 Dihedral : 8.083 123.210 2244 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 3.88 % Allowed : 14.24 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1882 helix: 0.84 (0.19), residues: 829 sheet: -0.96 (0.43), residues: 151 loop : -1.07 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 161 TYR 0.016 0.002 TYR F 217 PHE 0.021 0.002 PHE A 423 TRP 0.028 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (15054) covalent geometry : angle 0.61207 / 0.32 (20426) hydrogen bonds : bond 0.05272 / 3.50 ( 694) hydrogen bonds : angle 5.06306 / 3.44 ( 1974) metal coordination : bond 0.01700 / 1.07 ( 6) metal coordination : angle 13.41411 / 7.35 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 40 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7236 (mmm160) REVERT: A 155 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6518 (t0) REVERT: A 168 ASN cc_start: 0.8094 (m110) cc_final: 0.7641 (m110) REVERT: A 290 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7279 (mt-10) REVERT: A 430 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: B 112 MET cc_start: 0.8599 (mmp) cc_final: 0.7783 (mmp) REVERT: B 152 LYS cc_start: 0.8513 (mttp) cc_final: 0.7327 (mmtt) REVERT: C 117 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6833 (mtp85) REVERT: E 49 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7818 (tt) REVERT: E 113 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7086 (tp) REVERT: F 76 CYS cc_start: 0.3520 (OUTLIER) cc_final: 0.1625 (t) REVERT: F 208 ILE cc_start: 0.1351 (OUTLIER) cc_final: 0.0919 (tp) REVERT: F 214 MET cc_start: 0.5080 (ptp) cc_final: 0.4171 (ptp) REVERT: F 268 PHE cc_start: 0.7100 (m-80) cc_final: 0.6230 (m-80) REVERT: F 288 MET cc_start: 0.6433 (mmt) cc_final: 0.5993 (mmt) REVERT: F 305 MET cc_start: 0.7799 (mtm) cc_final: 0.7568 (mtm) REVERT: F 307 TYR cc_start: 0.8171 (t80) cc_final: 0.7715 (t80) REVERT: F 371 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7546 (pm20) outliers start: 60 outliers final: 41 residues processed: 219 average time/residue: 0.0948 time to fit residues: 33.0333 Evaluate side-chains 212 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 371 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.178554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129325 restraints weight = 15078.783| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.97 r_work: 0.3063 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15060 Z= 0.147 Angle : 0.605 23.376 20437 Z= 0.280 Chirality : 0.043 0.169 2316 Planarity : 0.005 0.046 2566 Dihedral : 7.807 109.292 2239 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 3.82 % Allowed : 15.34 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1882 helix: 0.98 (0.19), residues: 838 sheet: -0.89 (0.43), residues: 151 loop : -1.04 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 161 TYR 0.015 0.001 TYR F 217 PHE 0.014 0.001 PHE E 28 TRP 0.026 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (15054) covalent geometry : angle 0.52747 / 0.28 (20426) hydrogen bonds : bond 0.04457 / 2.98 ( 694) hydrogen bonds : angle 4.75492 / 3.23 ( 1974) metal coordination : bond 0.01325 / 0.73 ( 6) metal coordination : angle 12.81950 / 7.05 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.537 Fit side-chains REVERT: A 4 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 40 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7197 (mmm160) REVERT: A 155 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6455 (t0) REVERT: A 168 ASN cc_start: 0.8024 (m110) cc_final: 0.7526 (m110) REVERT: B 112 MET cc_start: 0.8603 (mmp) cc_final: 0.7758 (mmt) REVERT: B 152 LYS cc_start: 0.8496 (mttp) cc_final: 0.7287 (mmtt) REVERT: C 117 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6465 (mtp85) REVERT: C 166 THR cc_start: 0.8261 (p) cc_final: 0.7982 (p) REVERT: E 113 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6971 (tp) REVERT: F 1 MET cc_start: 0.7718 (tmm) cc_final: 0.7456 (tmm) REVERT: F 76 CYS cc_start: 0.3468 (OUTLIER) cc_final: 0.1433 (t) REVERT: F 214 MET cc_start: 0.5041 (ptp) cc_final: 0.4692 (ptp) REVERT: F 268 PHE cc_start: 0.7066 (m-80) cc_final: 0.6266 (m-80) REVERT: F 288 MET cc_start: 0.6364 (mmt) cc_final: 0.5989 (mmt) REVERT: F 307 TYR cc_start: 0.8107 (t80) cc_final: 0.7601 (t80) REVERT: F 371 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7581 (pm20) outliers start: 59 outliers final: 35 residues processed: 217 average time/residue: 0.0973 time to fit residues: 33.3185 Evaluate side-chains 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 371 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 152 optimal weight: 50.0000 chunk 21 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN B 78 GLN C 232 GLN F 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.179414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134490 restraints weight = 14959.728| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.75 r_work: 0.3107 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15060 Z= 0.131 Angle : 0.589 22.891 20437 Z= 0.273 Chirality : 0.043 0.177 2316 Planarity : 0.004 0.045 2566 Dihedral : 7.489 84.746 2236 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 3.56 % Allowed : 14.95 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 1882 helix: 1.09 (0.19), residues: 841 sheet: -0.99 (0.42), residues: 157 loop : -1.00 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 189 TYR 0.015 0.001 TYR F 217 PHE 0.013 0.001 PHE E 28 TRP 0.025 0.001 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (15054) covalent geometry : angle 0.51452 / 0.27 (20426) hydrogen bonds : bond 0.04152 / 2.79 ( 694) hydrogen bonds : angle 4.60669 / 3.14 ( 1974) metal coordination : bond 0.01270 / 0.71 ( 6) metal coordination : angle 12.38286 / 6.81 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.569 Fit side-chains REVERT: A 4 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 40 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7254 (mmm160) REVERT: A 155 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6482 (t0) REVERT: A 168 ASN cc_start: 0.8037 (m110) cc_final: 0.7513 (m110) REVERT: A 443 GLU cc_start: 0.7860 (tp30) cc_final: 0.7606 (tp30) REVERT: B 112 MET cc_start: 0.8573 (mmp) cc_final: 0.7769 (mmt) REVERT: B 152 LYS cc_start: 0.8569 (mttp) cc_final: 0.7421 (mmtt) REVERT: C 117 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6904 (mmt180) REVERT: C 166 THR cc_start: 0.8261 (p) cc_final: 0.7997 (p) REVERT: D 63 ARG cc_start: 0.7439 (ptt-90) cc_final: 0.7221 (ptt-90) REVERT: E 113 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7059 (tp) REVERT: F 13 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7298 (mp) REVERT: F 76 CYS cc_start: 0.3265 (OUTLIER) cc_final: 0.1011 (t) REVERT: F 214 MET cc_start: 0.5186 (ptp) cc_final: 0.4831 (ptp) REVERT: F 233 PRO cc_start: 0.5396 (Cg_exo) cc_final: 0.5136 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7045 (m-80) cc_final: 0.6383 (m-80) REVERT: F 288 MET cc_start: 0.6533 (mmt) cc_final: 0.6235 (mmt) REVERT: F 307 TYR cc_start: 0.8060 (t80) cc_final: 0.7600 (t80) REVERT: F 371 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7546 (pm20) outliers start: 55 outliers final: 36 residues processed: 212 average time/residue: 0.0955 time to fit residues: 31.9249 Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 371 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 0.0670 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.179230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.133331 restraints weight = 14904.861| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.69 r_work: 0.3095 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15060 Z= 0.136 Angle : 0.590 22.941 20437 Z= 0.273 Chirality : 0.043 0.181 2316 Planarity : 0.005 0.049 2566 Dihedral : 7.422 77.838 2236 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 3.88 % Allowed : 14.95 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1882 helix: 1.13 (0.19), residues: 841 sheet: -0.94 (0.42), residues: 157 loop : -0.97 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.013 0.001 TYR F 217 PHE 0.013 0.001 PHE E 28 TRP 0.026 0.001 TRP B 103 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (15054) covalent geometry : angle 0.51837 / 0.27 (20426) hydrogen bonds : bond 0.04124 / 2.77 ( 694) hydrogen bonds : angle 4.52622 / 3.09 ( 1974) metal coordination : bond 0.01281 / 0.70 ( 6) metal coordination : angle 12.18867 / 6.68 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.542 Fit side-chains REVERT: A 4 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8259 (mp) REVERT: A 40 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7317 (mmm160) REVERT: A 168 ASN cc_start: 0.8007 (m110) cc_final: 0.7495 (m110) REVERT: B 112 MET cc_start: 0.8532 (mmp) cc_final: 0.7754 (mmt) REVERT: B 152 LYS cc_start: 0.8587 (mttp) cc_final: 0.7430 (mmtt) REVERT: C 117 ARG cc_start: 0.7245 (mtt-85) cc_final: 0.6989 (mmt180) REVERT: C 166 THR cc_start: 0.8255 (p) cc_final: 0.8029 (p) REVERT: D 63 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.7195 (ptt-90) REVERT: D 119 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7616 (mm-30) REVERT: E 113 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6998 (tp) REVERT: F 13 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7335 (mp) REVERT: F 76 CYS cc_start: 0.3349 (OUTLIER) cc_final: 0.1100 (t) REVERT: F 208 ILE cc_start: 0.1074 (OUTLIER) cc_final: 0.0863 (tp) REVERT: F 214 MET cc_start: 0.5039 (ptp) cc_final: 0.4690 (ptp) REVERT: F 233 PRO cc_start: 0.5421 (Cg_exo) cc_final: 0.5175 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7072 (m-80) cc_final: 0.6444 (m-80) REVERT: F 288 MET cc_start: 0.6518 (mmt) cc_final: 0.6250 (mmt) REVERT: F 307 TYR cc_start: 0.8132 (t80) cc_final: 0.7609 (t80) outliers start: 60 outliers final: 46 residues processed: 213 average time/residue: 0.0977 time to fit residues: 32.8269 Evaluate side-chains 211 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 105 optimal weight: 0.0470 chunk 130 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 146 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 HIS F 112 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.182101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138026 restraints weight = 14838.188| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.71 r_work: 0.3145 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15060 Z= 0.097 Angle : 0.546 20.702 20437 Z= 0.252 Chirality : 0.041 0.160 2316 Planarity : 0.004 0.047 2566 Dihedral : 7.058 75.194 2230 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 2.85 % Allowed : 15.86 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1882 helix: 1.46 (0.19), residues: 834 sheet: -0.79 (0.42), residues: 161 loop : -0.84 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.016 0.001 TYR F 309 PHE 0.011 0.001 PHE E 28 TRP 0.023 0.001 TRP B 103 HIS 0.007 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (15054) covalent geometry : angle 0.47817 / 0.25 (20426) hydrogen bonds : bond 0.03514 / 2.38 ( 694) hydrogen bonds : angle 4.38153 / 3.00 ( 1974) metal coordination : bond 0.01180 / 0.65 ( 6) metal coordination : angle 11.40228 / 6.41 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.586 Fit side-chains REVERT: A 4 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 40 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7262 (mmm160) REVERT: A 168 ASN cc_start: 0.7936 (m110) cc_final: 0.7490 (m110) REVERT: B 112 MET cc_start: 0.8512 (mmp) cc_final: 0.7722 (mmt) REVERT: B 152 LYS cc_start: 0.8561 (mttp) cc_final: 0.7396 (mmtt) REVERT: C 117 ARG cc_start: 0.7239 (mtt-85) cc_final: 0.7004 (mmt180) REVERT: D 63 ARG cc_start: 0.7385 (ptt-90) cc_final: 0.7081 (ptt-90) REVERT: D 91 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8307 (mtmt) REVERT: D 119 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7581 (mm-30) REVERT: E 113 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6870 (tp) REVERT: F 76 CYS cc_start: 0.3149 (OUTLIER) cc_final: 0.0804 (t) REVERT: F 214 MET cc_start: 0.4981 (ptp) cc_final: 0.4447 (ptp) REVERT: F 233 PRO cc_start: 0.5392 (Cg_exo) cc_final: 0.5169 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7007 (m-80) cc_final: 0.6447 (m-80) REVERT: F 307 TYR cc_start: 0.8006 (t80) cc_final: 0.7408 (t80) outliers start: 44 outliers final: 35 residues processed: 209 average time/residue: 0.1021 time to fit residues: 33.3322 Evaluate side-chains 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 58 optimal weight: 0.0000 chunk 152 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.179692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3411 r_free = 0.3411 target = 0.132792 restraints weight = 14882.641| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.69 r_work: 0.3106 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15060 Z= 0.138 Angle : 0.579 22.602 20437 Z= 0.269 Chirality : 0.043 0.170 2316 Planarity : 0.004 0.046 2566 Dihedral : 7.094 73.825 2229 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 3.11 % Allowed : 16.12 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1882 helix: 1.31 (0.19), residues: 837 sheet: -0.84 (0.41), residues: 161 loop : -0.86 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.011 0.001 TYR F 217 PHE 0.019 0.001 PHE F 198 TRP 0.026 0.001 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (15054) covalent geometry : angle 0.51079 / 0.27 (20426) hydrogen bonds : bond 0.03984 / 2.67 ( 694) hydrogen bonds : angle 4.42621 / 3.02 ( 1974) metal coordination : bond 0.01230 / 0.68 ( 6) metal coordination : angle 11.78830 / 6.49 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8264 (mp) REVERT: A 40 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7325 (mmm160) REVERT: A 155 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6203 (t0) REVERT: A 168 ASN cc_start: 0.7958 (m110) cc_final: 0.7476 (m110) REVERT: A 443 GLU cc_start: 0.7762 (tp30) cc_final: 0.7530 (tp30) REVERT: B 112 MET cc_start: 0.8524 (mmp) cc_final: 0.7720 (mmt) REVERT: B 152 LYS cc_start: 0.8590 (mttp) cc_final: 0.7443 (mmtt) REVERT: C 117 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.7043 (mmt180) REVERT: D 63 ARG cc_start: 0.7469 (ptt-90) cc_final: 0.7190 (ptt-90) REVERT: D 119 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7604 (mm-30) REVERT: F 76 CYS cc_start: 0.3075 (OUTLIER) cc_final: 0.0791 (t) REVERT: F 214 MET cc_start: 0.4857 (ptp) cc_final: 0.4334 (ptp) REVERT: F 233 PRO cc_start: 0.5460 (Cg_exo) cc_final: 0.5255 (Cg_endo) REVERT: F 268 PHE cc_start: 0.6995 (m-80) cc_final: 0.6440 (m-80) REVERT: F 307 TYR cc_start: 0.8067 (t80) cc_final: 0.7406 (t80) REVERT: F 371 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7598 (pm20) outliers start: 48 outliers final: 37 residues processed: 198 average time/residue: 0.0981 time to fit residues: 30.5973 Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 371 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 166 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.176805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132292 restraints weight = 15045.379| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.82 r_work: 0.3061 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15060 Z= 0.204 Angle : 0.646 25.368 20437 Z= 0.303 Chirality : 0.045 0.167 2316 Planarity : 0.005 0.049 2566 Dihedral : 7.368 72.595 2227 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 3.43 % Allowed : 16.38 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1882 helix: 1.01 (0.19), residues: 834 sheet: -1.02 (0.41), residues: 157 loop : -0.96 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 403 TYR 0.017 0.002 TYR F 309 PHE 0.018 0.002 PHE F 198 TRP 0.030 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.20 (15054) covalent geometry : angle 0.57479 / 0.30 (20426) hydrogen bonds : bond 0.04818 / 3.20 ( 694) hydrogen bonds : angle 4.63953 / 3.16 ( 1974) metal coordination : bond 0.01441 / 0.77 ( 6) metal coordination : angle 12.71679 / 6.79 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 40 ARG cc_start: 0.7813 (mmm-85) cc_final: 0.7468 (mmm160) REVERT: A 155 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6273 (t0) REVERT: A 168 ASN cc_start: 0.8070 (m110) cc_final: 0.7534 (m110) REVERT: B 112 MET cc_start: 0.8576 (mmp) cc_final: 0.7739 (mmt) REVERT: B 152 LYS cc_start: 0.8627 (mttp) cc_final: 0.7466 (mmtt) REVERT: B 402 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8402 (mm-30) REVERT: C 117 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7080 (mmt180) REVERT: D 63 ARG cc_start: 0.7530 (ptt-90) cc_final: 0.7205 (ptt-90) REVERT: D 119 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7550 (mm-30) REVERT: F 13 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7405 (mp) REVERT: F 214 MET cc_start: 0.5063 (ptp) cc_final: 0.4500 (ptp) REVERT: F 233 PRO cc_start: 0.5516 (Cg_exo) cc_final: 0.5310 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7031 (m-80) cc_final: 0.6475 (m-80) REVERT: F 307 TYR cc_start: 0.8177 (t80) cc_final: 0.7616 (t80) REVERT: F 371 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7652 (pm20) outliers start: 53 outliers final: 45 residues processed: 209 average time/residue: 0.1037 time to fit residues: 34.2491 Evaluate side-chains 209 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 371 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 166 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.180568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.136452 restraints weight = 14978.750| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.75 r_work: 0.3123 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15060 Z= 0.111 Angle : 0.573 21.640 20437 Z= 0.265 Chirality : 0.042 0.164 2316 Planarity : 0.004 0.045 2566 Dihedral : 7.020 71.148 2227 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 2.52 % Allowed : 17.73 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1882 helix: 1.23 (0.19), residues: 843 sheet: -0.91 (0.43), residues: 148 loop : -0.86 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.020 0.001 TYR F 309 PHE 0.018 0.001 PHE F 198 TRP 0.023 0.001 TRP B 103 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15054) covalent geometry : angle 0.50417 / 0.26 (20426) hydrogen bonds : bond 0.03734 / 2.52 ( 694) hydrogen bonds : angle 4.45707 / 3.06 ( 1974) metal coordination : bond 0.01239 / 0.68 ( 6) metal coordination : angle 11.70720 / 6.52 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 40 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7427 (mmm160) REVERT: A 168 ASN cc_start: 0.8016 (m110) cc_final: 0.7495 (m110) REVERT: A 443 GLU cc_start: 0.7751 (tp30) cc_final: 0.7504 (tp30) REVERT: B 112 MET cc_start: 0.8558 (mmp) cc_final: 0.7784 (mmt) REVERT: B 152 LYS cc_start: 0.8571 (mttp) cc_final: 0.7423 (mmtt) REVERT: C 117 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7085 (mmt180) REVERT: D 63 ARG cc_start: 0.7399 (ptt-90) cc_final: 0.7118 (ptt-90) REVERT: D 119 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7482 (mm-30) REVERT: E 113 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6830 (tp) REVERT: F 214 MET cc_start: 0.5087 (ptp) cc_final: 0.4662 (ptp) REVERT: F 233 PRO cc_start: 0.5577 (Cg_exo) cc_final: 0.5368 (Cg_endo) REVERT: F 268 PHE cc_start: 0.6885 (m-80) cc_final: 0.6338 (m-80) REVERT: F 307 TYR cc_start: 0.8112 (t80) cc_final: 0.7472 (t80) outliers start: 39 outliers final: 31 residues processed: 196 average time/residue: 0.1067 time to fit residues: 32.4133 Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.178523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131017 restraints weight = 14927.393| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.79 r_work: 0.3080 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15060 Z= 0.158 Angle : 0.609 23.366 20437 Z= 0.283 Chirality : 0.044 0.168 2316 Planarity : 0.005 0.048 2566 Dihedral : 7.090 71.134 2227 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.46 % Allowed : 17.73 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1882 helix: 1.16 (0.19), residues: 834 sheet: -0.96 (0.41), residues: 157 loop : -0.88 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.012 0.001 TYR A 228 PHE 0.018 0.001 PHE F 198 TRP 0.027 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (15054) covalent geometry : angle 0.54007 / 0.28 (20426) hydrogen bonds : bond 0.04275 / 2.85 ( 694) hydrogen bonds : angle 4.51910 / 3.10 ( 1974) metal coordination : bond 0.01298 / 0.71 ( 6) metal coordination : angle 12.11012 / 6.60 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 40 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7489 (mmt90) REVERT: A 168 ASN cc_start: 0.8046 (m110) cc_final: 0.7508 (m110) REVERT: A 224 MET cc_start: 0.8640 (mtm) cc_final: 0.8321 (mtt) REVERT: B 112 MET cc_start: 0.8543 (mmp) cc_final: 0.7726 (mmt) REVERT: B 152 LYS cc_start: 0.8594 (mttp) cc_final: 0.7457 (mmtt) REVERT: C 117 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7113 (mmt180) REVERT: D 63 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7234 (ptt-90) REVERT: D 119 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7561 (mm-30) REVERT: E 51 ILE cc_start: 0.8259 (mm) cc_final: 0.8025 (mm) REVERT: F 214 MET cc_start: 0.5139 (ptp) cc_final: 0.4357 (ptp) REVERT: F 233 PRO cc_start: 0.5645 (Cg_exo) cc_final: 0.5430 (Cg_endo) REVERT: F 268 PHE cc_start: 0.6906 (m-80) cc_final: 0.6351 (m-80) REVERT: F 307 TYR cc_start: 0.8152 (t80) cc_final: 0.7492 (t80) outliers start: 38 outliers final: 34 residues processed: 192 average time/residue: 0.1089 time to fit residues: 32.7856 Evaluate side-chains 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 165 optimal weight: 30.0000 chunk 42 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.179245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136230 restraints weight = 14979.912| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.77 r_work: 0.3109 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15060 Z= 0.140 Angle : 0.595 22.891 20437 Z= 0.277 Chirality : 0.043 0.167 2316 Planarity : 0.004 0.046 2566 Dihedral : 6.939 70.386 2227 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.52 % Allowed : 17.73 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1882 helix: 1.15 (0.19), residues: 840 sheet: -0.91 (0.41), residues: 157 loop : -0.88 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.016 0.001 TYR F 309 PHE 0.017 0.001 PHE F 198 TRP 0.026 0.001 TRP B 103 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (15054) covalent geometry : angle 0.52736 / 0.28 (20426) hydrogen bonds : bond 0.04055 / 2.71 ( 694) hydrogen bonds : angle 4.48133 / 3.07 ( 1974) metal coordination : bond 0.01293 / 0.71 ( 6) metal coordination : angle 11.92685 / 6.54 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3834.75 seconds wall clock time: 66 minutes 29.89 seconds (3989.89 seconds total)