Starting phenix.real_space_refine on Sun Aug 24 23:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utt_42549/08_2025/8utt_42549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utt_42549/08_2025/8utt_42549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8utt_42549/08_2025/8utt_42549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utt_42549/08_2025/8utt_42549.map" model { file = "/net/cci-nas-00/data/ceres_data/8utt_42549/08_2025/8utt_42549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utt_42549/08_2025/8utt_42549.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 4 5.21 5 S 153 5.16 5 C 14835 2.51 5 N 4060 2.21 5 O 4673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23744 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3014 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "N" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3031 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 12, 'TRANS': 372} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "I" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Conformer: "B" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} bond proxies already assigned to first conformer: 3444 Chain: "S" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.46 residue: pdb=" N AALA B 430 " occ=0.54 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.46 residue: pdb=" N AASP B 431 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.46 residue: pdb=" N AGLU B 432 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.46 residue: pdb=" N ATHR I 429 " occ=0.52 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.48 residue: pdb=" N AALA I 430 " occ=0.52 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.48 residue: pdb=" N AASP I 431 " occ=0.52 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.48 residue: pdb=" N AGLU I 432 " occ=0.52 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.48 residue: pdb=" N AGLN I 433 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.48 Time building chain proxies: 7.51, per 1000 atoms: 0.32 Number of scatterers: 23744 At special positions: 0 Unit cell: (106.344, 113.94, 243.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 153 16.00 P 19 15.00 Mg 4 11.99 O 4673 8.00 N 4060 7.00 C 14835 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5546 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 24 sheets defined 48.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.522A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 88 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 134 Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.546A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 338 through 353 removed outlier: 3.669A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 385 Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 87 Processing helix chain 'N' and resid 102 through 109 removed outlier: 4.020A pdb=" N THR N 106 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 132 removed outlier: 3.682A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.552A pdb=" N ILE N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 296 removed outlier: 3.515A pdb=" N LYS N 266 " --> pdb=" O GLY N 262 " (cutoff:3.500A) Proline residue: N 292 - end of helix Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 337 through 349 removed outlier: 3.811A pdb=" N THR N 341 " --> pdb=" O ASN N 337 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 385 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.528A pdb=" N THR A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.875A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.102A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.612A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.594A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.806A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.059A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.245A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.516A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.216A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.038A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.149A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 4.020A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.333A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.804A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.750A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.664A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.690A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.575A pdb=" N HIS B 307 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.574A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.796A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.704A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.417A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.884A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.825A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.309A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.253A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.728A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.789A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.626A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.224A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.832A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.565A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.588A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.207A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.317A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.246A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.530A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.707A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 126 removed outlier: 3.865A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.579A pdb=" N SER I 145 " --> pdb=" O GLY I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.757A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.586A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.819A pdb=" N MET I 299 " --> pdb=" O SER I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.532A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.518A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.819A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 425 removed outlier: 4.125A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 3.918A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.323A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.586A pdb=" N GLN S 128 " --> pdb=" O LYS S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.101A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 197 removed outlier: 3.562A pdb=" N ASN S 186 " --> pdb=" O VAL S 182 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.711A pdb=" N LEU S 227 " --> pdb=" O THR S 223 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 243 No H-bonds generated for 'chain 'S' and resid 241 through 243' Processing helix chain 'S' and resid 251 through 260 removed outlier: 3.812A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.039A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.808A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU S 297 " --> pdb=" O ASN S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 337 removed outlier: 3.768A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR S 337 " --> pdb=" O ALA S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 3.939A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS S 394 " --> pdb=" O ARG S 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 4.346A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.124A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 56 removed outlier: 6.445A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 56 removed outlier: 6.445A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.266A pdb=" N LYS N 7 " --> pdb=" O MET N 327 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA N 329 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA N 9 " --> pdb=" O ALA N 329 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU N 331 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG N 11 " --> pdb=" O LEU N 331 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN N 90 " --> pdb=" O ARG N 324 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA N 326 " --> pdb=" O ASN N 90 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.266A pdb=" N LYS N 7 " --> pdb=" O MET N 327 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA N 329 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA N 9 " --> pdb=" O ALA N 329 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU N 331 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG N 11 " --> pdb=" O LEU N 331 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN N 90 " --> pdb=" O ARG N 324 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA N 326 " --> pdb=" O ASN N 90 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 29 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'N' and resid 205 through 206 removed outlier: 3.516A pdb=" N ALA N 206 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.487A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.370A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 135 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 246 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.648A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS E 139 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'I' and resid 90 through 91 removed outlier: 8.340A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC3, first strand: chain 'I' and resid 136 through 138 removed outlier: 6.345A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 65 through 68 removed outlier: 8.664A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU S 3 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE S 135 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE S 5 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL S 137 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE S 7 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'S' and resid 269 through 272 1149 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4559 1.33 - 1.45: 6225 1.45 - 1.58: 13180 1.58 - 1.71: 34 1.71 - 1.83: 244 Bond restraints: 24242 Sorted by residual: bond pdb=" C LYS K 299 " pdb=" N LYS K 300 " ideal model delta sigma weight residual 1.331 1.568 -0.238 1.33e-02 5.65e+03 3.19e+02 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.599 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.36e+01 ... (remaining 24237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 31759 2.41 - 4.83: 986 4.83 - 7.24: 138 7.24 - 9.66: 15 9.66 - 12.07: 8 Bond angle restraints: 32906 Sorted by residual: angle pdb=" O LYS K 299 " pdb=" C LYS K 299 " pdb=" N LYS K 300 " ideal model delta sigma weight residual 122.91 130.32 -7.41 1.19e+00 7.06e-01 3.88e+01 angle pdb=" CA LYS K 299 " pdb=" C LYS K 299 " pdb=" N LYS K 300 " ideal model delta sigma weight residual 114.98 106.67 8.31 1.34e+00 5.57e-01 3.85e+01 angle pdb=" CA PRO N 333 " pdb=" N PRO N 333 " pdb=" CD PRO N 333 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" C LYS K 299 " pdb=" N LYS K 300 " pdb=" CA LYS K 300 " ideal model delta sigma weight residual 120.71 113.75 6.96 1.42e+00 4.96e-01 2.40e+01 angle pdb=" C LYS K 296 " pdb=" N LYS K 297 " pdb=" CA LYS K 297 " ideal model delta sigma weight residual 121.54 130.62 -9.08 1.91e+00 2.74e-01 2.26e+01 ... (remaining 32901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.05: 14006 32.05 - 64.09: 606 64.09 - 96.14: 82 96.14 - 128.18: 24 128.18 - 160.23: 18 Dihedral angle restraints: 14736 sinusoidal: 6094 harmonic: 8642 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -90.96 160.23 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GTP S 501 " pdb=" O5' GTP S 501 " pdb=" PA GTP S 501 " pdb=" O3A GTP S 501 " ideal model delta sinusoidal sigma weight residual 69.27 -136.35 -154.38 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -37.70 142.29 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 14733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3302 0.100 - 0.199: 301 0.199 - 0.299: 6 0.299 - 0.398: 2 0.398 - 0.498: 2 Chirality restraints: 3613 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.66 -0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" C18 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" C17 TA1 I 502 " pdb=" C20 TA1 I 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.68 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3610 not shown) Planarity restraints: 4276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 B 502 " -0.219 2.00e-02 2.50e+03 1.82e-01 4.13e+02 pdb=" C30 TA1 B 502 " 0.062 2.00e-02 2.50e+03 pdb=" C31 TA1 B 502 " -0.157 2.00e-02 2.50e+03 pdb=" N01 TA1 B 502 " 0.298 2.00e-02 2.50e+03 pdb=" O14 TA1 B 502 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO K 292 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 363 " -0.056 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO K 364 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO K 364 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 364 " -0.046 5.00e-02 4.00e+02 ... (remaining 4273 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 5 1.93 - 2.67: 542 2.67 - 3.42: 33109 3.42 - 4.16: 53014 4.16 - 4.90: 99389 Nonbonded interactions: 186059 Sorted by model distance: nonbonded pdb="MG MG K 501 " pdb=" O2G ANP K 502 " model vdw 1.190 2.170 nonbonded pdb="MG MG K 501 " pdb=" PG ANP K 502 " model vdw 1.903 2.530 nonbonded pdb=" O1G GTP S 501 " pdb="MG MG S 502 " model vdw 1.921 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.929 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.932 2.170 ... (remaining 186054 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' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) selection = (chain 'S' and (resid 1 through 440 or resid 501 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 428 or resid 501 through 502)) selection = (chain 'I' and (resid 1 through 428 or resid 501 through 502)) } ncs_group { reference = (chain 'K' and resid 4 through 385) selection = (chain 'N' and resid 4 through 385) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.010 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.007 0.238 24243 Z= 0.401 Angle : 0.962 12.071 32906 Z= 0.549 Chirality : 0.055 0.498 3613 Planarity : 0.007 0.182 4276 Dihedral : 19.178 160.227 9190 Min Nonbonded Distance : 1.190 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.30 % Favored : 94.26 % Rotamer: Outliers : 1.60 % Allowed : 16.89 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 2969 helix: 0.84 (0.15), residues: 1222 sheet: -0.15 (0.22), residues: 533 loop : -1.54 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 221 TYR 0.026 0.002 TYR N 189 PHE 0.021 0.002 PHE B 367 TRP 0.014 0.002 TRP A 388 HIS 0.015 0.002 HIS S 107 Details of bonding type rmsd covalent geometry : bond 0.00720 (24242) covalent geometry : angle 0.96151 (32906) hydrogen bonds : bond 0.16469 ( 1089) hydrogen bonds : angle 6.10945 ( 3309) Misc. bond : bond 0.20765 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 524 time to evaluate : 1.023 Fit side-chains REVERT: K 35 THR cc_start: 0.8100 (m) cc_final: 0.7670 (m) REVERT: K 57 TRP cc_start: 0.7393 (t-100) cc_final: 0.6403 (t-100) REVERT: K 98 GLN cc_start: 0.7264 (pp30) cc_final: 0.7015 (pp30) REVERT: K 180 ASP cc_start: 0.8419 (t0) cc_final: 0.7811 (t0) REVERT: K 253 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: K 288 MET cc_start: 0.8556 (tmm) cc_final: 0.8171 (tmm) REVERT: N 13 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6340 (ttp-170) REVERT: N 159 ASN cc_start: 0.8875 (t0) cc_final: 0.8647 (t0) REVERT: N 254 ARG cc_start: 0.6126 (mtp-110) cc_final: 0.5475 (mtp-110) REVERT: E 221 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8420 (mtt-85) REVERT: E 414 GLU cc_start: 0.7852 (pt0) cc_final: 0.7336 (pt0) REVERT: I 162 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7341 (mmp80) REVERT: I 163 ILE cc_start: 0.8733 (mm) cc_final: 0.8501 (mt) REVERT: I 213 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7769 (ttm-80) REVERT: S 6 SER cc_start: 0.8853 (m) cc_final: 0.8560 (t) REVERT: S 24 TYR cc_start: 0.8023 (m-80) cc_final: 0.7666 (m-80) REVERT: S 50 ASN cc_start: 0.7419 (t0) cc_final: 0.7072 (t0) REVERT: S 217 LEU cc_start: 0.8988 (mt) cc_final: 0.8755 (tt) REVERT: S 420 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8169 (mt-10) REVERT: S 450 GLU cc_start: 0.3357 (OUTLIER) cc_final: 0.1504 (mm-30) outliers start: 37 outliers final: 10 residues processed: 542 average time/residue: 0.1826 time to fit residues: 152.1874 Evaluate side-chains 495 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 481 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 303 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 162 ARG Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS N 83 GLN N 171 HIS A 18 ASN A 107 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS B 279 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN E 107 HIS I 105 HIS I 204 ASN I 279 GLN I 332 ASN S 358 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.131306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093932 restraints weight = 44371.673| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.70 r_work: 0.3300 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24243 Z= 0.140 Angle : 0.627 10.875 32906 Z= 0.311 Chirality : 0.045 0.451 3613 Planarity : 0.005 0.092 4276 Dihedral : 13.352 155.419 3622 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.72 % Favored : 96.08 % Rotamer: Outliers : 2.66 % Allowed : 16.07 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.16), residues: 2969 helix: 1.56 (0.15), residues: 1244 sheet: 0.29 (0.22), residues: 526 loop : -1.26 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 391 TYR 0.026 0.001 TYR N 189 PHE 0.019 0.001 PHE B 367 TRP 0.017 0.001 TRP A 388 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00317 (24242) covalent geometry : angle 0.62701 (32906) hydrogen bonds : bond 0.04672 ( 1089) hydrogen bonds : angle 4.31123 ( 3309) Misc. bond : bond 0.00654 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 516 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: K 27 ILE cc_start: 0.8721 (mm) cc_final: 0.8430 (mm) REVERT: K 52 PHE cc_start: 0.8622 (m-80) cc_final: 0.8235 (m-10) REVERT: K 63 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6160 (pt0) REVERT: K 98 GLN cc_start: 0.7407 (pp30) cc_final: 0.7085 (pp30) REVERT: K 179 GLU cc_start: 0.8458 (tt0) cc_final: 0.8050 (tm-30) REVERT: K 253 GLU cc_start: 0.7886 (tp30) cc_final: 0.7655 (mm-30) REVERT: K 288 MET cc_start: 0.8421 (tmm) cc_final: 0.8073 (tmm) REVERT: N 30 MET cc_start: 0.6489 (pmm) cc_final: 0.5692 (pmm) REVERT: N 112 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6526 (pt0) REVERT: N 159 ASN cc_start: 0.8917 (t0) cc_final: 0.8647 (t0) REVERT: A 24 TYR cc_start: 0.8465 (m-80) cc_final: 0.8189 (m-80) REVERT: A 279 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8257 (mp0) REVERT: A 334 THR cc_start: 0.8990 (m) cc_final: 0.8641 (t) REVERT: B 188 SER cc_start: 0.8923 (t) cc_final: 0.8699 (p) REVERT: B 193 VAL cc_start: 0.8969 (p) cc_final: 0.8769 (p) REVERT: E 379 SER cc_start: 0.8924 (t) cc_final: 0.8340 (p) REVERT: E 414 GLU cc_start: 0.8045 (pt0) cc_final: 0.7634 (pt0) REVERT: E 445 GLU cc_start: 0.2506 (OUTLIER) cc_final: 0.2188 (tm-30) REVERT: I 136 THR cc_start: 0.8781 (m) cc_final: 0.8573 (p) REVERT: I 164 MET cc_start: 0.8417 (tpp) cc_final: 0.7929 (tpp) REVERT: I 213 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7921 (ttm-80) REVERT: I 388 MET cc_start: 0.8829 (mtp) cc_final: 0.8571 (ttm) REVERT: I 406 MET cc_start: 0.7763 (ttp) cc_final: 0.7500 (ttp) REVERT: I 417 ASP cc_start: 0.8530 (m-30) cc_final: 0.8218 (m-30) REVERT: S 1 MET cc_start: 0.6152 (tpp) cc_final: 0.5940 (tpp) REVERT: S 6 SER cc_start: 0.8866 (m) cc_final: 0.8584 (t) REVERT: S 15 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7236 (mm-40) REVERT: S 24 TYR cc_start: 0.8015 (m-80) cc_final: 0.7652 (m-80) REVERT: S 50 ASN cc_start: 0.7700 (t0) cc_final: 0.7011 (t0) REVERT: S 136 LEU cc_start: 0.7961 (mt) cc_final: 0.7671 (mp) REVERT: S 217 LEU cc_start: 0.9050 (mt) cc_final: 0.8754 (mt) REVERT: S 297 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7503 (mm-30) REVERT: S 377 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: S 450 GLU cc_start: 0.3778 (OUTLIER) cc_final: 0.3226 (mm-30) outliers start: 65 outliers final: 35 residues processed: 549 average time/residue: 0.1496 time to fit residues: 129.4174 Evaluate side-chains 505 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 465 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 292 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 187 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN N 66 ASN N 171 HIS A 15 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN E 28 HIS E 139 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.127198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090008 restraints weight = 44707.063| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.65 r_work: 0.3246 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 24243 Z= 0.210 Angle : 0.663 21.933 32906 Z= 0.327 Chirality : 0.047 0.447 3613 Planarity : 0.006 0.191 4276 Dihedral : 11.253 159.100 3598 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.09 % Favored : 95.71 % Rotamer: Outliers : 3.36 % Allowed : 16.93 % Favored : 79.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.16), residues: 2969 helix: 1.71 (0.15), residues: 1243 sheet: 0.30 (0.22), residues: 533 loop : -1.22 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 276 TYR 0.020 0.002 TYR K 74 PHE 0.021 0.002 PHE I 270 TRP 0.014 0.002 TRP B 344 HIS 0.027 0.002 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00505 (24242) covalent geometry : angle 0.66302 (32906) hydrogen bonds : bond 0.05222 ( 1089) hydrogen bonds : angle 4.20523 ( 3309) Misc. bond : bond 0.00941 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 485 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: K 15 PHE cc_start: 0.8513 (m-80) cc_final: 0.8091 (m-10) REVERT: K 27 ILE cc_start: 0.8552 (mm) cc_final: 0.8282 (mm) REVERT: K 52 PHE cc_start: 0.8613 (m-80) cc_final: 0.8401 (m-10) REVERT: K 98 GLN cc_start: 0.7512 (pp30) cc_final: 0.7128 (pp30) REVERT: K 179 GLU cc_start: 0.8540 (tt0) cc_final: 0.8221 (tm-30) REVERT: K 180 ASP cc_start: 0.8697 (t0) cc_final: 0.8155 (t0) REVERT: K 288 MET cc_start: 0.8473 (tmm) cc_final: 0.8067 (tmm) REVERT: K 293 ASN cc_start: 0.6563 (OUTLIER) cc_final: 0.6113 (m110) REVERT: N 159 ASN cc_start: 0.8976 (t0) cc_final: 0.8698 (t0) REVERT: N 347 TYR cc_start: 0.8474 (t80) cc_final: 0.7770 (t80) REVERT: A 24 TYR cc_start: 0.8554 (m-80) cc_final: 0.8156 (m-80) REVERT: A 123 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8223 (ttm170) REVERT: A 279 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8306 (mp0) REVERT: A 334 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8669 (t) REVERT: B 31 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7647 (t70) REVERT: B 73 MET cc_start: 0.8920 (mmt) cc_final: 0.8668 (mmm) REVERT: B 188 SER cc_start: 0.8959 (t) cc_final: 0.8756 (p) REVERT: B 197 ASP cc_start: 0.8140 (m-30) cc_final: 0.7929 (m-30) REVERT: B 209 ASP cc_start: 0.8426 (t70) cc_final: 0.8094 (t0) REVERT: B 282 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7612 (mmt-90) REVERT: E 414 GLU cc_start: 0.8059 (pt0) cc_final: 0.7668 (pt0) REVERT: E 445 GLU cc_start: 0.2743 (OUTLIER) cc_final: 0.2361 (tm-30) REVERT: I 73 MET cc_start: 0.8916 (mmt) cc_final: 0.8677 (mmt) REVERT: I 161 ASP cc_start: 0.8386 (t0) cc_final: 0.8041 (t0) REVERT: I 164 MET cc_start: 0.8464 (tpp) cc_final: 0.7983 (tpp) REVERT: I 213 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7925 (ttm-80) REVERT: I 316 ILE cc_start: 0.8747 (mm) cc_final: 0.8542 (mt) REVERT: I 388 MET cc_start: 0.8899 (mtp) cc_final: 0.8672 (ttm) REVERT: I 406 MET cc_start: 0.7808 (ttp) cc_final: 0.7498 (ttp) REVERT: S 1 MET cc_start: 0.6558 (tpp) cc_final: 0.6009 (tpp) REVERT: S 3 GLU cc_start: 0.7197 (pm20) cc_final: 0.6615 (mp0) REVERT: S 6 SER cc_start: 0.8929 (m) cc_final: 0.8639 (t) REVERT: S 15 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7475 (mm-40) REVERT: S 24 TYR cc_start: 0.8166 (m-80) cc_final: 0.7882 (m-80) REVERT: S 50 ASN cc_start: 0.7504 (t0) cc_final: 0.6515 (t0) REVERT: S 136 LEU cc_start: 0.8090 (mt) cc_final: 0.7744 (mp) REVERT: S 182 VAL cc_start: 0.7881 (m) cc_final: 0.7550 (m) REVERT: S 377 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8364 (ttm) REVERT: S 391 LEU cc_start: 0.8988 (tp) cc_final: 0.8714 (tp) REVERT: S 450 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3154 (mm-30) outliers start: 83 outliers final: 54 residues processed: 528 average time/residue: 0.1514 time to fit residues: 125.2188 Evaluate side-chains 510 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 449 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 303 PHE Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 332 ASN Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 316 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 58 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 132 optimal weight: 0.0570 chunk 225 optimal weight: 1.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN N 171 HIS A 18 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN I 332 ASN I 433 GLN A Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.126399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090085 restraints weight = 37221.812| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.38 r_work: 0.3237 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24243 Z= 0.210 Angle : 0.625 13.587 32906 Z= 0.313 Chirality : 0.047 0.436 3613 Planarity : 0.005 0.081 4276 Dihedral : 10.385 176.649 3598 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 3.75 % Allowed : 17.40 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.16), residues: 2969 helix: 1.75 (0.15), residues: 1245 sheet: 0.29 (0.22), residues: 539 loop : -1.20 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 276 TYR 0.021 0.002 TYR S 103 PHE 0.022 0.002 PHE I 270 TRP 0.013 0.001 TRP B 344 HIS 0.008 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00508 (24242) covalent geometry : angle 0.62509 (32906) hydrogen bonds : bond 0.05059 ( 1089) hydrogen bonds : angle 4.13679 ( 3309) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 466 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 6 VAL cc_start: 0.8843 (t) cc_final: 0.8629 (p) REVERT: K 27 ILE cc_start: 0.8345 (mm) cc_final: 0.8098 (mm) REVERT: K 98 GLN cc_start: 0.7673 (pp30) cc_final: 0.7389 (pp30) REVERT: K 179 GLU cc_start: 0.8669 (tt0) cc_final: 0.8158 (tm-30) REVERT: K 180 ASP cc_start: 0.8907 (t0) cc_final: 0.8160 (t0) REVERT: K 288 MET cc_start: 0.8489 (tmm) cc_final: 0.8136 (tmm) REVERT: N 115 GLN cc_start: 0.5403 (OUTLIER) cc_final: 0.4530 (mm110) REVERT: N 159 ASN cc_start: 0.9044 (t0) cc_final: 0.8771 (t0) REVERT: N 319 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8650 (mp) REVERT: N 347 TYR cc_start: 0.8496 (t80) cc_final: 0.7861 (t80) REVERT: A 24 TYR cc_start: 0.8675 (m-80) cc_final: 0.8287 (m-80) REVERT: A 230 LEU cc_start: 0.8804 (mt) cc_final: 0.8515 (mp) REVERT: A 279 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8504 (mp0) REVERT: A 334 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8758 (t) REVERT: A 379 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8564 (p) REVERT: B 31 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (t70) REVERT: B 188 SER cc_start: 0.9005 (t) cc_final: 0.8803 (p) REVERT: B 197 ASP cc_start: 0.8421 (m-30) cc_final: 0.8195 (m-30) REVERT: B 209 ASP cc_start: 0.8529 (t70) cc_final: 0.8163 (t0) REVERT: B 282 ARG cc_start: 0.8538 (mtp85) cc_final: 0.7847 (mmt-90) REVERT: B 407 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: E 24 TYR cc_start: 0.8823 (m-10) cc_final: 0.8619 (m-10) REVERT: E 275 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8768 (m) REVERT: E 379 SER cc_start: 0.9004 (t) cc_final: 0.8438 (p) REVERT: E 392 ASP cc_start: 0.8804 (m-30) cc_final: 0.8578 (m-30) REVERT: E 414 GLU cc_start: 0.8352 (pt0) cc_final: 0.7949 (pt0) REVERT: E 445 GLU cc_start: 0.2832 (OUTLIER) cc_final: 0.2443 (tm-30) REVERT: I 164 MET cc_start: 0.8576 (tpp) cc_final: 0.8055 (tpp) REVERT: I 209 ASP cc_start: 0.8468 (t70) cc_final: 0.8264 (t0) REVERT: I 213 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8240 (ttm-80) REVERT: I 274 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7985 (t) REVERT: I 363 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8684 (mtm) REVERT: I 406 MET cc_start: 0.7923 (ttp) cc_final: 0.7628 (ttp) REVERT: I 417 ASP cc_start: 0.8734 (m-30) cc_final: 0.8516 (m-30) REVERT: S 3 GLU cc_start: 0.7581 (pm20) cc_final: 0.6910 (mp0) REVERT: S 6 SER cc_start: 0.9033 (m) cc_final: 0.8741 (t) REVERT: S 15 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7551 (mm-40) REVERT: S 16 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7823 (mp) REVERT: S 20 CYS cc_start: 0.7832 (m) cc_final: 0.7177 (m) REVERT: S 24 TYR cc_start: 0.8308 (m-80) cc_final: 0.8059 (m-80) REVERT: S 50 ASN cc_start: 0.7627 (t0) cc_final: 0.6778 (t0) REVERT: S 55 GLU cc_start: 0.8165 (tt0) cc_final: 0.7838 (tt0) REVERT: S 182 VAL cc_start: 0.8090 (m) cc_final: 0.7754 (m) REVERT: S 297 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7755 (mm-30) REVERT: S 377 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8379 (ttm) REVERT: S 391 LEU cc_start: 0.9043 (tp) cc_final: 0.8763 (tp) REVERT: S 450 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.3350 (mm-30) outliers start: 92 outliers final: 59 residues processed: 522 average time/residue: 0.1503 time to fit residues: 123.3897 Evaluate side-chains 514 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 441 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 316 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 137 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS A 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090194 restraints weight = 34341.838| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.27 r_work: 0.3241 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24243 Z= 0.193 Angle : 0.598 13.903 32906 Z= 0.299 Chirality : 0.046 0.348 3613 Planarity : 0.005 0.081 4276 Dihedral : 10.087 178.524 3598 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.12 % Favored : 95.71 % Rotamer: Outliers : 3.64 % Allowed : 18.30 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.16), residues: 2969 helix: 1.85 (0.15), residues: 1245 sheet: 0.26 (0.22), residues: 557 loop : -1.21 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 162 TYR 0.021 0.001 TYR S 103 PHE 0.024 0.002 PHE I 270 TRP 0.012 0.001 TRP B 344 HIS 0.008 0.001 HIS S 406 Details of bonding type rmsd covalent geometry : bond 0.00467 (24242) covalent geometry : angle 0.59836 (32906) hydrogen bonds : bond 0.04801 ( 1089) hydrogen bonds : angle 4.07040 ( 3309) Misc. bond : bond 0.00940 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 460 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 44 LYS cc_start: 0.8958 (tptm) cc_final: 0.8367 (pptt) REVERT: K 98 GLN cc_start: 0.7726 (pp30) cc_final: 0.7410 (pp30) REVERT: K 105 TYR cc_start: 0.8490 (t80) cc_final: 0.8120 (t80) REVERT: K 142 VAL cc_start: 0.8547 (t) cc_final: 0.8311 (m) REVERT: K 166 LEU cc_start: 0.9085 (mm) cc_final: 0.8759 (mm) REVERT: K 179 GLU cc_start: 0.8611 (tt0) cc_final: 0.8158 (tm-30) REVERT: K 180 ASP cc_start: 0.8843 (t0) cc_final: 0.8243 (t0) REVERT: K 275 LEU cc_start: 0.9033 (mm) cc_final: 0.8721 (mp) REVERT: K 288 MET cc_start: 0.8351 (tmm) cc_final: 0.8053 (tmm) REVERT: N 91 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7796 (t) REVERT: N 115 GLN cc_start: 0.5476 (OUTLIER) cc_final: 0.4633 (mm-40) REVERT: N 159 ASN cc_start: 0.9059 (t0) cc_final: 0.8782 (t0) REVERT: N 178 VAL cc_start: 0.8877 (t) cc_final: 0.8616 (p) REVERT: N 319 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 24 TYR cc_start: 0.8671 (m-80) cc_final: 0.8398 (m-80) REVERT: A 195 LEU cc_start: 0.8573 (tp) cc_final: 0.8333 (tp) REVERT: A 216 ASN cc_start: 0.8845 (m-40) cc_final: 0.8599 (m110) REVERT: A 230 LEU cc_start: 0.8757 (mt) cc_final: 0.8478 (mp) REVERT: A 279 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8529 (mp0) REVERT: A 334 THR cc_start: 0.9032 (m) cc_final: 0.8721 (t) REVERT: A 377 MET cc_start: 0.8781 (ttt) cc_final: 0.8444 (ttt) REVERT: A 379 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 413 MET cc_start: 0.8967 (ttm) cc_final: 0.8695 (ttp) REVERT: B 31 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7858 (t70) REVERT: B 188 SER cc_start: 0.8994 (t) cc_final: 0.8753 (p) REVERT: B 197 ASP cc_start: 0.8381 (m-30) cc_final: 0.8141 (m-30) REVERT: B 282 ARG cc_start: 0.8545 (mtp85) cc_final: 0.7846 (mmt-90) REVERT: B 407 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: E 24 TYR cc_start: 0.8792 (m-10) cc_final: 0.8586 (m-10) REVERT: E 220 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7667 (tp30) REVERT: E 265 ILE cc_start: 0.8683 (pt) cc_final: 0.8315 (mt) REVERT: E 275 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (m) REVERT: E 392 ASP cc_start: 0.8707 (m-30) cc_final: 0.8494 (m-30) REVERT: E 445 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2497 (tm-30) REVERT: I 209 ASP cc_start: 0.8479 (t70) cc_final: 0.8249 (t0) REVERT: I 213 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8169 (ttm-80) REVERT: I 274 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8092 (t) REVERT: I 388 MET cc_start: 0.8980 (ttm) cc_final: 0.8623 (ttm) REVERT: I 406 MET cc_start: 0.7838 (ttp) cc_final: 0.7582 (ttp) REVERT: I 417 ASP cc_start: 0.8709 (m-30) cc_final: 0.8474 (m-30) REVERT: S 3 GLU cc_start: 0.7703 (pm20) cc_final: 0.7449 (pm20) REVERT: S 6 SER cc_start: 0.9038 (m) cc_final: 0.8681 (t) REVERT: S 16 ILE cc_start: 0.8495 (mt) cc_final: 0.7838 (mp) REVERT: S 20 CYS cc_start: 0.8007 (m) cc_final: 0.7459 (m) REVERT: S 24 TYR cc_start: 0.8435 (m-80) cc_final: 0.8208 (m-80) REVERT: S 50 ASN cc_start: 0.7490 (t0) cc_final: 0.6945 (t0) REVERT: S 120 ASP cc_start: 0.8551 (p0) cc_final: 0.8319 (m-30) REVERT: S 182 VAL cc_start: 0.8136 (m) cc_final: 0.7855 (m) REVERT: S 297 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7738 (mm-30) REVERT: S 377 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8305 (ttm) REVERT: S 391 LEU cc_start: 0.9049 (tp) cc_final: 0.8766 (tp) REVERT: S 413 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: S 450 GLU cc_start: 0.3985 (OUTLIER) cc_final: 0.3396 (mm-30) outliers start: 89 outliers final: 58 residues processed: 511 average time/residue: 0.1379 time to fit residues: 111.2424 Evaluate side-chains 520 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 450 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 316 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 256 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.128724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092326 restraints weight = 34529.552| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.33 r_work: 0.3298 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24243 Z= 0.125 Angle : 0.565 12.455 32906 Z= 0.281 Chirality : 0.044 0.317 3613 Planarity : 0.005 0.207 4276 Dihedral : 9.257 151.102 3598 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 3.21 % Allowed : 19.31 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2969 helix: 2.00 (0.15), residues: 1243 sheet: 0.46 (0.22), residues: 548 loop : -1.14 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.000 ARG B 276 TYR 0.020 0.001 TYR S 103 PHE 0.024 0.001 PHE I 270 TRP 0.014 0.001 TRP I 344 HIS 0.008 0.001 HIS S 406 Details of bonding type rmsd covalent geometry : bond 0.00289 (24242) covalent geometry : angle 0.56473 (32906) hydrogen bonds : bond 0.03960 ( 1089) hydrogen bonds : angle 3.90141 ( 3309) Misc. bond : bond 0.00925 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 470 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 44 LYS cc_start: 0.8958 (tptm) cc_final: 0.8369 (pptt) REVERT: K 46 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5679 (p) REVERT: K 57 TRP cc_start: 0.7760 (t-100) cc_final: 0.7502 (t-100) REVERT: K 74 TYR cc_start: 0.8220 (t80) cc_final: 0.7825 (t80) REVERT: K 98 GLN cc_start: 0.7716 (pp30) cc_final: 0.7413 (pp30) REVERT: K 105 TYR cc_start: 0.8484 (t80) cc_final: 0.8120 (t80) REVERT: K 142 VAL cc_start: 0.8497 (t) cc_final: 0.8285 (m) REVERT: K 179 GLU cc_start: 0.8610 (tt0) cc_final: 0.8267 (tm-30) REVERT: K 253 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7906 (mm-30) REVERT: K 288 MET cc_start: 0.8288 (tmm) cc_final: 0.8062 (tmm) REVERT: N 91 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7837 (t) REVERT: N 159 ASN cc_start: 0.9018 (t0) cc_final: 0.8753 (t0) REVERT: N 178 VAL cc_start: 0.8901 (t) cc_final: 0.8650 (p) REVERT: N 189 TYR cc_start: 0.4691 (t80) cc_final: 0.4399 (t80) REVERT: N 197 ASP cc_start: 0.8596 (t0) cc_final: 0.8079 (t0) REVERT: N 201 LYS cc_start: 0.8714 (tppt) cc_final: 0.8319 (mtmt) REVERT: A 24 TYR cc_start: 0.8668 (m-80) cc_final: 0.8376 (m-80) REVERT: A 216 ASN cc_start: 0.8842 (m-40) cc_final: 0.8611 (m110) REVERT: A 230 LEU cc_start: 0.8744 (mt) cc_final: 0.8460 (mp) REVERT: A 254 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7254 (mt-10) REVERT: A 279 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8547 (mp0) REVERT: A 379 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8530 (p) REVERT: B 31 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7843 (t70) REVERT: B 136 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8698 (p) REVERT: B 197 ASP cc_start: 0.8322 (m-30) cc_final: 0.8090 (m-30) REVERT: B 209 ASP cc_start: 0.8428 (t70) cc_final: 0.8154 (t0) REVERT: B 282 ARG cc_start: 0.8569 (mtp85) cc_final: 0.7864 (mmt-90) REVERT: B 313 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 328 GLU cc_start: 0.8428 (tt0) cc_final: 0.8200 (tt0) REVERT: B 407 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: E 220 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7614 (tp30) REVERT: E 265 ILE cc_start: 0.8575 (pt) cc_final: 0.8185 (mt) REVERT: E 275 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8741 (p) REVERT: E 379 SER cc_start: 0.9007 (t) cc_final: 0.8453 (p) REVERT: E 392 ASP cc_start: 0.8645 (m-30) cc_final: 0.8411 (m-30) REVERT: E 445 GLU cc_start: 0.2937 (OUTLIER) cc_final: 0.2521 (tm-30) REVERT: I 186 THR cc_start: 0.8788 (m) cc_final: 0.8490 (p) REVERT: I 209 ASP cc_start: 0.8453 (t70) cc_final: 0.8223 (t0) REVERT: I 213 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8181 (ttm-80) REVERT: I 406 MET cc_start: 0.7689 (ttp) cc_final: 0.7091 (ttp) REVERT: I 417 ASP cc_start: 0.8724 (m-30) cc_final: 0.8463 (m-30) REVERT: I 426 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8172 (tm-30) REVERT: S 6 SER cc_start: 0.9034 (m) cc_final: 0.8735 (t) REVERT: S 16 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7873 (mp) REVERT: S 20 CYS cc_start: 0.7913 (m) cc_final: 0.7502 (m) REVERT: S 36 MET cc_start: 0.7466 (ttm) cc_final: 0.7184 (ttm) REVERT: S 50 ASN cc_start: 0.7493 (t0) cc_final: 0.6915 (t0) REVERT: S 55 GLU cc_start: 0.8158 (tt0) cc_final: 0.7670 (mt-10) REVERT: S 85 GLN cc_start: 0.8779 (mm110) cc_final: 0.8562 (mm-40) REVERT: S 121 ARG cc_start: 0.6454 (mmm160) cc_final: 0.6195 (mmm160) REVERT: S 182 VAL cc_start: 0.8075 (m) cc_final: 0.7850 (m) REVERT: S 297 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7748 (mm-30) REVERT: S 355 ILE cc_start: 0.8547 (mp) cc_final: 0.8213 (mt) REVERT: S 377 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8250 (ttm) REVERT: S 391 LEU cc_start: 0.9048 (tp) cc_final: 0.8752 (tp) REVERT: S 450 GLU cc_start: 0.3872 (OUTLIER) cc_final: 0.3288 (mm-30) outliers start: 78 outliers final: 47 residues processed: 513 average time/residue: 0.1595 time to fit residues: 127.9104 Evaluate side-chains 505 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 446 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 191 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 268 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 160 optimal weight: 0.0040 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 90 ASN N 171 HIS N 318 ASN A 61 HIS A 309 HIS ** B 8 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 = 0.4105 r_free = 0.4105 target = 0.130051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093150 restraints weight = 37103.931| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.45 r_work: 0.3308 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24243 Z= 0.102 Angle : 0.546 9.277 32906 Z= 0.268 Chirality : 0.042 0.250 3613 Planarity : 0.004 0.081 4276 Dihedral : 8.965 151.564 3598 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 2.74 % Allowed : 19.43 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.16), residues: 2969 helix: 2.18 (0.15), residues: 1239 sheet: 0.56 (0.22), residues: 553 loop : -1.04 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 276 TYR 0.037 0.001 TYR S 24 PHE 0.023 0.001 PHE I 270 TRP 0.015 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 Details of bonding type rmsd covalent geometry : bond 0.00226 (24242) covalent geometry : angle 0.54582 (32906) hydrogen bonds : bond 0.03426 ( 1089) hydrogen bonds : angle 3.79331 ( 3309) Misc. bond : bond 0.00391 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 471 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: K 46 THR cc_start: 0.5858 (OUTLIER) cc_final: 0.5641 (p) REVERT: K 57 TRP cc_start: 0.7767 (t-100) cc_final: 0.7546 (t-100) REVERT: K 74 TYR cc_start: 0.8249 (t80) cc_final: 0.7833 (t80) REVERT: K 98 GLN cc_start: 0.7745 (pp30) cc_final: 0.7444 (pp30) REVERT: K 105 TYR cc_start: 0.8503 (t80) cc_final: 0.8159 (t80) REVERT: K 142 VAL cc_start: 0.8518 (t) cc_final: 0.8314 (m) REVERT: K 166 LEU cc_start: 0.8990 (mm) cc_final: 0.8721 (mm) REVERT: K 179 GLU cc_start: 0.8614 (tt0) cc_final: 0.8168 (tm-30) REVERT: K 180 ASP cc_start: 0.8868 (t0) cc_final: 0.8288 (t0) REVERT: K 275 LEU cc_start: 0.8969 (mm) cc_final: 0.8650 (mp) REVERT: N 159 ASN cc_start: 0.9023 (t0) cc_final: 0.8764 (t0) REVERT: N 178 VAL cc_start: 0.8894 (t) cc_final: 0.8642 (p) REVERT: N 189 TYR cc_start: 0.4830 (t80) cc_final: 0.4589 (t80) REVERT: N 197 ASP cc_start: 0.8626 (t0) cc_final: 0.8305 (t0) REVERT: N 201 LYS cc_start: 0.8691 (tppt) cc_final: 0.8239 (mtmm) REVERT: N 261 LYS cc_start: 0.8176 (mptt) cc_final: 0.7962 (mmtm) REVERT: N 349 ASP cc_start: 0.8611 (t0) cc_final: 0.8380 (t70) REVERT: A 24 TYR cc_start: 0.8673 (m-80) cc_final: 0.8380 (m-80) REVERT: A 49 PHE cc_start: 0.7582 (m-10) cc_final: 0.7286 (m-10) REVERT: A 216 ASN cc_start: 0.8856 (m-40) cc_final: 0.8645 (m110) REVERT: A 230 LEU cc_start: 0.8748 (mt) cc_final: 0.8468 (mp) REVERT: A 254 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7321 (mt-10) REVERT: A 279 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8548 (mp0) REVERT: A 379 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 31 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7831 (t70) REVERT: B 282 ARG cc_start: 0.8549 (mtp85) cc_final: 0.7837 (mmt-90) REVERT: B 407 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: E 322 ASP cc_start: 0.8806 (t0) cc_final: 0.8467 (t70) REVERT: E 379 SER cc_start: 0.9013 (t) cc_final: 0.8440 (p) REVERT: E 392 ASP cc_start: 0.8655 (m-30) cc_final: 0.8386 (m-30) REVERT: E 445 GLU cc_start: 0.2950 (OUTLIER) cc_final: 0.2598 (tm-30) REVERT: I 27 GLU cc_start: 0.8806 (tp30) cc_final: 0.8488 (tt0) REVERT: I 186 THR cc_start: 0.8764 (m) cc_final: 0.8427 (p) REVERT: I 209 ASP cc_start: 0.8448 (t70) cc_final: 0.8196 (t0) REVERT: I 213 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8228 (ttm-80) REVERT: I 288 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8182 (mm-30) REVERT: I 406 MET cc_start: 0.7679 (ttp) cc_final: 0.7358 (ttp) REVERT: I 417 ASP cc_start: 0.8732 (m-30) cc_final: 0.8463 (m-30) REVERT: S 6 SER cc_start: 0.9088 (m) cc_final: 0.8735 (t) REVERT: S 16 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.7874 (mp) REVERT: S 20 CYS cc_start: 0.7869 (m) cc_final: 0.7500 (m) REVERT: S 24 TYR cc_start: 0.8451 (m-80) cc_final: 0.8107 (m-80) REVERT: S 36 MET cc_start: 0.7386 (ttm) cc_final: 0.7151 (ttm) REVERT: S 50 ASN cc_start: 0.7354 (t0) cc_final: 0.6687 (t0) REVERT: S 55 GLU cc_start: 0.8152 (tt0) cc_final: 0.7613 (mt-10) REVERT: S 85 GLN cc_start: 0.8757 (mm110) cc_final: 0.8555 (mm-40) REVERT: S 115 ILE cc_start: 0.7622 (tp) cc_final: 0.7419 (tp) REVERT: S 297 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7675 (mm-30) REVERT: S 355 ILE cc_start: 0.8493 (mp) cc_final: 0.8159 (mt) REVERT: S 377 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8281 (ttm) REVERT: S 391 LEU cc_start: 0.9059 (tp) cc_final: 0.8763 (tp) REVERT: S 434 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8306 (tm-30) REVERT: S 450 GLU cc_start: 0.3855 (OUTLIER) cc_final: 0.3319 (mm-30) outliers start: 66 outliers final: 41 residues processed: 507 average time/residue: 0.1340 time to fit residues: 107.7798 Evaluate side-chains 502 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 453 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 422 TYR Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 432 TYR Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 162 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 293 ASN N 171 HIS E 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088190 restraints weight = 35314.588| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.29 r_work: 0.3225 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24243 Z= 0.272 Angle : 0.663 12.158 32906 Z= 0.330 Chirality : 0.047 0.343 3613 Planarity : 0.005 0.132 4276 Dihedral : 9.319 150.527 3598 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.26 % Favored : 95.57 % Rotamer: Outliers : 3.44 % Allowed : 19.00 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2969 helix: 1.94 (0.15), residues: 1237 sheet: 0.36 (0.22), residues: 557 loop : -1.20 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 276 TYR 0.025 0.002 TYR S 24 PHE 0.026 0.002 PHE B 367 TRP 0.013 0.002 TRP I 344 HIS 0.009 0.002 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00664 (24242) covalent geometry : angle 0.66301 (32906) hydrogen bonds : bond 0.05438 ( 1089) hydrogen bonds : angle 4.15039 ( 3309) Misc. bond : bond 0.00525 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 446 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 46 THR cc_start: 0.5853 (OUTLIER) cc_final: 0.5634 (p) REVERT: K 57 TRP cc_start: 0.7830 (t-100) cc_final: 0.7601 (t-100) REVERT: K 74 TYR cc_start: 0.8463 (t80) cc_final: 0.8179 (t80) REVERT: K 98 GLN cc_start: 0.7813 (pp30) cc_final: 0.7491 (pp30) REVERT: K 105 TYR cc_start: 0.8495 (t80) cc_final: 0.8127 (t80) REVERT: K 142 VAL cc_start: 0.8465 (t) cc_final: 0.8241 (m) REVERT: K 166 LEU cc_start: 0.9144 (mm) cc_final: 0.8862 (mm) REVERT: K 179 GLU cc_start: 0.8625 (tt0) cc_final: 0.8211 (tm-30) REVERT: K 180 ASP cc_start: 0.8850 (t0) cc_final: 0.8259 (t0) REVERT: K 275 LEU cc_start: 0.9057 (mm) cc_final: 0.8732 (mp) REVERT: K 293 ASN cc_start: 0.6643 (OUTLIER) cc_final: 0.6285 (m110) REVERT: K 339 ASP cc_start: 0.8209 (m-30) cc_final: 0.7890 (m-30) REVERT: N 115 GLN cc_start: 0.5391 (OUTLIER) cc_final: 0.4390 (mm-40) REVERT: N 159 ASN cc_start: 0.9047 (t0) cc_final: 0.8732 (t0) REVERT: N 178 VAL cc_start: 0.8914 (t) cc_final: 0.8637 (p) REVERT: N 189 TYR cc_start: 0.5044 (t80) cc_final: 0.4809 (t80) REVERT: N 197 ASP cc_start: 0.8595 (t0) cc_final: 0.8011 (t0) REVERT: N 201 LYS cc_start: 0.8731 (tppt) cc_final: 0.8247 (mtmm) REVERT: A 24 TYR cc_start: 0.8716 (m-80) cc_final: 0.8429 (m-80) REVERT: A 216 ASN cc_start: 0.8895 (m-40) cc_final: 0.8660 (m110) REVERT: A 230 LEU cc_start: 0.8825 (mt) cc_final: 0.8548 (mp) REVERT: A 379 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8562 (p) REVERT: A 413 MET cc_start: 0.9135 (ttm) cc_final: 0.8821 (ttp) REVERT: B 31 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7858 (t70) REVERT: B 407 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: E 265 ILE cc_start: 0.8767 (pt) cc_final: 0.8428 (mt) REVERT: E 392 ASP cc_start: 0.8686 (m-30) cc_final: 0.8368 (m-30) REVERT: E 429 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8497 (mt-10) REVERT: I 209 ASP cc_start: 0.8509 (t70) cc_final: 0.8279 (t0) REVERT: I 213 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8214 (ttm-80) REVERT: I 282 ARG cc_start: 0.8881 (ttm110) cc_final: 0.8493 (mtp85) REVERT: S 6 SER cc_start: 0.9108 (m) cc_final: 0.8702 (t) REVERT: S 16 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.7941 (mp) REVERT: S 20 CYS cc_start: 0.8079 (m) cc_final: 0.7573 (m) REVERT: S 24 TYR cc_start: 0.8511 (m-80) cc_final: 0.8249 (m-80) REVERT: S 35 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7426 (mp10) REVERT: S 36 MET cc_start: 0.7557 (ttm) cc_final: 0.7137 (ttm) REVERT: S 50 ASN cc_start: 0.7528 (t0) cc_final: 0.7005 (t0) REVERT: S 55 GLU cc_start: 0.8083 (tt0) cc_final: 0.7518 (mt-10) REVERT: S 196 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7424 (tm-30) REVERT: S 297 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7781 (mm-30) REVERT: S 355 ILE cc_start: 0.8604 (mp) cc_final: 0.8371 (mt) REVERT: S 377 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8329 (ttm) REVERT: S 417 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7424 (mt-10) REVERT: S 422 ARG cc_start: 0.8358 (tpt90) cc_final: 0.7861 (tpt90) REVERT: S 434 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8363 (tm-30) REVERT: S 450 GLU cc_start: 0.3755 (OUTLIER) cc_final: 0.3174 (mm-30) outliers start: 84 outliers final: 58 residues processed: 495 average time/residue: 0.1644 time to fit residues: 128.3715 Evaluate side-chains 507 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 440 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 4 CYS Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 428 LEU Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 191 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN I 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.127420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090649 restraints weight = 38071.150| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.47 r_work: 0.3281 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24243 Z= 0.124 Angle : 0.589 11.602 32906 Z= 0.287 Chirality : 0.043 0.302 3613 Planarity : 0.005 0.086 4276 Dihedral : 9.047 151.855 3598 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Rotamer: Outliers : 2.54 % Allowed : 20.05 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.16), residues: 2969 helix: 2.08 (0.15), residues: 1233 sheet: 0.51 (0.22), residues: 554 loop : -1.10 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 276 TYR 0.025 0.001 TYR S 24 PHE 0.022 0.001 PHE I 270 TRP 0.014 0.001 TRP A 388 HIS 0.007 0.001 HIS S 406 Details of bonding type rmsd covalent geometry : bond 0.00287 (24242) covalent geometry : angle 0.58890 (32906) hydrogen bonds : bond 0.03951 ( 1089) hydrogen bonds : angle 3.96121 ( 3309) Misc. bond : bond 0.00417 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 456 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: K 46 THR cc_start: 0.5810 (OUTLIER) cc_final: 0.5593 (p) REVERT: K 57 TRP cc_start: 0.7806 (t-100) cc_final: 0.7555 (t-100) REVERT: K 74 TYR cc_start: 0.8304 (t80) cc_final: 0.7985 (t80) REVERT: K 98 GLN cc_start: 0.7794 (pp30) cc_final: 0.7485 (pp30) REVERT: K 105 TYR cc_start: 0.8522 (t80) cc_final: 0.8186 (t80) REVERT: K 166 LEU cc_start: 0.9064 (mm) cc_final: 0.8773 (mm) REVERT: K 179 GLU cc_start: 0.8607 (tt0) cc_final: 0.8181 (tm-30) REVERT: K 180 ASP cc_start: 0.8866 (t0) cc_final: 0.8280 (t0) REVERT: K 275 LEU cc_start: 0.8985 (mm) cc_final: 0.8654 (mp) REVERT: K 331 LEU cc_start: 0.8562 (mt) cc_final: 0.8310 (mp) REVERT: N 159 ASN cc_start: 0.9038 (t0) cc_final: 0.8756 (t0) REVERT: N 178 VAL cc_start: 0.8898 (t) cc_final: 0.8665 (p) REVERT: N 197 ASP cc_start: 0.8596 (t0) cc_final: 0.8280 (t0) REVERT: N 201 LYS cc_start: 0.8715 (tppt) cc_final: 0.8270 (mtmm) REVERT: A 24 TYR cc_start: 0.8634 (m-80) cc_final: 0.8258 (m-80) REVERT: A 230 LEU cc_start: 0.8764 (mt) cc_final: 0.8477 (mp) REVERT: A 254 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7347 (mt-10) REVERT: A 279 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8570 (mp0) REVERT: A 379 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 31 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7822 (t70) REVERT: B 407 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: E 265 ILE cc_start: 0.8582 (pt) cc_final: 0.8187 (mt) REVERT: E 379 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8446 (p) REVERT: E 392 ASP cc_start: 0.8627 (m-30) cc_final: 0.8393 (m-30) REVERT: I 209 ASP cc_start: 0.8457 (t70) cc_final: 0.8216 (t0) REVERT: I 213 ARG cc_start: 0.8564 (ttm110) cc_final: 0.8228 (ttm-80) REVERT: I 282 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8442 (mtp85) REVERT: I 330 MET cc_start: 0.8535 (mmt) cc_final: 0.8194 (mmt) REVERT: I 406 MET cc_start: 0.7544 (ttp) cc_final: 0.7302 (ttp) REVERT: S 6 SER cc_start: 0.9117 (m) cc_final: 0.8715 (t) REVERT: S 16 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.7983 (mp) REVERT: S 20 CYS cc_start: 0.8011 (m) cc_final: 0.7619 (m) REVERT: S 24 TYR cc_start: 0.8544 (m-80) cc_final: 0.8330 (m-80) REVERT: S 35 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7385 (mp10) REVERT: S 36 MET cc_start: 0.7563 (ttm) cc_final: 0.7204 (ttm) REVERT: S 50 ASN cc_start: 0.7357 (t0) cc_final: 0.6721 (t0) REVERT: S 55 GLU cc_start: 0.8100 (tt0) cc_final: 0.7587 (mt-10) REVERT: S 297 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7750 (mm-30) REVERT: S 355 ILE cc_start: 0.8537 (mp) cc_final: 0.8195 (mt) REVERT: S 377 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: S 422 ARG cc_start: 0.8353 (tpt90) cc_final: 0.7804 (tpt90) REVERT: S 434 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8408 (tm-30) REVERT: S 450 GLU cc_start: 0.3773 (OUTLIER) cc_final: 0.3210 (mm-30) outliers start: 61 outliers final: 46 residues processed: 487 average time/residue: 0.1434 time to fit residues: 110.3342 Evaluate side-chains 498 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 444 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 428 LEU Chi-restraints excluded: chain S residue 432 TYR Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 182 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 overall best weight: 1.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 293 ASN A 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.126957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090309 restraints weight = 34724.351| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.33 r_work: 0.3284 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24243 Z= 0.145 Angle : 0.603 12.922 32906 Z= 0.293 Chirality : 0.044 0.292 3613 Planarity : 0.005 0.097 4276 Dihedral : 8.992 152.428 3598 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 2.50 % Allowed : 20.25 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2969 helix: 2.09 (0.15), residues: 1233 sheet: 0.59 (0.22), residues: 546 loop : -1.08 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 276 TYR 0.030 0.001 TYR N 189 PHE 0.022 0.001 PHE I 270 TRP 0.012 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 Details of bonding type rmsd covalent geometry : bond 0.00345 (24242) covalent geometry : angle 0.60317 (32906) hydrogen bonds : bond 0.04180 ( 1089) hydrogen bonds : angle 3.95166 ( 3309) Misc. bond : bond 0.00570 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 449 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 29 GLN cc_start: 0.7377 (tm-30) cc_final: 0.7173 (tm-30) REVERT: K 46 THR cc_start: 0.5795 (OUTLIER) cc_final: 0.5578 (p) REVERT: K 57 TRP cc_start: 0.7791 (t-100) cc_final: 0.7563 (t-100) REVERT: K 74 TYR cc_start: 0.8362 (t80) cc_final: 0.8065 (t80) REVERT: K 98 GLN cc_start: 0.7782 (pp30) cc_final: 0.7476 (pp30) REVERT: K 105 TYR cc_start: 0.8525 (t80) cc_final: 0.8192 (t80) REVERT: K 166 LEU cc_start: 0.9077 (mm) cc_final: 0.8777 (mm) REVERT: K 179 GLU cc_start: 0.8624 (tt0) cc_final: 0.8199 (tm-30) REVERT: K 180 ASP cc_start: 0.8867 (t0) cc_final: 0.8296 (t0) REVERT: K 275 LEU cc_start: 0.8975 (mm) cc_final: 0.8646 (mp) REVERT: K 293 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6468 (m110) REVERT: K 331 LEU cc_start: 0.8560 (mt) cc_final: 0.8332 (mp) REVERT: N 108 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7105 (mtt) REVERT: N 178 VAL cc_start: 0.8897 (t) cc_final: 0.8665 (p) REVERT: N 197 ASP cc_start: 0.8579 (t0) cc_final: 0.8257 (t0) REVERT: N 201 LYS cc_start: 0.8716 (tppt) cc_final: 0.8255 (mtmm) REVERT: A 24 TYR cc_start: 0.8668 (m-80) cc_final: 0.8290 (m-80) REVERT: A 49 PHE cc_start: 0.7750 (m-10) cc_final: 0.7490 (m-10) REVERT: A 230 LEU cc_start: 0.8771 (mt) cc_final: 0.8486 (mp) REVERT: A 254 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7334 (mt-10) REVERT: A 279 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8567 (mp0) REVERT: A 379 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8511 (p) REVERT: B 31 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7819 (t70) REVERT: B 407 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: E 24 TYR cc_start: 0.8773 (m-80) cc_final: 0.8564 (m-10) REVERT: E 265 ILE cc_start: 0.8675 (pt) cc_final: 0.8319 (mt) REVERT: E 322 ASP cc_start: 0.8802 (t0) cc_final: 0.8487 (t70) REVERT: E 379 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8434 (p) REVERT: E 392 ASP cc_start: 0.8605 (m-30) cc_final: 0.8259 (m-30) REVERT: E 429 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8473 (mt-10) REVERT: I 209 ASP cc_start: 0.8478 (t70) cc_final: 0.8247 (t0) REVERT: I 213 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8276 (ttm-80) REVERT: I 282 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8429 (mtp85) REVERT: I 330 MET cc_start: 0.8574 (mmt) cc_final: 0.8217 (mmt) REVERT: I 406 MET cc_start: 0.7593 (ttp) cc_final: 0.7345 (ttp) REVERT: S 6 SER cc_start: 0.9134 (m) cc_final: 0.8719 (t) REVERT: S 16 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.7972 (mp) REVERT: S 20 CYS cc_start: 0.8055 (m) cc_final: 0.7668 (m) REVERT: S 35 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7376 (mp10) REVERT: S 36 MET cc_start: 0.7512 (ttm) cc_final: 0.7128 (ttm) REVERT: S 50 ASN cc_start: 0.7331 (t0) cc_final: 0.6689 (t0) REVERT: S 55 GLU cc_start: 0.8091 (tt0) cc_final: 0.7573 (mt-10) REVERT: S 297 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7735 (mm-30) REVERT: S 355 ILE cc_start: 0.8547 (mp) cc_final: 0.8204 (mt) REVERT: S 377 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: S 417 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6837 (mt-10) REVERT: S 420 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7734 (mp0) REVERT: S 422 ARG cc_start: 0.8369 (tpt90) cc_final: 0.7826 (tpt90) REVERT: S 434 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8397 (tm-30) outliers start: 60 outliers final: 46 residues processed: 479 average time/residue: 0.1443 time to fit residues: 109.1190 Evaluate side-chains 501 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 446 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 188 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 293 ASN A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.126819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090499 restraints weight = 34416.569| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.23 r_work: 0.3296 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24243 Z= 0.146 Angle : 0.605 13.312 32906 Z= 0.294 Chirality : 0.044 0.302 3613 Planarity : 0.005 0.145 4276 Dihedral : 8.846 152.565 3594 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 2.70 % Allowed : 20.09 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2969 helix: 2.10 (0.15), residues: 1233 sheet: 0.61 (0.22), residues: 540 loop : -1.09 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG B 276 TYR 0.048 0.001 TYR S 24 PHE 0.022 0.001 PHE I 270 TRP 0.012 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 Details of bonding type rmsd covalent geometry : bond 0.00349 (24242) covalent geometry : angle 0.60477 (32906) hydrogen bonds : bond 0.04126 ( 1089) hydrogen bonds : angle 3.95352 ( 3309) Misc. bond : bond 0.00613 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7268.14 seconds wall clock time: 124 minutes 40.71 seconds (7480.71 seconds total)