Starting phenix.real_space_refine on Mon May 26 19:13:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vct_43140/05_2025/8vct_43140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vct_43140/05_2025/8vct_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_43140/05_2025/8vct_43140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vct_43140/05_2025/8vct_43140.map" model { file = "/net/cci-nas-00/data/ceres_data/8vct_43140/05_2025/8vct_43140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vct_43140/05_2025/8vct_43140.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.35, per 1000 atoms: 0.60 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: 7.35 Conformation dependent library (CDL) restraints added in 3.6 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: 9.23 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: 9.67 Time building geometry restraints manager: 8.46 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=" CG PRO A 406 " pdb=" CD PRO A 406 " ideal model delta sigma weight residual 1.503 1.407 0.096 3.40e-02 8.65e+02 8.01e+00 bond pdb=" CB PRO A 406 " pdb=" CG PRO A 406 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.71e+00 bond pdb=" CA CYS C 184 " pdb=" C CYS C 184 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.72e-02 3.38e+03 2.31e+00 bond pdb=" C VAL A 405 " pdb=" N PRO A 406 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.31e-02 5.83e+03 1.92e+00 bond pdb=" CA MET B 255 " pdb=" C MET B 255 " ideal model delta sigma weight residual 1.518 1.573 -0.055 4.01e-02 6.22e+02 1.91e+00 ... (remaining 29765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 40179 2.49 - 4.97: 495 4.97 - 7.46: 82 7.46 - 9.95: 8 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=" CA PRO A 406 " pdb=" N PRO A 406 " pdb=" CD PRO A 406 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.92e+01 angle pdb=" N PRO A 406 " pdb=" CD PRO A 406 " pdb=" CG PRO A 406 " ideal model delta sigma weight residual 103.20 97.11 6.09 1.50e+00 4.44e-01 1.65e+01 angle pdb=" N TRP A 336 " pdb=" CA TRP A 336 " pdb=" CB TRP A 336 " ideal model delta sigma weight residual 110.39 116.47 -6.08 1.66e+00 3.63e-01 1.34e+01 angle pdb=" CA LEU B 475 " pdb=" CB LEU B 475 " pdb=" CG LEU B 475 " ideal model delta sigma weight residual 116.30 128.74 -12.44 3.50e+00 8.16e-02 1.26e+01 ... (remaining 40761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 17011 35.88 - 71.77: 721 71.77 - 107.65: 48 107.65 - 143.54: 6 143.54 - 179.42: 2 Dihedral angle restraints: 17788 sinusoidal: 8046 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 17785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3916 0.056 - 0.112: 620 0.112 - 0.169: 53 0.169 - 0.225: 0 0.225 - 0.281: 1 Chirality restraints: 4590 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=" CB VAL E 405 " pdb=" CA VAL E 405 " pdb=" CG1 VAL E 405 " pdb=" CG2 VAL E 405 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB THR G 299 " pdb=" CA THR G 299 " pdb=" OG1 THR G 299 " pdb=" CG2 THR G 299 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 4587 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 485 or resid 601 through 602)) selection = chain 'B' selection = (chain 'E' and (resid 4 through 485 or resid 601 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: 2.870 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: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 72.250 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29778 Z= 0.136 Angle : 0.688 12.437 40772 Z= 0.354 Chirality : 0.041 0.281 4590 Planarity : 0.005 0.131 4878 Dihedral : 18.146 179.420 11492 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.078 0.003 TRP A 336 HIS 0.004 0.001 HIS Y 236 PHE 0.024 0.001 PHE B 464 TYR 0.024 0.001 TYR Y 284 ARG 0.017 0.000 ARG X 224 Details of bonding type rmsd hydrogen bonds : bond 0.18214 ( 1166) hydrogen bonds : angle 6.33156 ( 3275) metal coordination : bond 0.01091 ( 8) metal coordination : angle 2.13103 ( 6) covalent geometry : bond 0.00290 (29770) covalent geometry : angle 0.68805 (40766) *********************** 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 : 2.796 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: 0.6271 (tpt90) REVERT: C 320 LEU cc_start: 0.7923 (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: 0.8528 (mp) REVERT: A 344 MET cc_start: 0.8633 (tpt) cc_final: 0.8375 (tpt) REVERT: A 402 ASP cc_start: 0.4764 (t70) cc_final: 0.4305 (t0) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.3841 time to fit residues: 254.7511 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 : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 1.9990 chunk 259 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 199 optimal weight: 0.0970 chunk 310 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 440 GLN Y 51 HIS 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 = 0.181586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152708 restraints weight = 44880.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153105 restraints weight = 113196.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151869 restraints weight = 59398.190| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29778 Z= 0.166 Angle : 0.657 11.148 40772 Z= 0.330 Chirality : 0.041 0.176 4590 Planarity : 0.005 0.069 4878 Dihedral : 18.273 131.328 4874 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 1.17 % Allowed : 9.76 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3318 helix: 0.04 (0.13), residues: 1660 sheet: -0.42 (0.39), residues: 177 loop : -1.50 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 482 HIS 0.009 0.001 HIS C 383 PHE 0.015 0.001 PHE F 464 TYR 0.017 0.001 TYR F 158 ARG 0.005 0.000 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 1166) hydrogen bonds : angle 4.81922 ( 3275) metal coordination : bond 0.01437 ( 8) metal coordination : angle 2.55533 ( 6) covalent geometry : bond 0.00388 (29770) covalent geometry : angle 0.65613 (40766) *********************** 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 377 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 343 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7418 (pp30) cc_final: 0.7204 (pp30) REVERT: G 306 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7319 (tm-30) REVERT: E 207 ARG cc_start: 0.6969 (ttt-90) cc_final: 0.6114 (tpt90) REVERT: F 192 ASP cc_start: 0.8002 (p0) cc_final: 0.7588 (p0) REVERT: C 198 ASN cc_start: 0.7794 (t0) cc_final: 0.7437 (t0) REVERT: C 390 ARG cc_start: 0.7395 (ttp-110) cc_final: 0.7177 (tpm170) REVERT: B 123 GLU cc_start: 0.6380 (tt0) cc_final: 0.6146 (tt0) REVERT: Y 221 PHE cc_start: 0.6276 (t80) cc_final: 0.5772 (t80) REVERT: A 344 MET cc_start: 0.8471 (tpt) cc_final: 0.8044 (tpt) REVERT: A 383 HIS cc_start: 0.6734 (m-70) cc_final: 0.6176 (m-70) REVERT: A 402 ASP cc_start: 0.4629 (t70) cc_final: 0.4176 (t0) outliers start: 34 outliers final: 25 residues processed: 363 average time/residue: 0.3952 time to fit residues: 228.9812 Evaluate side-chains 318 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 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 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 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 210 GLU Chi-restraints excluded: chain Y residue 270 TRP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 192 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 169 optimal weight: 0.0270 chunk 324 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 306 optimal weight: 0.1980 chunk 159 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 58 HIS Y 305 GLN A 104 HIS ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149323 restraints weight = 44854.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149806 restraints weight = 112055.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150558 restraints weight = 77546.947| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29778 Z= 0.169 Angle : 0.635 11.699 40772 Z= 0.321 Chirality : 0.041 0.165 4590 Planarity : 0.005 0.059 4878 Dihedral : 18.145 126.911 4874 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3318 helix: 0.14 (0.13), residues: 1657 sheet: -0.45 (0.39), residues: 177 loop : -1.53 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 482 HIS 0.008 0.001 HIS C 383 PHE 0.014 0.002 PHE B 464 TYR 0.018 0.001 TYR Y 284 ARG 0.009 0.000 ARG E 280 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1166) hydrogen bonds : angle 4.61801 ( 3275) metal coordination : bond 0.01280 ( 8) metal coordination : angle 2.47042 ( 6) covalent geometry : bond 0.00400 (29770) covalent geometry : angle 0.63410 (40766) *********************** 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 378 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7648 (pp30) cc_final: 0.7386 (pp30) REVERT: G 306 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7338 (tm-30) REVERT: X 27 VAL cc_start: 0.8328 (p) cc_final: 0.8119 (p) REVERT: E 207 ARG cc_start: 0.7008 (ttt-90) cc_final: 0.6068 (tpt90) REVERT: F 192 ASP cc_start: 0.8010 (p0) cc_final: 0.7715 (p0) REVERT: C 198 ASN cc_start: 0.8000 (t0) cc_final: 0.7595 (t0) REVERT: B 123 GLU cc_start: 0.6434 (tt0) cc_final: 0.6216 (tt0) REVERT: B 344 MET cc_start: 0.8387 (ttm) cc_final: 0.7904 (ttm) REVERT: A 344 MET cc_start: 0.8451 (tpt) cc_final: 0.8232 (tpt) REVERT: A 383 HIS cc_start: 0.6795 (m-70) cc_final: 0.6177 (m-70) REVERT: A 402 ASP cc_start: 0.4661 (t70) cc_final: 0.4127 (t0) outliers start: 54 outliers final: 38 residues processed: 362 average time/residue: 0.3961 time to fit residues: 229.2340 Evaluate side-chains 336 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 3.009 ------------------------------------------------------------------------------- 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 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 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 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 108 LEU Chi-restraints excluded: chain Y residue 210 GLU 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 192 ASP Chi-restraints excluded: chain A residue 294 ASP 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 338 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 337 optimal weight: 0.0010 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 319 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 119 ASN ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN Y 58 HIS Y 131 GLN Y 305 GLN A 473 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158409 restraints weight = 45295.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157072 restraints weight = 100964.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153560 restraints weight = 54052.203| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29778 Z= 0.107 Angle : 0.579 10.825 40772 Z= 0.289 Chirality : 0.039 0.186 4590 Planarity : 0.004 0.062 4878 Dihedral : 17.974 127.414 4874 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.17 % Allowed : 14.72 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3318 helix: 0.43 (0.13), residues: 1643 sheet: -0.14 (0.39), residues: 175 loop : -1.38 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 482 HIS 0.006 0.001 HIS C 383 PHE 0.015 0.001 PHE Y 221 TYR 0.016 0.001 TYR Y 284 ARG 0.005 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1166) hydrogen bonds : angle 4.34575 ( 3275) metal coordination : bond 0.00964 ( 8) metal coordination : angle 2.06508 ( 6) covalent geometry : bond 0.00226 (29770) covalent geometry : angle 0.57850 (40766) *********************** 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 370 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 336 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7787 (pp30) cc_final: 0.7484 (pp30) REVERT: G 306 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7237 (tm-30) REVERT: X 27 VAL cc_start: 0.8404 (p) cc_final: 0.8180 (p) REVERT: X 107 MET cc_start: 0.8180 (tmm) cc_final: 0.7923 (tpp) REVERT: E 207 ARG cc_start: 0.6985 (ttt-90) cc_final: 0.6003 (tpt90) REVERT: C 104 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7401 (t-90) REVERT: B 32 GLU cc_start: 0.5761 (pp20) cc_final: 0.5348 (pp20) REVERT: Y 32 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5316 (mt) REVERT: A 383 HIS cc_start: 0.6655 (m-70) cc_final: 0.5995 (m-70) outliers start: 34 outliers final: 18 residues processed: 361 average time/residue: 0.4032 time to fit residues: 229.6953 Evaluate side-chains 326 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 306 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 413 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 355 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 336 TRP 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 336 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 chunk 138 optimal weight: 2.9990 chunk 278 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 283 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 overall best weight: 0.8538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS Y 105 HIS ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155588 restraints weight = 45055.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156611 restraints weight = 109186.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156641 restraints weight = 62927.949| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29778 Z= 0.112 Angle : 0.571 9.986 40772 Z= 0.285 Chirality : 0.038 0.146 4590 Planarity : 0.004 0.065 4878 Dihedral : 17.901 127.594 4874 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.83 % Allowed : 15.24 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3318 helix: 0.50 (0.13), residues: 1661 sheet: -0.08 (0.39), residues: 175 loop : -1.32 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 482 HIS 0.006 0.000 HIS C 383 PHE 0.014 0.001 PHE E 351 TYR 0.017 0.001 TYR Y 284 ARG 0.006 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1166) hydrogen bonds : angle 4.25849 ( 3275) metal coordination : bond 0.00891 ( 8) metal coordination : angle 2.07465 ( 6) covalent geometry : bond 0.00253 (29770) covalent geometry : angle 0.57003 (40766) *********************** 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 375 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7921 (pp30) cc_final: 0.7567 (pp30) REVERT: G 306 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7147 (tm-30) REVERT: X 27 VAL cc_start: 0.8331 (p) cc_final: 0.8099 (p) REVERT: E 207 ARG cc_start: 0.6991 (ttt-90) cc_final: 0.6054 (tpt90) REVERT: C 104 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7541 (t-90) REVERT: B 32 GLU cc_start: 0.5769 (pp20) cc_final: 0.5367 (pp20) REVERT: Y 32 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5239 (mt) REVERT: Y 221 PHE cc_start: 0.6109 (t80) cc_final: 0.5678 (t80) REVERT: Y 282 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.5709 (t80) outliers start: 53 outliers final: 27 residues processed: 357 average time/residue: 0.4014 time to fit residues: 225.5257 Evaluate side-chains 327 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain X residue 175 LEU 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 63 CYS 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 385 MET Chi-restraints excluded: chain C residue 389 LEU 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 404 VAL Chi-restraints excluded: chain Y residue 32 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 336 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 206 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 308 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 311 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** F 208 HIS C 355 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN Y 39 ASN A 235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151519 restraints weight = 44950.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152402 restraints weight = 117767.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152994 restraints weight = 68398.100| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2071 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 : 0.607 10.486 40772 Z= 0.304 Chirality : 0.040 0.152 4590 Planarity : 0.004 0.067 4878 Dihedral : 17.895 134.101 4874 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 2.10 % Allowed : 16.17 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3318 helix: 0.48 (0.13), residues: 1669 sheet: -0.18 (0.38), residues: 175 loop : -1.37 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 482 HIS 0.005 0.001 HIS B 208 PHE 0.015 0.001 PHE X 160 TYR 0.025 0.001 TYR B 375 ARG 0.006 0.000 ARG F 160 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 1166) hydrogen bonds : angle 4.31637 ( 3275) metal coordination : bond 0.01087 ( 8) metal coordination : angle 2.17795 ( 6) covalent geometry : bond 0.00360 (29770) covalent geometry : angle 0.60664 (40766) *********************** 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 375 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 314 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7968 (pp30) cc_final: 0.7524 (pp30) REVERT: G 268 THR cc_start: 0.6450 (OUTLIER) cc_final: 0.6163 (m) REVERT: G 306 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7294 (tm-30) REVERT: X 27 VAL cc_start: 0.8419 (p) cc_final: 0.8166 (p) REVERT: E 207 ARG cc_start: 0.7092 (ttt-90) cc_final: 0.6066 (tpt90) REVERT: F 192 ASP cc_start: 0.8032 (p0) cc_final: 0.7657 (p0) REVERT: C 11 ARG cc_start: 0.6827 (ttp-170) cc_final: 0.5897 (ptp-170) REVERT: C 104 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7691 (t-90) REVERT: C 235 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: B 32 GLU cc_start: 0.5825 (pp20) cc_final: 0.5333 (pp20) REVERT: B 52 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6319 (pp30) REVERT: Y 32 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5118 (mt) REVERT: Y 282 PHE cc_start: 0.5982 (OUTLIER) cc_final: 0.5780 (t80) outliers start: 61 outliers final: 43 residues processed: 355 average time/residue: 0.3948 time to fit residues: 223.6954 Evaluate side-chains 352 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU 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 268 THR Chi-restraints excluded: chain G residue 336 TRP Chi-restraints excluded: chain G residue 366 ILE Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 175 LEU 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 446 MET 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 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 235 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 389 LEU 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 320 LEU 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 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 92 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 176 HIS 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 107 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 174 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 296 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.4122 r_free = 0.4122 target = 0.181563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151439 restraints weight = 44784.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152964 restraints weight = 111484.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152521 restraints weight = 56300.996| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2224 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= 0.161 Angle : 0.624 12.042 40772 Z= 0.313 Chirality : 0.040 0.154 4590 Planarity : 0.004 0.067 4878 Dihedral : 17.910 139.229 4874 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 2.14 % Allowed : 16.76 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3318 helix: 0.45 (0.13), residues: 1666 sheet: -0.22 (0.39), residues: 175 loop : -1.40 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 482 HIS 0.005 0.001 HIS B 208 PHE 0.017 0.002 PHE B 311 TYR 0.023 0.001 TYR B 375 ARG 0.007 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1166) hydrogen bonds : angle 4.35789 ( 3275) metal coordination : bond 0.01151 ( 8) metal coordination : angle 2.26338 ( 6) covalent geometry : bond 0.00386 (29770) covalent geometry : angle 0.62345 (40766) *********************** 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 368 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 3.024 Fit side-chains revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7981 (pp30) cc_final: 0.7493 (pp30) REVERT: G 306 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7294 (tm-30) REVERT: X 27 VAL cc_start: 0.8416 (p) cc_final: 0.8162 (p) REVERT: E 207 ARG cc_start: 0.6982 (ttt-90) cc_final: 0.6038 (tpt90) REVERT: F 192 ASP cc_start: 0.8123 (p0) cc_final: 0.7832 (p0) REVERT: C 11 ARG cc_start: 0.6863 (ttp-170) cc_final: 0.6243 (ptp90) REVERT: C 198 ASN cc_start: 0.8143 (t0) cc_final: 0.7719 (t0) REVERT: C 235 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: C 390 ARG cc_start: 0.7789 (tpm170) cc_final: 0.7517 (ttp-110) REVERT: B 32 GLU cc_start: 0.5934 (pp20) cc_final: 0.5447 (pp20) REVERT: B 52 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6326 (pp30) REVERT: Y 32 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5177 (mt) REVERT: A 146 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7816 (mp) outliers start: 62 outliers final: 48 residues processed: 346 average time/residue: 0.3950 time to fit residues: 218.3082 Evaluate side-chains 351 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 3.180 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain G residue 254 THR 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 X residue 16 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 175 LEU 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 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 235 GLN 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 C residue 389 LEU 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 320 LEU 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 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 92 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 146 LEU 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 190 optimal weight: 0.0980 chunk 189 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 237 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4127 r_free = 0.4127 target = 0.182042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151347 restraints weight = 45011.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152429 restraints weight = 113789.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152494 restraints weight = 61010.692| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2315 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= 0.142 Angle : 0.614 10.943 40772 Z= 0.306 Chirality : 0.040 0.143 4590 Planarity : 0.004 0.068 4878 Dihedral : 17.873 140.991 4874 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.21 % Allowed : 17.24 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3318 helix: 0.46 (0.13), residues: 1666 sheet: -0.22 (0.38), residues: 175 loop : -1.35 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 482 HIS 0.006 0.001 HIS C 383 PHE 0.017 0.001 PHE Y 221 TYR 0.026 0.001 TYR Y 284 ARG 0.006 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 1166) hydrogen bonds : angle 4.32743 ( 3275) metal coordination : bond 0.01051 ( 8) metal coordination : angle 2.19443 ( 6) covalent geometry : bond 0.00335 (29770) covalent geometry : angle 0.61337 (40766) *********************** 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 370 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.7988 (pp30) cc_final: 0.7499 (pp30) REVERT: G 306 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7288 (tm-30) REVERT: X 27 VAL cc_start: 0.8404 (p) cc_final: 0.8150 (p) REVERT: E 207 ARG cc_start: 0.6962 (ttt-90) cc_final: 0.6041 (tpt90) REVERT: F 192 ASP cc_start: 0.8096 (p0) cc_final: 0.7810 (p0) REVERT: C 11 ARG cc_start: 0.6719 (ttp-170) cc_final: 0.5939 (ptp90) REVERT: C 198 ASN cc_start: 0.8158 (t0) cc_final: 0.7770 (t0) REVERT: C 235 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 390 ARG cc_start: 0.7747 (tpm170) cc_final: 0.7454 (ttp-110) REVERT: B 32 GLU cc_start: 0.5954 (pp20) cc_final: 0.5469 (pp20) REVERT: B 52 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6316 (pp30) REVERT: Y 32 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5155 (mt) REVERT: Y 227 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 146 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7813 (mp) outliers start: 64 outliers final: 46 residues processed: 352 average time/residue: 0.3982 time to fit residues: 224.4761 Evaluate side-chains 347 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 2.746 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR 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 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 63 CYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 413 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 235 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 389 LEU 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 B residue 444 TYR Chi-restraints excluded: chain Y residue 32 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 105 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 176 HIS 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 22 optimal weight: 0.3980 chunk 191 optimal weight: 0.3980 chunk 176 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 106 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.184857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155636 restraints weight = 44768.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156884 restraints weight = 110879.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156626 restraints weight = 56513.134| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29778 Z= 0.109 Angle : 0.589 10.674 40772 Z= 0.292 Chirality : 0.039 0.144 4590 Planarity : 0.004 0.069 4878 Dihedral : 17.771 137.350 4874 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.83 % Allowed : 17.59 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3318 helix: 0.59 (0.13), residues: 1663 sheet: -0.05 (0.38), residues: 174 loop : -1.27 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 482 HIS 0.003 0.001 HIS C 383 PHE 0.019 0.001 PHE Y 221 TYR 0.031 0.001 TYR Y 284 ARG 0.015 0.000 ARG X 224 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 1166) hydrogen bonds : angle 4.20780 ( 3275) metal coordination : bond 0.00878 ( 8) metal coordination : angle 2.03153 ( 6) covalent geometry : bond 0.00240 (29770) covalent geometry : angle 0.58805 (40766) *********************** 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 377 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.8007 (pp30) cc_final: 0.7515 (pp30) REVERT: G 268 THR cc_start: 0.6258 (OUTLIER) cc_final: 0.5879 (m) REVERT: G 306 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7217 (tm-30) REVERT: X 27 VAL cc_start: 0.8404 (p) cc_final: 0.8130 (p) REVERT: E 207 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.6037 (tpt90) REVERT: F 192 ASP cc_start: 0.7914 (p0) cc_final: 0.7658 (p0) REVERT: C 11 ARG cc_start: 0.6510 (ttp-170) cc_final: 0.5506 (ptp90) REVERT: C 104 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7564 (t-90) REVERT: C 198 ASN cc_start: 0.8076 (t0) cc_final: 0.7688 (t0) REVERT: C 308 TRP cc_start: 0.6394 (OUTLIER) cc_final: 0.5970 (t-100) REVERT: B 32 GLU cc_start: 0.5907 (pp20) cc_final: 0.5428 (pp20) REVERT: B 52 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6345 (pp30) REVERT: Y 32 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5226 (mt) REVERT: Y 227 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7290 (tm-30) REVERT: Y 260 LEU cc_start: 0.7304 (mm) cc_final: 0.6766 (mt) REVERT: A 146 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7737 (mp) outliers start: 53 outliers final: 40 residues processed: 359 average time/residue: 0.3855 time to fit residues: 222.6168 Evaluate side-chains 350 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU 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 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 25 GLU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL 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 133 LEU Chi-restraints excluded: chain F residue 275 PHE 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 355 GLN Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 183 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 B residue 444 TYR Chi-restraints excluded: chain Y residue 32 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 146 LEU 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 228 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 241 optimal weight: 0.0980 chunk 134 optimal weight: 0.6980 chunk 323 optimal weight: 0.9990 chunk 271 optimal weight: 0.0050 chunk 338 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156347 restraints weight = 45267.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157695 restraints weight = 111252.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157382 restraints weight = 53925.438| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29778 Z= 0.111 Angle : 0.597 10.775 40772 Z= 0.295 Chirality : 0.039 0.143 4590 Planarity : 0.004 0.071 4878 Dihedral : 17.706 135.567 4874 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 1.72 % Allowed : 18.03 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3318 helix: 0.59 (0.13), residues: 1672 sheet: 0.07 (0.39), residues: 174 loop : -1.26 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP E 482 HIS 0.003 0.000 HIS C 383 PHE 0.015 0.001 PHE Y 221 TYR 0.019 0.001 TYR Y 284 ARG 0.011 0.000 ARG X 224 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1166) hydrogen bonds : angle 4.19871 ( 3275) metal coordination : bond 0.00801 ( 8) metal coordination : angle 2.00135 ( 6) covalent geometry : bond 0.00246 (29770) covalent geometry : angle 0.59674 (40766) ********************** 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 368 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 GLN cc_start: 0.8023 (pp30) cc_final: 0.7539 (pp30) REVERT: G 268 THR cc_start: 0.6167 (OUTLIER) cc_final: 0.5883 (m) REVERT: G 306 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7207 (tm-30) REVERT: X 27 VAL cc_start: 0.8356 (p) cc_final: 0.8085 (p) REVERT: E 207 ARG cc_start: 0.6976 (ttt-90) cc_final: 0.6014 (tpt90) REVERT: F 45 GLN cc_start: 0.6131 (mm-40) cc_final: 0.5547 (pp30) REVERT: F 192 ASP cc_start: 0.7894 (p0) cc_final: 0.7610 (p0) REVERT: C 104 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7595 (t-90) REVERT: C 198 ASN cc_start: 0.8046 (t0) cc_final: 0.7637 (t0) REVERT: C 373 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7660 (tt0) REVERT: B 32 GLU cc_start: 0.5905 (pp20) cc_final: 0.5425 (pp20) REVERT: B 52 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6308 (pp30) REVERT: B 62 ILE cc_start: 0.9047 (tp) cc_final: 0.8635 (tp) REVERT: Y 32 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5139 (mt) REVERT: Y 104 VAL cc_start: 0.6280 (m) cc_final: 0.5799 (p) REVERT: Y 227 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7292 (tm-30) REVERT: Y 260 LEU cc_start: 0.7248 (mm) cc_final: 0.6764 (mt) REVERT: A 146 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7749 (mp) outliers start: 50 outliers final: 39 residues processed: 354 average time/residue: 0.3866 time to fit residues: 219.7620 Evaluate side-chains 350 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 306 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU 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 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 25 GLU Chi-restraints excluded: chain E residue 52 GLN 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 133 LEU Chi-restraints excluded: chain F residue 275 PHE 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 385 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 183 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 B residue 444 TYR Chi-restraints excluded: chain Y residue 32 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 146 LEU 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 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 338 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 305 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.180728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151894 restraints weight = 45092.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152671 restraints weight = 110718.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151171 restraints weight = 55108.768| |-----------------------------------------------------------------------------| 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) = 0.150 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29778 Z= 0.183 Angle : 0.663 11.186 40772 Z= 0.330 Chirality : 0.041 0.159 4590 Planarity : 0.005 0.069 4878 Dihedral : 17.776 144.677 4874 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 1.76 % Allowed : 18.24 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3318 helix: 0.41 (0.13), residues: 1667 sheet: 0.03 (0.39), residues: 169 loop : -1.35 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP E 482 HIS 0.005 0.001 HIS B 383 PHE 0.019 0.002 PHE B 311 TYR 0.021 0.002 TYR Y 284 ARG 0.011 0.000 ARG X 224 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 1166) hydrogen bonds : angle 4.37554 ( 3275) metal coordination : bond 0.01125 ( 8) metal coordination : angle 2.23637 ( 6) covalent geometry : bond 0.00441 (29770) covalent geometry : angle 0.66267 (40766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8107.74 seconds wall clock time: 143 minutes 9.66 seconds (8589.66 seconds total)