Starting phenix.real_space_refine on Thu Sep 18 06:03:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud4_64061/09_2025/9ud4_64061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud4_64061/09_2025/9ud4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ud4_64061/09_2025/9ud4_64061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud4_64061/09_2025/9ud4_64061.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud4_64061/09_2025/9ud4_64061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud4_64061/09_2025/9ud4_64061.cif" } 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-2.0-5805/lib/python3.9/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, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.12, per 1000 atoms: 0.28 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: 1.19 Conformation dependent library (CDL) restraints added in 681.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.54 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: 2.40 Time building geometry restraints manager: 1.62 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: 2.230 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.130 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 aren 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 covalent geometry : bond 0.00347 (15054) covalent geometry : angle 0.60440 (20426) hydrogen bonds : bond 0.14311 ( 694) hydrogen bonds : angle 6.18716 ( 1974) metal coordination : bond 0.00950 ( 6) metal coordination : angle 14.67130 ( 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 : 0.513 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: 0.8031 (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: 0.1195 time to fit residues: 35.6911 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 : 0.571 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8191 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 aren 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 covalent geometry : bond 0.00568 (15054) covalent geometry : angle 0.61207 (20426) hydrogen bonds : bond 0.05272 ( 694) hydrogen bonds : angle 5.06306 ( 1974) metal coordination : bond 0.01700 ( 6) metal coordination : angle 13.41411 ( 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 : 0.617 Fit side-chains 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: 0.7280 (mt-10) REVERT: A 430 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: B 112 MET cc_start: 0.8600 (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: 0.3519 (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: 0.8170 (t80) cc_final: 0.7716 (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: 0.1098 time to fit residues: 37.9921 Evaluate side-chains 211 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3887 r_free = 0.3887 target = 0.178450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132168 restraints weight = 15100.647| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.78 r_work: 0.3082 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15060 Z= 0.149 Angle : 0.607 23.378 20437 Z= 0.282 Chirality : 0.043 0.169 2316 Planarity : 0.005 0.046 2566 Dihedral : 7.810 109.315 2239 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.81 % 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 aren not related in a simple way. whole: -0.19 (0.19), residues: 1882 helix: 0.98 (0.19), residues: 838 sheet: -0.90 (0.43), residues: 151 loop : -1.03 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 189 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 covalent geometry : bond 0.00363 (15054) covalent geometry : angle 0.52940 (20426) hydrogen bonds : bond 0.04492 ( 694) hydrogen bonds : angle 4.76295 ( 1974) metal coordination : bond 0.01347 ( 6) metal coordination : angle 12.81318 ( 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 228 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8369 (mp) REVERT: A 40 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7311 (mmm160) REVERT: A 155 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6363 (t0) REVERT: A 168 ASN cc_start: 0.8050 (m110) cc_final: 0.7567 (m110) REVERT: B 112 MET cc_start: 0.8571 (mmp) cc_final: 0.7737 (mmt) REVERT: B 152 LYS cc_start: 0.8568 (mttp) cc_final: 0.7382 (mmtt) REVERT: C 117 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6618 (mtp85) REVERT: C 166 THR cc_start: 0.8275 (p) cc_final: 0.8000 (p) REVERT: E 113 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7090 (tp) REVERT: F 1 MET cc_start: 0.7704 (tmm) cc_final: 0.7480 (tmm) REVERT: F 76 CYS cc_start: 0.3369 (OUTLIER) cc_final: 0.1314 (t) REVERT: F 214 MET cc_start: 0.5154 (ptp) cc_final: 0.4823 (ptp) REVERT: F 268 PHE cc_start: 0.7103 (m-80) cc_final: 0.6329 (m-80) REVERT: F 288 MET cc_start: 0.6504 (mmt) cc_final: 0.6126 (mmt) REVERT: F 307 TYR cc_start: 0.8114 (t80) cc_final: 0.7640 (t80) REVERT: F 371 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7649 (pm20) outliers start: 59 outliers final: 36 residues processed: 216 average time/residue: 0.1093 time to fit residues: 37.4382 Evaluate side-chains 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 196 ASN 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: 1.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 152 optimal weight: 50.0000 chunk 21 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 78 GLN C 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.178628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134392 restraints weight = 14982.237| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.80 r_work: 0.3089 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15060 Z= 0.147 Angle : 0.600 23.481 20437 Z= 0.278 Chirality : 0.043 0.168 2316 Planarity : 0.005 0.048 2566 Dihedral : 7.552 82.705 2236 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 4.01 % Allowed : 14.69 % 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 aren not related in a simple way. whole: -0.15 (0.19), residues: 1882 helix: 1.02 (0.19), residues: 841 sheet: -0.99 (0.42), residues: 157 loop : -1.01 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 161 TYR 0.014 0.001 TYR F 217 PHE 0.013 0.001 PHE E 28 TRP 0.026 0.001 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00358 (15054) covalent geometry : angle 0.52441 (20426) hydrogen bonds : bond 0.04315 ( 694) hydrogen bonds : angle 4.63739 ( 1974) metal coordination : bond 0.01297 ( 6) metal coordination : angle 12.53869 ( 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 229 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 40 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7294 (mmm160) REVERT: A 155 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6519 (t0) REVERT: A 168 ASN cc_start: 0.8038 (m110) cc_final: 0.7523 (m110) REVERT: B 112 MET cc_start: 0.8575 (mmp) cc_final: 0.7777 (mmt) REVERT: B 152 LYS cc_start: 0.8580 (mttp) cc_final: 0.7439 (mmtt) REVERT: C 117 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6940 (mmt180) REVERT: C 166 THR cc_start: 0.8267 (p) cc_final: 0.8013 (p) REVERT: D 63 ARG cc_start: 0.7467 (ptt-90) cc_final: 0.7240 (ptt-90) REVERT: E 113 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7078 (tp) REVERT: F 13 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7315 (mp) REVERT: F 76 CYS cc_start: 0.3258 (OUTLIER) cc_final: 0.0982 (t) REVERT: F 214 MET cc_start: 0.5255 (ptp) cc_final: 0.4904 (ptp) REVERT: F 233 PRO cc_start: 0.5405 (Cg_exo) cc_final: 0.5145 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7052 (m-80) cc_final: 0.6391 (m-80) REVERT: F 288 MET cc_start: 0.6505 (mmt) cc_final: 0.6156 (mmt) REVERT: F 305 MET cc_start: 0.7871 (mtm) cc_final: 0.7639 (mtp) REVERT: F 307 TYR cc_start: 0.8117 (t80) cc_final: 0.7644 (t80) REVERT: F 371 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7555 (pm20) outliers start: 62 outliers final: 44 residues processed: 213 average time/residue: 0.1104 time to fit residues: 37.1877 Evaluate side-chains 209 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 C residue 234 THR 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 31 VAL Chi-restraints excluded: chain E residue 73 VAL 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 196 ASN 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: 0.0980 chunk 84 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS F 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.178010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133783 restraints weight = 14953.459| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.78 r_work: 0.3088 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15060 Z= 0.155 Angle : 0.604 23.707 20437 Z= 0.279 Chirality : 0.044 0.184 2316 Planarity : 0.005 0.047 2566 Dihedral : 7.590 78.012 2236 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 15.08 % Favored : 81.04 % 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 aren not related in a simple way. whole: -0.13 (0.19), residues: 1882 helix: 1.02 (0.19), residues: 842 sheet: -0.97 (0.42), residues: 157 loop : -0.99 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.014 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 B 328 Details of bonding type rmsd covalent geometry : bond 0.00383 (15054) covalent geometry : angle 0.53055 (20426) hydrogen bonds : bond 0.04367 ( 694) hydrogen bonds : angle 4.60066 ( 1974) metal coordination : bond 0.01333 ( 6) metal coordination : angle 12.44681 ( 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 228 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 40 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7327 (mmm160) REVERT: A 168 ASN cc_start: 0.8034 (m110) cc_final: 0.7490 (m110) REVERT: B 112 MET cc_start: 0.8552 (mmp) cc_final: 0.7730 (mmt) REVERT: B 152 LYS cc_start: 0.8613 (mttp) cc_final: 0.7447 (mmtt) REVERT: C 117 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.7014 (mmt180) REVERT: C 166 THR cc_start: 0.8257 (p) cc_final: 0.8022 (p) REVERT: D 63 ARG cc_start: 0.7499 (ptt-90) cc_final: 0.7241 (ptt-90) REVERT: D 115 MET cc_start: 0.7177 (tpp) cc_final: 0.6958 (tpt) REVERT: D 119 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7634 (mm-30) REVERT: F 13 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7350 (mp) REVERT: F 76 CYS cc_start: 0.3160 (OUTLIER) cc_final: 0.0772 (t) REVERT: F 214 MET cc_start: 0.5014 (ptp) cc_final: 0.4675 (ptp) REVERT: F 233 PRO cc_start: 0.5434 (Cg_exo) cc_final: 0.5175 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7047 (m-80) cc_final: 0.6428 (m-80) REVERT: F 288 MET cc_start: 0.6598 (mmt) cc_final: 0.6342 (mmt) REVERT: F 307 TYR cc_start: 0.8137 (t80) cc_final: 0.7618 (t80) REVERT: F 371 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7532 (pm20) outliers start: 60 outliers final: 47 residues processed: 215 average time/residue: 0.1124 time to fit residues: 37.9547 Evaluate side-chains 212 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 265 ILE 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 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 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 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 196 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 0.0030 chunk 164 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3896 r_free = 0.3896 target = 0.179438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131258 restraints weight = 14881.591| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.90 r_work: 0.3081 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1413 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= 0.129 Angle : 0.577 22.815 20437 Z= 0.266 Chirality : 0.043 0.166 2316 Planarity : 0.004 0.045 2566 Dihedral : 7.386 75.275 2230 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 3.75 % Allowed : 15.60 % Favored : 80.65 % 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 aren not related in a simple way. whole: 0.00 (0.20), residues: 1882 helix: 1.15 (0.19), residues: 843 sheet: -0.87 (0.44), residues: 148 loop : -0.94 (0.20), residues: 891 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 0.012 0.001 PHE E 28 TRP 0.025 0.001 TRP B 103 HIS 0.011 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00309 (15054) covalent geometry : angle 0.50395 (20426) hydrogen bonds : bond 0.04047 ( 694) hydrogen bonds : angle 4.50272 ( 1974) metal coordination : bond 0.01283 ( 6) metal coordination : angle 12.10305 ( 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 229 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8218 (mp) REVERT: A 40 ARG cc_start: 0.7636 (mmm-85) cc_final: 0.7227 (mmm160) REVERT: A 168 ASN cc_start: 0.7990 (m110) cc_final: 0.7468 (m110) REVERT: B 112 MET cc_start: 0.8581 (mmp) cc_final: 0.7782 (mmt) REVERT: B 152 LYS cc_start: 0.8535 (mttp) cc_final: 0.7347 (mmtt) REVERT: C 117 ARG cc_start: 0.7276 (mtt-85) cc_final: 0.6986 (mmt180) REVERT: D 63 ARG cc_start: 0.7361 (ptt-90) cc_final: 0.7094 (ptt-90) REVERT: D 119 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7535 (mm-30) REVERT: D 147 THR cc_start: 0.8181 (m) cc_final: 0.7830 (p) REVERT: F 76 CYS cc_start: 0.3242 (OUTLIER) cc_final: 0.0943 (t) REVERT: F 214 MET cc_start: 0.4817 (ptp) cc_final: 0.4280 (ptp) REVERT: F 233 PRO cc_start: 0.5377 (Cg_exo) cc_final: 0.5175 (Cg_endo) REVERT: F 268 PHE cc_start: 0.6993 (m-80) cc_final: 0.6392 (m-80) REVERT: F 288 MET cc_start: 0.6464 (mmt) cc_final: 0.6249 (mmt) REVERT: F 307 TYR cc_start: 0.8098 (t80) cc_final: 0.7522 (t80) outliers start: 58 outliers final: 47 residues processed: 215 average time/residue: 0.1163 time to fit residues: 39.0494 Evaluate side-chains 209 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 265 ILE 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 C residue 203 ILE Chi-restraints excluded: chain D residue 25 VAL 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 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 196 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 152 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** F 176 HIS ** 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 = 0.3891 r_free = 0.3891 target = 0.178985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132054 restraints weight = 14902.807| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.77 r_work: 0.3086 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15060 Z= 0.141 Angle : 0.588 23.117 20437 Z= 0.272 Chirality : 0.043 0.187 2316 Planarity : 0.005 0.046 2566 Dihedral : 7.306 73.932 2229 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 3.88 % Allowed : 15.60 % Favored : 80.52 % 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 aren not related in a simple way. whole: -0.03 (0.19), residues: 1882 helix: 1.14 (0.19), residues: 836 sheet: -0.87 (0.44), residues: 148 loop : -0.97 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.017 0.001 TYR F 309 PHE 0.012 0.001 PHE E 28 TRP 0.026 0.001 TRP B 103 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00344 (15054) covalent geometry : angle 0.51783 (20426) hydrogen bonds : bond 0.04117 ( 694) hydrogen bonds : angle 4.48644 ( 1974) metal coordination : bond 0.01323 ( 6) metal coordination : angle 12.02151 ( 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 226 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 40 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7362 (mmm160) REVERT: A 168 ASN cc_start: 0.8018 (m110) cc_final: 0.7498 (m110) REVERT: A 443 GLU cc_start: 0.7831 (tp30) cc_final: 0.7566 (tp30) REVERT: B 112 MET cc_start: 0.8528 (mmp) cc_final: 0.7707 (mmt) REVERT: B 152 LYS cc_start: 0.8598 (mttp) cc_final: 0.7450 (mmtt) REVERT: C 117 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7083 (mmt180) REVERT: D 63 ARG cc_start: 0.7449 (ptt-90) cc_final: 0.7140 (ptt-90) REVERT: D 119 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7606 (mm-30) REVERT: F 13 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7341 (mp) REVERT: F 76 CYS cc_start: 0.3166 (OUTLIER) cc_final: 0.0741 (t) REVERT: F 214 MET cc_start: 0.4929 (ptp) cc_final: 0.4390 (ptp) REVERT: F 233 PRO cc_start: 0.5494 (Cg_exo) cc_final: 0.5291 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7042 (m-80) cc_final: 0.6481 (m-80) REVERT: F 288 MET cc_start: 0.6630 (mmt) cc_final: 0.6413 (mmt) REVERT: F 307 TYR cc_start: 0.8091 (t80) cc_final: 0.7523 (t80) outliers start: 60 outliers final: 53 residues processed: 213 average time/residue: 0.1092 time to fit residues: 36.8369 Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 303 VAL 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 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 265 ILE 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 C residue 203 ILE 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 196 ASN 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=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: 2.9990 chunk 33 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3875 r_free = 0.3875 target = 0.177325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133339 restraints weight = 15064.768| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.78 r_work: 0.3082 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15060 Z= 0.184 Angle : 0.623 24.330 20437 Z= 0.290 Chirality : 0.045 0.174 2316 Planarity : 0.005 0.050 2566 Dihedral : 7.362 73.173 2229 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 3.95 % Allowed : 15.92 % Favored : 80.13 % 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 aren not related in a simple way. whole: -0.14 (0.19), residues: 1882 helix: 1.03 (0.19), residues: 834 sheet: -0.95 (0.43), residues: 148 loop : -1.00 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.013 0.001 TYR D 141 PHE 0.014 0.001 PHE A 423 TRP 0.028 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00463 (15054) covalent geometry : angle 0.55223 (20426) hydrogen bonds : bond 0.04521 ( 694) hydrogen bonds : angle 4.57782 ( 1974) metal coordination : bond 0.01384 ( 6) metal coordination : angle 12.41763 ( 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 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 40 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7390 (mmm160) REVERT: A 168 ASN cc_start: 0.8053 (m110) cc_final: 0.7527 (m110) REVERT: A 224 MET cc_start: 0.8623 (mtt) cc_final: 0.8372 (mtt) REVERT: B 112 MET cc_start: 0.8562 (mmp) cc_final: 0.7730 (mmt) REVERT: B 152 LYS cc_start: 0.8627 (mttp) cc_final: 0.7467 (mmtt) REVERT: C 117 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7112 (mmt180) REVERT: D 119 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 13 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7429 (mp) REVERT: F 214 MET cc_start: 0.5072 (ptp) cc_final: 0.4506 (ptp) REVERT: F 233 PRO cc_start: 0.5475 (Cg_exo) cc_final: 0.5251 (Cg_endo) REVERT: F 268 PHE cc_start: 0.7078 (m-80) cc_final: 0.6518 (m-80) REVERT: F 288 MET cc_start: 0.6686 (mmt) cc_final: 0.6382 (mmt) REVERT: F 307 TYR cc_start: 0.8154 (t80) cc_final: 0.7653 (t80) REVERT: F 371 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7631 (pm20) outliers start: 61 outliers final: 54 residues processed: 210 average time/residue: 0.1106 time to fit residues: 36.8875 Evaluate side-chains 214 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 196 THR 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 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 265 ILE 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 C residue 203 ILE 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 D residue 145 LEU 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 196 ASN 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: 0.7980 chunk 8 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 144 optimal weight: 0.0030 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 68 optimal weight: 0.0000 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** F 176 HIS ** 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 = 0.3916 r_free = 0.3916 target = 0.181441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.133270 restraints weight = 14952.497| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.88 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15060 Z= 0.104 Angle : 0.564 20.903 20437 Z= 0.261 Chirality : 0.042 0.169 2316 Planarity : 0.004 0.043 2566 Dihedral : 6.789 71.670 2227 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 2.72 % Allowed : 17.41 % Favored : 79.87 % 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 aren not related in a simple way. whole: 0.25 (0.20), residues: 1882 helix: 1.38 (0.19), residues: 833 sheet: -0.83 (0.42), residues: 152 loop : -0.80 (0.20), residues: 897 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 0.012 0.001 PHE E 28 TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00236 (15054) covalent geometry : angle 0.49803 (20426) hydrogen bonds : bond 0.03567 ( 694) hydrogen bonds : angle 4.40100 ( 1974) metal coordination : bond 0.01225 ( 6) metal coordination : angle 11.44521 ( 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 210 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 40 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7186 (mmt-90) REVERT: A 168 ASN cc_start: 0.7927 (m110) cc_final: 0.7472 (m110) REVERT: B 112 MET cc_start: 0.8577 (mmp) cc_final: 0.7808 (mmt) REVERT: B 152 LYS cc_start: 0.8509 (mttp) cc_final: 0.7338 (mmtt) REVERT: C 117 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7045 (mmt180) REVERT: D 63 ARG cc_start: 0.7299 (ptt-90) cc_final: 0.6972 (ptt-90) REVERT: D 119 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7409 (mm-30) REVERT: F 214 MET cc_start: 0.4994 (ptp) cc_final: 0.4198 (ptp) REVERT: F 233 PRO cc_start: 0.5595 (Cg_exo) cc_final: 0.5392 (Cg_endo) REVERT: F 268 PHE cc_start: 0.6902 (m-80) cc_final: 0.6338 (m-80) REVERT: F 307 TYR cc_start: 0.8062 (t80) cc_final: 0.7544 (t80) outliers start: 42 outliers final: 36 residues processed: 201 average time/residue: 0.1143 time to fit residues: 35.6631 Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 212 ASP 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 271 SER Chi-restraints excluded: chain B residue 366 VAL 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 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 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 196 ASN 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 57 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3866 r_free = 0.3866 target = 0.176435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131971 restraints weight = 14977.040| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.72 r_work: 0.3068 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15060 Z= 0.219 Angle : 0.658 25.263 20437 Z= 0.309 Chirality : 0.046 0.189 2316 Planarity : 0.005 0.053 2566 Dihedral : 7.040 72.019 2226 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.59 % Allowed : 17.67 % 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 aren not related in a simple way. whole: -0.15 (0.19), residues: 1882 helix: 1.00 (0.19), residues: 827 sheet: -0.83 (0.44), residues: 142 loop : -0.99 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.014 0.002 TYR D 141 PHE 0.018 0.002 PHE A 58 TRP 0.031 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00552 (15054) covalent geometry : angle 0.58865 (20426) hydrogen bonds : bond 0.04883 ( 694) hydrogen bonds : angle 4.64839 ( 1974) metal coordination : bond 0.01493 ( 6) metal coordination : angle 12.72287 ( 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 198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 40 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.7535 (mmt90) REVERT: A 168 ASN cc_start: 0.8077 (m110) cc_final: 0.7544 (m110) REVERT: B 112 MET cc_start: 0.8572 (mmp) cc_final: 0.7726 (mmt) REVERT: B 152 LYS cc_start: 0.8622 (mttp) cc_final: 0.7471 (mmtt) REVERT: C 117 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7113 (mmt180) REVERT: D 119 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7554 (mm-30) REVERT: F 13 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7441 (mp) REVERT: F 214 MET cc_start: 0.5103 (ptp) cc_final: 0.4536 (ptp) REVERT: F 233 PRO cc_start: 0.5673 (Cg_exo) cc_final: 0.5456 (Cg_endo) REVERT: F 268 PHE cc_start: 0.6967 (m-80) cc_final: 0.6242 (m-80) REVERT: F 307 TYR cc_start: 0.8200 (t80) cc_final: 0.7728 (t80) outliers start: 40 outliers final: 35 residues processed: 191 average time/residue: 0.1133 time to fit residues: 34.0105 Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 212 ASP 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 271 SER Chi-restraints excluded: chain B residue 366 VAL 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 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 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 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 196 ASN 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: 1.9990 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 165 optimal weight: 40.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.179335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134431 restraints weight = 14963.202| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.76 r_work: 0.3100 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15060 Z= 0.130 Angle : 0.593 22.728 20437 Z= 0.275 Chirality : 0.043 0.198 2316 Planarity : 0.004 0.052 2566 Dihedral : 6.797 70.914 2226 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 18.06 % Favored : 79.35 % 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 aren not related in a simple way. whole: -0.00 (0.19), residues: 1882 helix: 1.15 (0.19), residues: 835 sheet: -0.87 (0.44), residues: 143 loop : -0.94 (0.20), residues: 904 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 0.012 0.001 PHE A 58 TRP 0.024 0.001 TRP B 103 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00317 (15054) covalent geometry : angle 0.52383 (20426) hydrogen bonds : bond 0.03999 ( 694) hydrogen bonds : angle 4.49421 ( 1974) metal coordination : bond 0.01329 ( 6) metal coordination : angle 12.01569 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.60 seconds wall clock time: 73 minutes 59.58 seconds (4439.58 seconds total)