Starting phenix.real_space_refine on Sat Aug 8 14:07:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vct_43140/08_2026/8vct_43140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vct_43140/08_2026/8vct_43140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vct_43140/08_2026/8vct_43140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vct_43140/08_2026/8vct_43140.map" model { file = "/net/cci-nas-00/data/ceres_data/8vct_43140/08_2026/8vct_43140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vct_43140/08_2026/8vct_43140.cif" } resolution = 3.83 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 114 5.49 5 Mg 6 5.21 5 S 100 5.16 5 C 18034 2.51 5 N 5184 2.21 5 O 5560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29000 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3138 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain breaks: 1 Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "E" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "F" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "C" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3138 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain breaks: 1 Chain: "B" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "Y" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 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: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4133 SG CYS X 124 23.526 63.726 82.695 1.00 38.81 S ATOM 4154 SG CYS X 127 23.361 67.519 83.111 1.00 39.84 S ATOM 4372 SG CYS X 152 23.193 65.229 86.219 1.00 56.49 S ATOM 23429 SG CYS Y 124 94.735 32.656 41.863 1.00 59.32 S ATOM 23450 SG CYS Y 127 97.751 32.334 44.183 1.00 52.60 S ATOM 23668 SG CYS Y 152 98.032 34.436 40.844 1.00 64.30 S Time building chain proxies: 6.50, per 1000 atoms: 0.22 Number of scatterers: 29000 At special positions: 0 Unit cell: (186.39, 148.77, 166.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 100 16.00 P 114 15.00 Mg 6 11.99 O 5560 8.00 N 5184 7.00 C 18034 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: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb=" ZN Y 601 " pdb="ZN ZN Y 601 " - pdb=" ND1 HIS Y 155 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 124 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 127 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 152 " Number of angles added : 6 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6296 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 17 sheets defined 57.7% alpha, 4.5% beta 48 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 32 through 41 removed outlier: 3.548A pdb=" N ALA G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA G 38 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.641A pdb=" N ASP G 50 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 64 removed outlier: 3.602A pdb=" N HIS G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 89 removed outlier: 4.241A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 115 removed outlier: 4.051A pdb=" N GLY G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 149 removed outlier: 3.744A pdb=" N SER G 145 " --> pdb=" O GLY G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 181 through 188 removed outlier: 3.752A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 204 removed outlier: 3.614A pdb=" N ARG G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.611A pdb=" N ALA G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.641A pdb=" N SER G 240 " --> pdb=" O LEU G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 258 removed outlier: 4.320A pdb=" N PHE G 252 " --> pdb=" O MET G 248 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 271 through 277 removed outlier: 4.022A pdb=" N PHE G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 317 removed outlier: 3.869A pdb=" N ILE G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 341 removed outlier: 3.565A pdb=" N ARG G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 362 removed outlier: 3.628A pdb=" N LYS G 349 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.618A pdb=" N LEU G 379 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 392 removed outlier: 3.546A pdb=" N LEU G 386 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA G 388 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 399 removed outlier: 3.870A pdb=" N ARG G 399 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 23 removed outlier: 3.684A pdb=" N THR X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY X 21 " --> pdb=" O ILE X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 removed outlier: 3.637A pdb=" N LEU X 32 " --> pdb=" O SER X 28 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU X 33 " --> pdb=" O PRO X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 58 removed outlier: 3.750A pdb=" N HIS X 58 " --> pdb=" O VAL X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 76 through 79 Processing helix chain 'X' and resid 80 through 85 removed outlier: 3.626A pdb=" N VAL X 84 " --> pdb=" O TYR X 80 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 80 through 85' Processing helix chain 'X' and resid 85 through 98 removed outlier: 3.989A pdb=" N ILE X 93 " --> pdb=" O ARG X 89 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG X 94 " --> pdb=" O ASP X 90 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR X 98 " --> pdb=" O ARG X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 108 removed outlier: 4.160A pdb=" N HIS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU X 106 " --> pdb=" O GLY X 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.735A pdb=" N VAL X 128 " --> pdb=" O CYS X 124 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU X 130 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 168 removed outlier: 3.604A pdb=" N HIS X 168 " --> pdb=" O VAL X 165 " (cutoff:3.500A) Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 205 through 210 removed outlier: 4.182A pdb=" N GLU X 210 " --> pdb=" O ARG X 207 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 229 removed outlier: 4.237A pdb=" N LEU X 229 " --> pdb=" O LEU X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 240 through 250 removed outlier: 3.507A pdb=" N VAL X 246 " --> pdb=" O VAL X 242 " (cutoff:3.500A) Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 269 through 276 Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.781A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.641A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 53 removed outlier: 3.691A pdb=" N LYS E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.881A pdb=" N ARG E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 68 Processing helix chain 'E' and resid 73 through 89 removed outlier: 3.911A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 78 " --> pdb=" O GLY E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 Processing helix chain 'E' and resid 141 through 151 removed outlier: 3.584A pdb=" N SER E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.768A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.513A pdb=" N ARG E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 224 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.853A pdb=" N SER E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 243' Processing helix chain 'E' and resid 244 through 260 removed outlier: 3.665A pdb=" N ILE E 259 " --> pdb=" O MET E 255 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 275 removed outlier: 3.706A pdb=" N ILE E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 281 removed outlier: 3.832A pdb=" N SER E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.740A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.951A pdb=" N TRP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 362 removed outlier: 3.533A pdb=" N VAL E 347 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 382 through 392 removed outlier: 3.611A pdb=" N ARG E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 400 removed outlier: 3.527A pdb=" N TYR E 400 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 421 Processing helix chain 'E' and resid 426 through 436 removed outlier: 4.192A pdb=" N LYS E 430 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA E 431 " --> pdb=" O PRO E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 449 removed outlier: 3.851A pdb=" N MET E 446 " --> pdb=" O HIS E 442 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E 449 " --> pdb=" O LEU E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 467 removed outlier: 3.520A pdb=" N LEU E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 474 through 485 removed outlier: 3.817A pdb=" N LEU E 478 " --> pdb=" O LYS E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.673A pdb=" N ALA F 26 " --> pdb=" O PHE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 37 removed outlier: 4.091A pdb=" N ALA F 37 " --> pdb=" O SER F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 51 removed outlier: 3.762A pdb=" N LEU F 51 " --> pdb=" O SER F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 64 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 75 through 89 removed outlier: 3.664A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 114 removed outlier: 4.206A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 removed outlier: 3.887A pdb=" N ARG F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 195 removed outlier: 3.886A pdb=" N ILE F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.973A pdb=" N SER F 218 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.820A pdb=" N HIS F 236 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 268 through 276 removed outlier: 4.027A pdb=" N ARG F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE F 274 " --> pdb=" O LYS F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 removed outlier: 4.091A pdb=" N ARG F 284 " --> pdb=" O ARG F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 317 Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.534A pdb=" N ARG F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 362 removed outlier: 3.583A pdb=" N VAL F 347 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.862A pdb=" N LEU F 379 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 400 Processing helix chain 'F' and resid 407 through 424 removed outlier: 3.599A pdb=" N ILE F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 420 " --> pdb=" O GLN F 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 440 through 451 removed outlier: 3.694A pdb=" N LEU F 445 " --> pdb=" O ARG F 441 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N MET F 446 " --> pdb=" O HIS F 442 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU F 447 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU F 449 " --> pdb=" O LEU F 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP F 450 " --> pdb=" O MET F 446 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR F 451 " --> pdb=" O LEU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 467 removed outlier: 3.704A pdb=" N PHE F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F 465 " --> pdb=" O LYS F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 485 Proline residue: F 477 - end of helix removed outlier: 3.961A pdb=" N LEU F 480 " --> pdb=" O LEU F 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.782A pdb=" N ALA C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.685A pdb=" N LEU C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.611A pdb=" N HIS C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 removed outlier: 4.447A pdb=" N LEU C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.955A pdb=" N GLY C 108 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.535A pdb=" N SER C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.605A pdb=" N PHE C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 4.040A pdb=" N ARG C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.198A pdb=" N ALA C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.874A pdb=" N HIS C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.864A pdb=" N MET C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.519A pdb=" N PHE C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.780A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 378 Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 382 through 392 removed outlier: 4.196A pdb=" N ALA C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 65 through 68 Processing helix chain 'B' and resid 73 through 88 removed outlier: 4.474A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 4.327A pdb=" N HIS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.565A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.966A pdb=" N SER B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.862A pdb=" N HIS B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 238 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.529A pdb=" N PHE B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 270 through 276 removed outlier: 4.006A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.535A pdb=" N ARG B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.635A pdb=" N ILE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.574A pdb=" N ARG B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.627A pdb=" N VAL B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 378 Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.593A pdb=" N SER B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 removed outlier: 3.682A pdb=" N TYR B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 421 Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.777A pdb=" N LEU B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 452 through 467 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 471 through 485 Proline residue: B 477 - end of helix removed outlier: 3.811A pdb=" N GLU B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 24 removed outlier: 3.551A pdb=" N THR Y 16 " --> pdb=" O LEU Y 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY Y 21 " --> pdb=" O ILE Y 17 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 36 removed outlier: 3.944A pdb=" N LEU Y 32 " --> pdb=" O SER Y 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU Y 33 " --> pdb=" O PRO Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 59 Processing helix chain 'Y' and resid 66 through 74 Processing helix chain 'Y' and resid 76 through 79 removed outlier: 3.548A pdb=" N LEU Y 79 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 76 through 79' Processing helix chain 'Y' and resid 80 through 85 removed outlier: 3.797A pdb=" N VAL Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY Y 85 " --> pdb=" O ALA Y 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 80 through 85' Processing helix chain 'Y' and resid 85 through 97 removed outlier: 3.677A pdb=" N ILE Y 93 " --> pdb=" O ARG Y 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Y 94 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU Y 97 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 107 removed outlier: 3.521A pdb=" N VAL Y 104 " --> pdb=" O ALA Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.846A pdb=" N VAL Y 128 " --> pdb=" O CYS Y 124 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA Y 129 " --> pdb=" O PRO Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 201 through 203 No H-bonds generated for 'chain 'Y' and resid 201 through 203' Processing helix chain 'Y' and resid 214 through 230 removed outlier: 3.715A pdb=" N TRP Y 218 " --> pdb=" O SER Y 214 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR Y 219 " --> pdb=" O LEU Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 240 through 250 Processing helix chain 'Y' and resid 251 through 259 Processing helix chain 'Y' and resid 269 through 277 removed outlier: 3.837A pdb=" N PHE Y 275 " --> pdb=" O LEU Y 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG Y 276 " --> pdb=" O LYS Y 272 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS Y 277 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing helix chain 'Y' and resid 283 through 295 removed outlier: 4.014A pdb=" N HIS Y 287 " --> pdb=" O SER Y 283 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 310 removed outlier: 3.940A pdb=" N LEU Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.933A pdb=" N ALA A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.552A pdb=" N LYS A 53 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.971A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.801A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.961A pdb=" N ARG A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.545A pdb=" N LEU A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.514A pdb=" N HIS A 236 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.822A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.276A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 4.337A pdb=" N GLU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.545A pdb=" N ILE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.585A pdb=" N ARG A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.937A pdb=" N VAL A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.644A pdb=" N ARG A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 440 through 448 removed outlier: 4.088A pdb=" N TYR A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 455 through 467 removed outlier: 3.811A pdb=" N LYS A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 Proline residue: A 477 - end of helix removed outlier: 3.651A pdb=" N GLU A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.139A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 169 through 173 removed outlier: 3.572A pdb=" N MET G 264 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU G 132 " --> pdb=" O LEU G 265 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY G 267 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU G 134 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER G 131 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE G 291 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU G 133 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 299 through 300 removed outlier: 3.611A pdb=" N GLN G 300 " --> pdb=" O LYS G 303 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS G 303 " --> pdb=" O GLN G 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'X' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.303A pdb=" N LEU E 132 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY E 267 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 134 " --> pdb=" O GLY E 267 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE E 172 " --> pdb=" O ASP E 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 156 through 158 removed outlier: 3.745A pdb=" N GLN E 166 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 225 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 299 through 300 Processing sheet with id=AA8, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.505A pdb=" N TYR F 158 " --> pdb=" O ILE F 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 169 through 173 Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 7 removed outlier: 6.143A pdb=" N ILE C 6 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 226 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 168 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 232 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 264 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 132 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY C 267 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 134 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER C 131 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.410A pdb=" N ILE B 6 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 164 " --> pdb=" O HIS B 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.543A pdb=" N LEU B 132 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 291 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 135 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 120 through 123 removed outlier: 4.127A pdb=" N PHE Y 121 " --> pdb=" O PHE Y 161 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE Y 161 " --> pdb=" O PHE Y 121 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR Y 123 " --> pdb=" O VAL Y 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.909A pdb=" N GLY A 267 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 229 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 266 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 231 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 156 through 158 removed outlier: 3.585A pdb=" N ILE A 157 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 166 " --> pdb=" O ILE A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 299 through 300 1045 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 9657 1.36 - 1.51: 8160 1.51 - 1.66: 11787 1.66 - 1.80: 104 1.80 - 1.95: 62 Bond restraints: 29770 Sorted by residual: bond pdb=" O3B AGS C 601 " pdb=" PB AGS C 601 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O3B AGS G 601 " pdb=" PB AGS G 601 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O3A AGS C 601 " pdb=" PA AGS C 601 " ideal model delta sigma weight residual 1.664 1.583 0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O3A AGS G 601 " pdb=" PA AGS G 601 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C3' DT I 25 " pdb=" C2' DT I 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 29765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 40086 2.49 - 4.97: 570 4.97 - 7.46: 87 7.46 - 9.95: 21 9.95 - 12.44: 2 Bond angle restraints: 40766 Sorted by residual: angle pdb=" C LEU X 76 " pdb=" N PHE X 77 " pdb=" CA PHE X 77 " ideal model delta sigma weight residual 120.06 125.94 -5.88 1.19e+00 7.06e-01 2.45e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT I 12 " pdb=" C4 DT I 12 " pdb=" O4 DT I 12 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4 DT I 35 " pdb=" C4 DT I 35 " pdb=" C5 DT I 35 " ideal model delta sigma weight residual 124.90 121.81 3.09 7.00e-01 2.04e+00 1.94e+01 angle pdb=" N3 DT I 36 " pdb=" C4 DT I 36 " pdb=" O4 DT I 36 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 40761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 17011 35.88 - 71.77: 731 71.77 - 107.65: 76 107.65 - 143.54: 4 143.54 - 179.42: 2 Dihedral angle restraints: 17824 sinusoidal: 8082 harmonic: 9742 Sorted by residual: dihedral pdb=" C5' ADP E 601 " pdb=" O5' ADP E 601 " pdb=" PA ADP E 601 " pdb=" O2A ADP E 601 " ideal model delta sinusoidal sigma weight residual 300.00 120.58 179.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 96.68 -156.68 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 75.67 -135.67 1 2.00e+01 2.50e-03 4.12e+01 ... (remaining 17821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3834 0.056 - 0.112: 692 0.112 - 0.169: 57 0.169 - 0.225: 0 0.225 - 0.281: 3 Chirality restraints: 4586 Sorted by residual: chirality pdb=" CB VAL E 404 " pdb=" CA VAL E 404 " pdb=" CG1 VAL E 404 " pdb=" CG2 VAL E 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' AGS G 601 " pdb=" C2' AGS G 601 " pdb=" C4' AGS G 601 " pdb=" O3' AGS G 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' AGS C 601 " pdb=" C2' AGS C 601 " pdb=" C4' AGS C 601 " pdb=" O3' AGS C 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4583 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 405 " 0.088 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO A 406 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 406 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 406 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 336 " 0.025 2.00e-02 2.50e+03 2.88e-02 2.08e+01 pdb=" CG TRP A 336 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 336 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 336 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 336 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 336 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 336 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 336 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 336 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 336 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 482 " -0.018 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" CG TRP E 482 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 482 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP E 482 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 482 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 482 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 482 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 482 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 482 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E 482 " 0.006 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 244 2.64 - 3.20: 25147 3.20 - 3.77: 42757 3.77 - 4.33: 55593 4.33 - 4.90: 90287 Nonbonded interactions: 214028 Sorted by model distance: nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C 602 " model vdw 2.070 2.170 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 2.105 2.170 nonbonded pdb=" OE2 GLU E 233 " pdb="MG MG E 602 " model vdw 2.112 2.170 nonbonded pdb=" OG1 THR E 143 " pdb="MG MG E 602 " model vdw 2.128 2.170 nonbonded pdb=" O1B ADP B 601 " pdb="MG MG B 602 " model vdw 2.137 2.170 ... (remaining 214023 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 602) selection = chain 'B' selection = (chain 'E' and resid 4 through 602) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.61 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.870 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 29778 Z= 0.243 Angle : 0.737 12.437 40772 Z= 0.426 Chirality : 0.042 0.281 4586 Planarity : 0.005 0.131 4878 Dihedral : 18.517 179.420 11528 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3318 helix: -0.06 (0.13), residues: 1606 sheet: -0.48 (0.40), residues: 177 loop : -1.47 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG X 224 TYR 0.024 0.001 TYR Y 284 PHE 0.024 0.001 PHE B 464 TRP 0.078 0.003 TRP A 336 HIS 0.004 0.001 HIS Y 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.24 (29770) covalent geometry : angle 0.73679 / 0.43 (40766) hydrogen bonds : bond 0.18214 / 12.08 ( 1166) hydrogen bonds : angle 6.33156 / 4.50 ( 3275) metal coordination : bond 0.01091 / 0.64 ( 8) metal coordination : angle 2.13103 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 198 ASN cc_start: 0.8049 (p0) cc_final: 0.7721 (p0) REVERT: E 207 ARG cc_start: 0.6858 (ttt-90) cc_final: 0.6270 (tpt90) REVERT: C 320 LEU cc_start: 0.7924 (mt) cc_final: 0.7658 (tt) REVERT: C 334 ASP cc_start: 0.6724 (t0) cc_final: 0.6509 (t0) REVERT: C 390 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.7018 (tpm170) REVERT: Y 284 TYR cc_start: 0.7152 (p90) cc_final: 0.6754 (p90) REVERT: A 105 LEU cc_start: 0.8736 (mp) cc_final: 0.8529 (mp) REVERT: A 344 MET cc_start: 0.8633 (tpt) cc_final: 0.8374 (tpt) REVERT: A 402 ASP cc_start: 0.4764 (t70) cc_final: 0.4304 (t0) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.1730 time to fit residues: 116.0987 Evaluate side-chains 309 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 101 GLN ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN C 60 HIS C 246 GLN C 257 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 440 GLN Y 51 HIS A 52 GLN A 235 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.181812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152833 restraints weight = 45856.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153329 restraints weight = 114263.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152125 restraints weight = 58785.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150995 restraints weight = 68207.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151449 restraints weight = 49260.724| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29778 Z= 0.227 Angle : 0.730 11.462 40772 Z= 0.370 Chirality : 0.045 0.199 4586 Planarity : 0.005 0.065 4878 Dihedral : 18.990 141.324 4910 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 1.45 % Allowed : 9.79 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3318 helix: -0.09 (0.13), residues: 1652 sheet: -0.36 (0.41), residues: 164 loop : -1.60 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 224 TYR 0.018 0.002 TYR X 14 PHE 0.019 0.002 PHE B 464 TRP 0.043 0.002 TRP E 482 HIS 0.008 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (29770) covalent geometry : angle 0.72909 / 0.37 (40766) hydrogen bonds : bond 0.05836 / 3.99 ( 1166) hydrogen bonds : angle 5.04951 / 3.62 ( 3275) metal coordination : bond 0.01549 / 1.04 ( 8) metal coordination : angle 2.77367 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 339 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7331 (pp30) cc_final: 0.7109 (pp30) REVERT: G 306 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7409 (tm-30) REVERT: E 207 ARG cc_start: 0.7039 (ttt-90) cc_final: 0.6074 (tpt90) REVERT: F 192 ASP cc_start: 0.8108 (p0) cc_final: 0.7669 (p0) REVERT: C 198 ASN cc_start: 0.7950 (t0) cc_final: 0.7621 (t0) REVERT: C 390 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7164 (tpm170) REVERT: B 123 GLU cc_start: 0.6433 (tt0) cc_final: 0.6232 (tt0) REVERT: B 181 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7680 (mttt) REVERT: Y 221 PHE cc_start: 0.6317 (t80) cc_final: 0.5767 (t80) REVERT: A 344 MET cc_start: 0.8606 (tpt) cc_final: 0.8177 (tpt) REVERT: A 383 HIS cc_start: 0.6775 (m-70) cc_final: 0.6217 (m-70) REVERT: A 402 ASP cc_start: 0.4796 (t70) cc_final: 0.4330 (t0) outliers start: 42 outliers final: 29 residues processed: 365 average time/residue: 0.1643 time to fit residues: 96.1706 Evaluate side-chains 327 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 294 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 31 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 40.0000 chunk 244 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 52 GLN G 176 HIS ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 101 GLN ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Y 131 GLN Y 305 GLN A 235 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.181415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151386 restraints weight = 45278.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152438 restraints weight = 110758.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152047 restraints weight = 60310.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152260 restraints weight = 42367.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152594 restraints weight = 36218.023| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29778 Z= 0.165 Angle : 0.652 12.026 40772 Z= 0.329 Chirality : 0.042 0.185 4586 Planarity : 0.005 0.058 4878 Dihedral : 18.739 126.659 4910 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.90 % Allowed : 13.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3318 helix: 0.04 (0.13), residues: 1661 sheet: -0.27 (0.40), residues: 164 loop : -1.59 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 280 TYR 0.017 0.001 TYR Y 284 PHE 0.016 0.002 PHE Y 139 TRP 0.041 0.002 TRP E 482 HIS 0.011 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (29770) covalent geometry : angle 0.65111 / 0.33 (40766) hydrogen bonds : bond 0.05003 / 3.43 ( 1166) hydrogen bonds : angle 4.76503 / 3.43 ( 3275) metal coordination : bond 0.01225 / 0.80 ( 8) metal coordination : angle 2.41689 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7573 (pp30) cc_final: 0.7319 (pp30) REVERT: G 306 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7333 (tm-30) REVERT: E 203 TYR cc_start: 0.5879 (m-80) cc_final: 0.5638 (m-80) REVERT: E 207 ARG cc_start: 0.6984 (ttt-90) cc_final: 0.6107 (tpt90) REVERT: C 235 GLN cc_start: 0.7321 (tp40) cc_final: 0.6979 (tm-30) REVERT: B 32 GLU cc_start: 0.5821 (pp20) cc_final: 0.5449 (pp20) REVERT: Y 32 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5444 (mt) REVERT: A 383 HIS cc_start: 0.6658 (m-70) cc_final: 0.6032 (m-70) REVERT: A 402 ASP cc_start: 0.4746 (t70) cc_final: 0.4202 (t0) outliers start: 55 outliers final: 43 residues processed: 344 average time/residue: 0.1580 time to fit residues: 88.5551 Evaluate side-chains 331 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 299 optimal weight: 20.0000 chunk 157 optimal weight: 0.0170 chunk 122 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Y 58 HIS Y 305 GLN A 235 GLN A 473 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153279 restraints weight = 44877.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153103 restraints weight = 107634.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150868 restraints weight = 54969.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149810 restraints weight = 69009.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150063 restraints weight = 56018.892| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29778 Z= 0.134 Angle : 0.620 11.863 40772 Z= 0.312 Chirality : 0.041 0.212 4586 Planarity : 0.004 0.057 4878 Dihedral : 18.545 125.678 4910 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.93 % Allowed : 15.17 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3318 helix: 0.16 (0.13), residues: 1665 sheet: -0.21 (0.40), residues: 164 loop : -1.55 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 333 TYR 0.023 0.001 TYR B 375 PHE 0.013 0.001 PHE B 464 TRP 0.048 0.002 TRP E 482 HIS 0.008 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (29770) covalent geometry : angle 0.61899 / 0.31 (40766) hydrogen bonds : bond 0.04435 / 3.06 ( 1166) hydrogen bonds : angle 4.62501 / 3.34 ( 3275) metal coordination : bond 0.01078 / 0.70 ( 8) metal coordination : angle 2.44581 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 ASN cc_start: 0.7835 (m-40) cc_final: 0.7159 (m-40) REVERT: G 45 GLN cc_start: 0.7724 (pp30) cc_final: 0.7458 (pp30) REVERT: G 306 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7306 (tm-30) REVERT: E 207 ARG cc_start: 0.6932 (ttt-90) cc_final: 0.6046 (tpt90) REVERT: F 192 ASP cc_start: 0.8015 (p0) cc_final: 0.7606 (p0) REVERT: C 104 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: C 235 GLN cc_start: 0.7364 (tp40) cc_final: 0.6986 (tm-30) REVERT: B 32 GLU cc_start: 0.5800 (pp20) cc_final: 0.5319 (pp20) REVERT: Y 221 PHE cc_start: 0.6079 (t80) cc_final: 0.5820 (t80) REVERT: A 344 MET cc_start: 0.8183 (tpt) cc_final: 0.7695 (tpt) REVERT: A 383 HIS cc_start: 0.6667 (m-70) cc_final: 0.6018 (m-70) outliers start: 56 outliers final: 41 residues processed: 348 average time/residue: 0.1622 time to fit residues: 92.1893 Evaluate side-chains 326 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 135 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 290 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Y 58 HIS Y 305 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152744 restraints weight = 45025.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152328 restraints weight = 115806.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150922 restraints weight = 58011.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150052 restraints weight = 60703.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150414 restraints weight = 47447.473| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29778 Z= 0.141 Angle : 0.614 11.677 40772 Z= 0.309 Chirality : 0.041 0.177 4586 Planarity : 0.004 0.061 4878 Dihedral : 18.398 125.691 4910 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.34 % Allowed : 16.00 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3318 helix: 0.20 (0.13), residues: 1674 sheet: -0.34 (0.38), residues: 177 loop : -1.51 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 333 TYR 0.023 0.001 TYR B 337 PHE 0.017 0.001 PHE Y 282 TRP 0.044 0.002 TRP E 482 HIS 0.010 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (29770) covalent geometry : angle 0.61346 / 0.31 (40766) hydrogen bonds : bond 0.04298 / 2.97 ( 1166) hydrogen bonds : angle 4.53813 / 3.27 ( 3275) metal coordination : bond 0.01102 / 0.73 ( 8) metal coordination : angle 2.39484 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 302 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7834 (pp30) cc_final: 0.7451 (pp30) REVERT: G 306 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 207 ARG cc_start: 0.6945 (ttt-90) cc_final: 0.6064 (tpt90) REVERT: F 192 ASP cc_start: 0.8029 (p0) cc_final: 0.7710 (p0) REVERT: C 104 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7694 (t-90) REVERT: C 126 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.7174 (tpp-160) REVERT: C 235 GLN cc_start: 0.7396 (tp40) cc_final: 0.7042 (tm-30) REVERT: C 390 ARG cc_start: 0.7873 (tpm170) cc_final: 0.7360 (ttp-110) REVERT: B 32 GLU cc_start: 0.5890 (pp20) cc_final: 0.5390 (pp20) REVERT: B 344 MET cc_start: 0.8358 (ttm) cc_final: 0.7939 (ttm) REVERT: Y 32 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5301 (mt) REVERT: Y 282 PHE cc_start: 0.6132 (t80) cc_final: 0.5597 (t80) REVERT: A 383 HIS cc_start: 0.6705 (m-70) cc_final: 0.6006 (m-70) outliers start: 68 outliers final: 47 residues processed: 351 average time/residue: 0.1593 time to fit residues: 90.7541 Evaluate side-chains 336 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 280 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 172 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS Y 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150664 restraints weight = 45026.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151712 restraints weight = 111524.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151317 restraints weight = 58212.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151431 restraints weight = 42686.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151740 restraints weight = 36511.859| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29778 Z= 0.158 Angle : 0.631 11.822 40772 Z= 0.316 Chirality : 0.041 0.175 4586 Planarity : 0.004 0.066 4878 Dihedral : 18.291 127.113 4910 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 2.59 % Allowed : 16.59 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3318 helix: 0.23 (0.13), residues: 1667 sheet: -0.34 (0.38), residues: 177 loop : -1.55 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 202 TYR 0.012 0.001 TYR Y 284 PHE 0.017 0.002 PHE Y 282 TRP 0.055 0.002 TRP E 482 HIS 0.008 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (29770) covalent geometry : angle 0.62993 / 0.32 (40766) hydrogen bonds : bond 0.04400 / 3.03 ( 1166) hydrogen bonds : angle 4.52226 / 3.26 ( 3275) metal coordination : bond 0.01210 / 0.81 ( 8) metal coordination : angle 2.48949 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 306 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7926 (pp30) cc_final: 0.7502 (pp30) REVERT: G 306 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 207 ARG cc_start: 0.6957 (ttt-90) cc_final: 0.6082 (tpt90) REVERT: F 192 ASP cc_start: 0.8049 (p0) cc_final: 0.7770 (p0) REVERT: C 104 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7758 (t-90) REVERT: C 198 ASN cc_start: 0.8157 (t0) cc_final: 0.7776 (t0) REVERT: B 32 GLU cc_start: 0.5934 (pp20) cc_final: 0.5456 (pp20) REVERT: B 344 MET cc_start: 0.8350 (ttm) cc_final: 0.7972 (ttm) REVERT: Y 32 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.5354 (mt) REVERT: A 383 HIS cc_start: 0.6534 (m-70) cc_final: 0.5902 (m-70) outliers start: 75 outliers final: 50 residues processed: 361 average time/residue: 0.1612 time to fit residues: 95.0549 Evaluate side-chains 343 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain Y residue 271 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 309 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 296 optimal weight: 0.5980 chunk 319 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 320 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 319 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS Y 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154157 restraints weight = 45028.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154017 restraints weight = 114033.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152906 restraints weight = 58596.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151962 restraints weight = 65811.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152421 restraints weight = 47792.781| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29778 Z= 0.125 Angle : 0.609 11.421 40772 Z= 0.304 Chirality : 0.040 0.166 4586 Planarity : 0.004 0.068 4878 Dihedral : 18.158 126.614 4910 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 2.14 % Allowed : 17.55 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3318 helix: 0.31 (0.13), residues: 1683 sheet: -0.29 (0.38), residues: 177 loop : -1.48 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 238 TYR 0.011 0.001 TYR Y 123 PHE 0.019 0.001 PHE Y 282 TRP 0.054 0.002 TRP E 482 HIS 0.006 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (29770) covalent geometry : angle 0.60848 / 0.30 (40766) hydrogen bonds : bond 0.03951 / 2.74 ( 1166) hydrogen bonds : angle 4.41235 / 3.18 ( 3275) metal coordination : bond 0.01038 / 0.67 ( 8) metal coordination : angle 2.29947 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7960 (pp30) cc_final: 0.7486 (pp30) REVERT: G 268 THR cc_start: 0.6351 (OUTLIER) cc_final: 0.6107 (m) REVERT: G 306 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7303 (tm-30) REVERT: E 207 ARG cc_start: 0.6956 (ttt-90) cc_final: 0.6052 (tpt90) REVERT: C 104 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7694 (t-90) REVERT: C 126 ARG cc_start: 0.7522 (tpp-160) cc_final: 0.7076 (mmp80) REVERT: C 198 ASN cc_start: 0.8196 (t0) cc_final: 0.7822 (t0) REVERT: C 235 GLN cc_start: 0.7371 (tp40) cc_final: 0.7048 (tm-30) REVERT: B 32 GLU cc_start: 0.5999 (pp20) cc_final: 0.5478 (pp20) REVERT: B 52 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6339 (pp30) REVERT: Y 32 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5279 (mt) REVERT: A 318 LEU cc_start: 0.7837 (mp) cc_final: 0.7613 (mp) REVERT: A 383 HIS cc_start: 0.6633 (m-70) cc_final: 0.5978 (m-70) outliers start: 62 outliers final: 43 residues processed: 362 average time/residue: 0.1604 time to fit residues: 92.9628 Evaluate side-chains 352 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 336 TRP Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 325 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 224 optimal weight: 0.0470 chunk 87 optimal weight: 7.9990 chunk 278 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 273 optimal weight: 0.0870 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154095 restraints weight = 45247.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154375 restraints weight = 109565.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152829 restraints weight = 56078.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152208 restraints weight = 58879.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152380 restraints weight = 47523.684| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29778 Z= 0.132 Angle : 0.617 11.284 40772 Z= 0.308 Chirality : 0.040 0.160 4586 Planarity : 0.004 0.067 4878 Dihedral : 18.091 129.193 4910 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 2.45 % Allowed : 17.52 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3318 helix: 0.32 (0.13), residues: 1691 sheet: -0.21 (0.38), residues: 175 loop : -1.48 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 11 TYR 0.014 0.001 TYR B 375 PHE 0.014 0.001 PHE Y 221 TRP 0.052 0.002 TRP E 482 HIS 0.005 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (29770) covalent geometry : angle 0.61631 / 0.31 (40766) hydrogen bonds : bond 0.03923 / 2.72 ( 1166) hydrogen bonds : angle 4.37626 / 3.16 ( 3275) metal coordination : bond 0.01057 / 0.70 ( 8) metal coordination : angle 2.29764 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7990 (pp30) cc_final: 0.7494 (pp30) REVERT: G 268 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.6052 (m) REVERT: G 306 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 207 ARG cc_start: 0.6923 (ttt-90) cc_final: 0.6034 (tpt90) REVERT: E 435 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.3077 (mt) REVERT: C 11 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6903 (ttp-170) REVERT: C 58 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (ttp80) REVERT: C 104 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7666 (t-90) REVERT: C 198 ASN cc_start: 0.8199 (t0) cc_final: 0.7773 (t0) REVERT: C 235 GLN cc_start: 0.7348 (tp40) cc_final: 0.7003 (tm-30) REVERT: B 32 GLU cc_start: 0.6006 (pp20) cc_final: 0.5482 (pp20) REVERT: B 52 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6403 (pp30) REVERT: Y 32 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5278 (mt) REVERT: A 383 HIS cc_start: 0.6695 (m-70) cc_final: 0.6042 (m-70) outliers start: 71 outliers final: 50 residues processed: 367 average time/residue: 0.1604 time to fit residues: 95.6080 Evaluate side-chains 351 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 336 TRP Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 TRP Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 308 TRP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 71 optimal weight: 50.0000 chunk 260 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 190 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 309 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 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 = 0.4108 r_free = 0.4108 target = 0.180059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149744 restraints weight = 45073.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150447 restraints weight = 124574.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150698 restraints weight = 65179.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151693 restraints weight = 40956.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151742 restraints weight = 34249.581| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29778 Z= 0.201 Angle : 0.678 12.057 40772 Z= 0.339 Chirality : 0.043 0.182 4586 Planarity : 0.004 0.070 4878 Dihedral : 18.152 134.258 4910 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.82 % Rotamer: Outliers : 2.14 % Allowed : 18.62 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3318 helix: 0.21 (0.13), residues: 1694 sheet: -0.44 (0.38), residues: 179 loop : -1.54 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 11 TYR 0.013 0.002 TYR X 14 PHE 0.018 0.002 PHE X 161 TRP 0.048 0.002 TRP E 482 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (29770) covalent geometry : angle 0.67761 / 0.34 (40766) hydrogen bonds : bond 0.04444 / 3.05 ( 1166) hydrogen bonds : angle 4.49547 / 3.24 ( 3275) metal coordination : bond 0.01371 / 0.92 ( 8) metal coordination : angle 2.48622 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7996 (pp30) cc_final: 0.7465 (pp30) REVERT: G 306 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7387 (tm-30) REVERT: E 207 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6099 (tpt90) REVERT: E 435 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.2978 (mt) REVERT: C 104 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7850 (t-90) REVERT: C 126 ARG cc_start: 0.7492 (tpp-160) cc_final: 0.7092 (mmp80) REVERT: C 198 ASN cc_start: 0.8296 (t0) cc_final: 0.7927 (t0) REVERT: C 235 GLN cc_start: 0.7530 (tp40) cc_final: 0.7149 (tm-30) REVERT: B 32 GLU cc_start: 0.6069 (pp20) cc_final: 0.5530 (pp20) REVERT: B 52 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6434 (pp30) REVERT: Y 32 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5169 (mt) REVERT: A 383 HIS cc_start: 0.6608 (m-70) cc_final: 0.5959 (m90) outliers start: 62 outliers final: 54 residues processed: 346 average time/residue: 0.1549 time to fit residues: 86.8568 Evaluate side-chains 352 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 336 TRP Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain Y residue 282 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 225 optimal weight: 3.9990 chunk 79 optimal weight: 50.0000 chunk 161 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 242 optimal weight: 0.9980 chunk 75 optimal weight: 50.0000 chunk 123 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** 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 = 0.4106 r_free = 0.4106 target = 0.180026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151315 restraints weight = 44624.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151601 restraints weight = 117964.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150084 restraints weight = 56315.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150283 restraints weight = 42196.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150666 restraints weight = 33353.593| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29778 Z= 0.151 Angle : 0.651 11.804 40772 Z= 0.325 Chirality : 0.041 0.163 4586 Planarity : 0.004 0.070 4878 Dihedral : 18.101 133.805 4910 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 2.14 % Allowed : 18.83 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3318 helix: 0.23 (0.13), residues: 1692 sheet: -0.28 (0.38), residues: 175 loop : -1.52 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 11 TYR 0.027 0.001 TYR E 444 PHE 0.015 0.001 PHE X 161 TRP 0.048 0.002 TRP E 482 HIS 0.004 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (29770) covalent geometry : angle 0.65006 / 0.32 (40766) hydrogen bonds : bond 0.04125 / 2.83 ( 1166) hydrogen bonds : angle 4.44965 / 3.21 ( 3275) metal coordination : bond 0.01150 / 0.76 ( 8) metal coordination : angle 2.35939 / 1.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: G 45 GLN cc_start: 0.8012 (pp30) cc_final: 0.7489 (pp30) REVERT: G 306 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7329 (tm-30) REVERT: E 207 ARG cc_start: 0.6951 (ttt-90) cc_final: 0.5990 (tpt90) REVERT: E 344 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7010 (tpt) REVERT: E 435 LEU cc_start: 0.4330 (OUTLIER) cc_final: 0.3180 (mt) REVERT: F 192 ASP cc_start: 0.8130 (p0) cc_final: 0.7766 (p0) REVERT: C 11 ARG cc_start: 0.7104 (ttp-170) cc_final: 0.6804 (ptp-170) REVERT: C 126 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.7214 (mmp80) REVERT: C 198 ASN cc_start: 0.8269 (t0) cc_final: 0.7941 (t0) REVERT: C 217 MET cc_start: 0.7389 (ttt) cc_final: 0.7137 (ttt) REVERT: C 235 GLN cc_start: 0.7452 (tp40) cc_final: 0.7079 (tm-30) REVERT: B 32 GLU cc_start: 0.6060 (pp20) cc_final: 0.5574 (pp20) REVERT: B 52 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6422 (pp30) REVERT: Y 32 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5292 (mt) REVERT: A 383 HIS cc_start: 0.6598 (m-70) cc_final: 0.5932 (m90) outliers start: 62 outliers final: 55 residues processed: 348 average time/residue: 0.1558 time to fit residues: 87.5090 Evaluate side-chains 348 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 336 TRP Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 482 TRP Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 32 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 210 GLU Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain Y residue 271 LEU Chi-restraints excluded: chain Y residue 282 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 336 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 142 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 333 optimal weight: 3.9990 chunk 337 optimal weight: 4.9990 chunk 165 optimal weight: 0.0570 chunk 12 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 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 = 0.4129 r_free = 0.4129 target = 0.182121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152594 restraints weight = 45413.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154030 restraints weight = 111974.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153759 restraints weight = 54359.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153897 restraints weight = 40846.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154273 restraints weight = 34266.382| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29778 Z= 0.134 Angle : 0.641 11.548 40772 Z= 0.319 Chirality : 0.041 0.221 4586 Planarity : 0.004 0.072 4878 Dihedral : 18.018 133.979 4910 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.17 % Allowed : 18.90 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3318 helix: 0.30 (0.13), residues: 1664 sheet: -0.22 (0.38), residues: 175 loop : -1.45 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 441 TYR 0.044 0.001 TYR E 444 PHE 0.017 0.001 PHE Y 221 TRP 0.048 0.002 TRP E 482 HIS 0.004 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (29770) covalent geometry : angle 0.64000 / 0.32 (40766) hydrogen bonds : bond 0.03931 / 2.71 ( 1166) hydrogen bonds : angle 4.41809 / 3.18 ( 3275) metal coordination : bond 0.01051 / 0.69 ( 8) metal coordination : angle 2.29066 / 1.06 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3762.35 seconds wall clock time: 65 minutes 56.03 seconds (3956.03 seconds total)