Starting phenix.real_space_refine on Fri Jun 20 12:01:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utt_42549/06_2025/8utt_42549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utt_42549/06_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_42549/06_2025/8utt_42549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utt_42549/06_2025/8utt_42549.map" model { file = "/net/cci-nas-00/data/ceres_data/8utt_42549/06_2025/8utt_42549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utt_42549/06_2025/8utt_42549.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.80, per 1000 atoms: 0.75 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: 5.88 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.58 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: 8.33 Time building geometry restraints manager: 6.96 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 or resid 502)) selection = (chain 'I' and (resid 1 through 428 or resid 501 or resid 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: 194.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 57.680 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (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 TRP 0.014 0.002 TRP A 388 HIS 0.015 0.002 HIS S 107 PHE 0.021 0.002 PHE B 367 TYR 0.026 0.002 TYR N 189 ARG 0.018 0.001 ARG E 221 Details of bonding type rmsd hydrogen bonds : bond 0.16469 ( 1089) hydrogen bonds : angle 6.10945 ( 3309) covalent geometry : bond 0.00720 (24242) covalent geometry : angle 0.96151 (32906) 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 : 2.951 Fit side-chains REVERT: K 35 THR cc_start: 0.8100 (m) cc_final: 0.7267 (m) REVERT: K 52 PHE cc_start: 0.8339 (m-80) cc_final: 0.7943 (m-80) 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: 0.6342 (ttp-170) REVERT: N 159 ASN cc_start: 0.8875 (t0) cc_final: 0.8671 (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: 0.8559 (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: 0.6900 (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: 0.4009 time to fit residues: 334.7447 Evaluate side-chains 494 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 480 time to evaluate : 2.934 ------------------------------------------------------------------------------- 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 249 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 15 GLN A 18 ASN A 107 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS B 279 GLN B 292 GLN E 28 HIS 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.129370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092966 restraints weight = 34441.949| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.32 r_work: 0.3303 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 24243 Z= 0.170 Angle : 0.640 11.309 32906 Z= 0.318 Chirality : 0.045 0.291 3613 Planarity : 0.005 0.090 4276 Dihedral : 13.483 155.053 3622 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.78 % Favored : 96.01 % Rotamer: Outliers : 3.24 % Allowed : 15.64 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2969 helix: 1.54 (0.15), residues: 1235 sheet: 0.17 (0.22), residues: 536 loop : -1.26 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.008 0.001 HIS E 107 PHE 0.020 0.002 PHE B 367 TYR 0.025 0.001 TYR N 189 ARG 0.006 0.001 ARG I 391 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 1089) hydrogen bonds : angle 4.35166 ( 3309) covalent geometry : bond 0.00405 (24242) covalent geometry : angle 0.64033 (32906) Misc. bond : bond 0.00800 ( 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 591 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 511 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: K 27 ILE cc_start: 0.8720 (mm) cc_final: 0.8428 (mm) REVERT: K 98 GLN cc_start: 0.7570 (pp30) cc_final: 0.7256 (pp30) REVERT: K 179 GLU cc_start: 0.8543 (tt0) cc_final: 0.8137 (tm-30) REVERT: K 180 ASP cc_start: 0.8739 (t0) cc_final: 0.8280 (t0) REVERT: K 253 GLU cc_start: 0.7987 (tp30) cc_final: 0.7756 (mm-30) REVERT: K 288 MET cc_start: 0.8466 (tmm) cc_final: 0.8135 (tmm) REVERT: N 159 ASN cc_start: 0.8955 (t0) cc_final: 0.8678 (t0) REVERT: N 171 HIS cc_start: 0.8738 (t-90) cc_final: 0.8446 (t-90) REVERT: N 347 TYR cc_start: 0.8425 (t80) cc_final: 0.7417 (t80) REVERT: A 24 TYR cc_start: 0.8586 (m-80) cc_final: 0.8272 (m-80) REVERT: A 279 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8415 (mp0) REVERT: A 334 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 188 SER cc_start: 0.9014 (t) cc_final: 0.8792 (p) REVERT: B 212 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: E 92 LEU cc_start: 0.8853 (mt) cc_final: 0.8626 (mm) REVERT: E 379 SER cc_start: 0.9016 (t) cc_final: 0.8429 (p) REVERT: E 445 GLU cc_start: 0.2398 (OUTLIER) cc_final: 0.2006 (tm-30) REVERT: I 136 THR cc_start: 0.8849 (m) cc_final: 0.8625 (p) REVERT: I 164 MET cc_start: 0.8572 (tpp) cc_final: 0.8100 (tpp) REVERT: I 213 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8044 (ttm-80) REVERT: I 363 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8568 (mtm) REVERT: I 388 MET cc_start: 0.8885 (mtp) cc_final: 0.8638 (ttm) REVERT: I 406 MET cc_start: 0.7985 (ttp) cc_final: 0.7698 (ttp) REVERT: I 417 ASP cc_start: 0.8717 (m-30) cc_final: 0.8461 (m-30) REVERT: S 1 MET cc_start: 0.6344 (tpp) cc_final: 0.5799 (tpp) REVERT: S 3 GLU cc_start: 0.7095 (mp0) cc_final: 0.6877 (mp0) REVERT: S 6 SER cc_start: 0.8917 (m) cc_final: 0.8628 (t) REVERT: S 15 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7331 (mm-40) REVERT: S 24 TYR cc_start: 0.8140 (m-80) cc_final: 0.7763 (m-80) REVERT: S 50 ASN cc_start: 0.7813 (t0) cc_final: 0.6836 (t0) REVERT: S 136 LEU cc_start: 0.8055 (mt) cc_final: 0.7777 (mp) REVERT: S 217 LEU cc_start: 0.9077 (mt) cc_final: 0.8736 (mt) REVERT: S 242 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8104 (pp) REVERT: S 297 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7640 (mm-30) REVERT: S 377 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8320 (ttm) REVERT: S 390 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8033 (mtm110) REVERT: S 450 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.3321 (mm-30) outliers start: 80 outliers final: 44 residues processed: 546 average time/residue: 0.3669 time to fit residues: 311.9696 Evaluate side-chains 520 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 468 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 28 ILE Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 62 VAL 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 259 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 334 THR 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 212 PHE Chi-restraints excluded: chain B residue 342 VAL 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 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 166 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU 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 202 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 268 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.128174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.091928 restraints weight = 34428.197| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.29 r_work: 0.3290 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24243 Z= 0.176 Angle : 0.612 10.401 32906 Z= 0.304 Chirality : 0.046 0.645 3613 Planarity : 0.006 0.199 4276 Dihedral : 11.237 157.756 3598 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.16 % Favored : 95.64 % Rotamer: Outliers : 3.21 % Allowed : 17.16 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2969 helix: 1.73 (0.15), residues: 1241 sheet: 0.26 (0.22), residues: 535 loop : -1.21 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.027 0.001 HIS A 266 PHE 0.020 0.002 PHE B 367 TYR 0.020 0.001 TYR K 74 ARG 0.039 0.001 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1089) hydrogen bonds : angle 4.16864 ( 3309) covalent geometry : bond 0.00422 (24242) covalent geometry : angle 0.61204 (32906) Misc. bond : bond 0.00384 ( 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 561 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 482 time to evaluate : 2.813 Fit side-chains REVERT: K 15 PHE cc_start: 0.8520 (m-80) cc_final: 0.8105 (m-10) REVERT: K 27 ILE cc_start: 0.8561 (mm) cc_final: 0.8302 (mm) REVERT: K 52 PHE cc_start: 0.8605 (m-80) cc_final: 0.8338 (m-10) REVERT: K 98 GLN cc_start: 0.7545 (pp30) cc_final: 0.7169 (pp30) REVERT: K 179 GLU cc_start: 0.8593 (tt0) cc_final: 0.8136 (tm-30) REVERT: K 180 ASP cc_start: 0.8818 (t0) cc_final: 0.8027 (t0) REVERT: K 253 GLU cc_start: 0.8161 (tp30) cc_final: 0.7927 (mm-30) REVERT: K 288 MET cc_start: 0.8494 (tmm) cc_final: 0.8103 (tmm) REVERT: K 293 ASN cc_start: 0.6536 (OUTLIER) cc_final: 0.6077 (m110) REVERT: N 56 TYR cc_start: 0.6035 (m-10) cc_final: 0.5834 (m-10) REVERT: N 159 ASN cc_start: 0.8993 (t0) cc_final: 0.8713 (t0) REVERT: N 347 TYR cc_start: 0.8480 (t80) cc_final: 0.7747 (t80) REVERT: A 24 TYR cc_start: 0.8621 (m-80) cc_final: 0.8239 (m-80) REVERT: A 123 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8358 (ttm170) REVERT: A 279 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8454 (mp0) REVERT: A 334 THR cc_start: 0.9056 (m) cc_final: 0.8737 (t) REVERT: B 31 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7815 (t70) REVERT: B 73 MET cc_start: 0.8967 (mmt) cc_final: 0.8707 (mmm) REVERT: B 188 SER cc_start: 0.9029 (t) cc_final: 0.8816 (p) REVERT: B 197 ASP cc_start: 0.8264 (m-30) cc_final: 0.8005 (m-30) REVERT: B 209 ASP cc_start: 0.8578 (t70) cc_final: 0.8231 (t0) REVERT: B 282 ARG cc_start: 0.8437 (mtp85) cc_final: 0.7720 (mmt-90) REVERT: B 323 MET cc_start: 0.8735 (mmp) cc_final: 0.8501 (mmt) REVERT: E 379 SER cc_start: 0.9003 (t) cc_final: 0.8399 (p) REVERT: E 392 ASP cc_start: 0.8664 (t0) cc_final: 0.8451 (m-30) REVERT: E 445 GLU cc_start: 0.2634 (OUTLIER) cc_final: 0.2223 (tm-30) REVERT: I 73 MET cc_start: 0.8935 (mmt) cc_final: 0.8713 (mmt) REVERT: I 161 ASP cc_start: 0.8605 (t0) cc_final: 0.8250 (t0) REVERT: I 164 MET cc_start: 0.8581 (tpp) cc_final: 0.8144 (tpp) REVERT: I 213 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8038 (ttm-80) REVERT: I 406 MET cc_start: 0.7925 (ttp) cc_final: 0.7112 (ttp) REVERT: I 410 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8123 (mt-10) REVERT: S 1 MET cc_start: 0.6537 (tpp) cc_final: 0.6316 (tpp) REVERT: S 6 SER cc_start: 0.8984 (m) cc_final: 0.8682 (t) REVERT: S 15 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: S 24 TYR cc_start: 0.8190 (m-80) cc_final: 0.7795 (m-80) REVERT: S 50 ASN cc_start: 0.7902 (t0) cc_final: 0.7104 (t0) REVERT: S 136 LEU cc_start: 0.8144 (mt) cc_final: 0.7816 (mp) REVERT: S 377 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: S 391 LEU cc_start: 0.9008 (tp) cc_final: 0.8730 (tp) REVERT: S 422 ARG cc_start: 0.8144 (tpt90) cc_final: 0.7903 (tpt90) REVERT: S 450 GLU cc_start: 0.3844 (OUTLIER) cc_final: 0.3061 (mm-30) outliers start: 79 outliers final: 56 residues processed: 522 average time/residue: 0.3495 time to fit residues: 285.8453 Evaluate side-chains 521 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 459 time to evaluate : 2.533 ------------------------------------------------------------------------------- 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 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain A residue 62 VAL 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 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 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 218 THR 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 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 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 450 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 283 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 293 ASN K 318 ASN N 270 ASN A 216 ASN B 298 ASN I 332 ASN I 433 GLN A Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.125700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088797 restraints weight = 44880.230| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.65 r_work: 0.3203 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24243 Z= 0.225 Angle : 0.627 8.584 32906 Z= 0.316 Chirality : 0.048 0.509 3613 Planarity : 0.005 0.081 4276 Dihedral : 10.386 179.782 3598 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 3.79 % Allowed : 17.83 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2969 helix: 1.69 (0.15), residues: 1247 sheet: 0.23 (0.22), residues: 541 loop : -1.22 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.009 0.001 HIS A 266 PHE 0.023 0.002 PHE B 367 TYR 0.017 0.002 TYR E 224 ARG 0.005 0.001 ARG E 221 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 1089) hydrogen bonds : angle 4.19338 ( 3309) covalent geometry : bond 0.00546 (24242) covalent geometry : angle 0.62712 (32906) Misc. bond : bond 0.00383 ( 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 565 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 472 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 27 ILE cc_start: 0.8337 (mm) cc_final: 0.8100 (mm) REVERT: K 52 PHE cc_start: 0.8634 (m-80) cc_final: 0.8425 (m-10) REVERT: K 98 GLN cc_start: 0.7597 (pp30) cc_final: 0.7324 (pp30) REVERT: K 179 GLU cc_start: 0.8535 (tt0) cc_final: 0.8176 (tm-30) REVERT: K 180 ASP cc_start: 0.8747 (t0) cc_final: 0.8010 (t0) REVERT: K 288 MET cc_start: 0.8464 (tmm) cc_final: 0.8094 (tmm) REVERT: N 13 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5596 (ppt170) REVERT: N 115 GLN cc_start: 0.5391 (OUTLIER) cc_final: 0.4512 (mm110) REVERT: N 159 ASN cc_start: 0.9024 (t0) cc_final: 0.8755 (t0) REVERT: N 189 TYR cc_start: 0.4750 (t80) cc_final: 0.4498 (t80) REVERT: N 319 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8644 (mp) REVERT: N 347 TYR cc_start: 0.8496 (t80) cc_final: 0.8055 (t80) REVERT: A 24 TYR cc_start: 0.8595 (m-80) cc_final: 0.8318 (m-80) REVERT: A 279 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8336 (mp0) REVERT: A 334 THR cc_start: 0.9002 (m) cc_final: 0.8707 (t) REVERT: A 379 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 31 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7626 (t70) REVERT: B 188 SER cc_start: 0.8992 (t) cc_final: 0.8782 (p) REVERT: B 197 ASP cc_start: 0.8205 (m-30) cc_final: 0.7979 (m-30) REVERT: B 209 ASP cc_start: 0.8403 (t70) cc_final: 0.8061 (t0) REVERT: B 282 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7734 (mmt-90) REVERT: B 407 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: E 24 TYR cc_start: 0.8760 (m-10) cc_final: 0.8544 (m-10) REVERT: E 275 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8726 (m) REVERT: E 379 SER cc_start: 0.8933 (t) cc_final: 0.8343 (p) REVERT: E 392 ASP cc_start: 0.8528 (t0) cc_final: 0.8276 (m-30) REVERT: E 429 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8243 (mt-10) REVERT: E 445 GLU cc_start: 0.3017 (OUTLIER) cc_final: 0.2659 (tm-30) REVERT: I 164 MET cc_start: 0.8484 (tpp) cc_final: 0.7937 (tpp) REVERT: I 209 ASP cc_start: 0.8320 (t70) cc_final: 0.8082 (t0) REVERT: I 213 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8029 (ttm-80) REVERT: I 406 MET cc_start: 0.7764 (ttp) cc_final: 0.7473 (ttp) REVERT: I 417 ASP cc_start: 0.8524 (m-30) cc_final: 0.8303 (m-30) REVERT: S 1 MET cc_start: 0.6756 (tpp) cc_final: 0.6136 (tpp) REVERT: S 3 GLU cc_start: 0.7494 (pm20) cc_final: 0.6816 (mp0) REVERT: S 6 SER cc_start: 0.8983 (m) cc_final: 0.8635 (t) REVERT: S 15 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: S 50 ASN cc_start: 0.8091 (t0) cc_final: 0.7165 (t0) REVERT: S 182 VAL cc_start: 0.8080 (m) cc_final: 0.7733 (m) REVERT: S 297 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7664 (mm-30) REVERT: S 377 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8287 (ttm) REVERT: S 391 LEU cc_start: 0.9035 (tp) cc_final: 0.8764 (tp) REVERT: S 450 GLU cc_start: 0.3704 (OUTLIER) cc_final: 0.2974 (mm-30) outliers start: 93 outliers final: 65 residues processed: 526 average time/residue: 0.3476 time to fit residues: 286.5004 Evaluate side-chains 526 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 450 time to evaluate : 2.696 ------------------------------------------------------------------------------- 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 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 13 ARG 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 62 VAL 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 236 SER Chi-restraints excluded: chain A residue 259 LEU 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 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 136 THR 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 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 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 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 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 217 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 126 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4096 r_free = 0.4096 target = 0.129126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092457 restraints weight = 37358.986| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.45 r_work: 0.3283 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24243 Z= 0.119 Angle : 0.560 14.617 32906 Z= 0.278 Chirality : 0.044 0.347 3613 Planarity : 0.005 0.118 4276 Dihedral : 9.443 150.468 3598 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 2.62 % Allowed : 19.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2969 helix: 1.90 (0.15), residues: 1252 sheet: 0.42 (0.22), residues: 541 loop : -1.13 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.008 0.001 HIS N 171 PHE 0.027 0.001 PHE K 303 TYR 0.015 0.001 TYR K 105 ARG 0.040 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 1089) hydrogen bonds : angle 3.92555 ( 3309) covalent geometry : bond 0.00270 (24242) covalent geometry : angle 0.55997 (32906) Misc. bond : bond 0.00985 ( 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 540 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 477 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 6 VAL cc_start: 0.8852 (t) cc_final: 0.8650 (p) REVERT: K 44 LYS cc_start: 0.8934 (tptm) cc_final: 0.8343 (pptt) REVERT: K 74 TYR cc_start: 0.8262 (t80) cc_final: 0.7811 (t80) REVERT: K 98 GLN cc_start: 0.7745 (pp30) cc_final: 0.7458 (pp30) REVERT: K 105 TYR cc_start: 0.8483 (t80) cc_final: 0.8119 (t80) REVERT: K 142 VAL cc_start: 0.8533 (t) cc_final: 0.8249 (m) REVERT: K 179 GLU cc_start: 0.8613 (tt0) cc_final: 0.8266 (tm-30) REVERT: K 180 ASP cc_start: 0.8829 (t0) cc_final: 0.8199 (t0) REVERT: K 212 GLU cc_start: 0.8559 (mp0) cc_final: 0.8289 (mp0) REVERT: K 275 LEU cc_start: 0.9050 (mm) cc_final: 0.8722 (mp) REVERT: K 288 MET cc_start: 0.8238 (tmm) cc_final: 0.7978 (tmm) REVERT: N 13 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5452 (ppt170) REVERT: N 91 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7754 (t) REVERT: N 159 ASN cc_start: 0.9032 (t0) cc_final: 0.8817 (t0) REVERT: N 178 VAL cc_start: 0.8873 (t) cc_final: 0.8617 (p) REVERT: N 319 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8641 (mp) REVERT: N 347 TYR cc_start: 0.8485 (t80) cc_final: 0.7872 (t80) REVERT: A 3 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 24 TYR cc_start: 0.8651 (m-80) cc_final: 0.8403 (m-80) REVERT: A 230 LEU cc_start: 0.8756 (mt) cc_final: 0.8464 (mp) REVERT: A 279 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8516 (mp0) REVERT: A 379 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 31 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7839 (t70) REVERT: B 136 THR cc_start: 0.8962 (m) cc_final: 0.8684 (p) REVERT: B 197 ASP cc_start: 0.8313 (m-30) cc_final: 0.8091 (m-30) REVERT: B 209 ASP cc_start: 0.8485 (t70) cc_final: 0.8147 (t0) REVERT: B 282 ARG cc_start: 0.8534 (mtp85) cc_final: 0.7838 (mmt-90) REVERT: B 328 GLU cc_start: 0.8445 (tt0) cc_final: 0.8232 (tt0) REVERT: B 407 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: E 220 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7602 (tp30) REVERT: E 265 ILE cc_start: 0.8510 (pt) cc_final: 0.8056 (mt) REVERT: E 275 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (m) REVERT: E 379 SER cc_start: 0.9017 (t) cc_final: 0.8467 (p) REVERT: E 392 ASP cc_start: 0.8717 (t0) cc_final: 0.8400 (m-30) REVERT: E 445 GLU cc_start: 0.2930 (OUTLIER) cc_final: 0.2491 (tm-30) REVERT: I 186 THR cc_start: 0.8806 (m) cc_final: 0.8512 (p) REVERT: I 209 ASP cc_start: 0.8441 (t70) cc_final: 0.8215 (t0) REVERT: I 213 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8254 (ttm-80) REVERT: I 406 MET cc_start: 0.7741 (ttp) cc_final: 0.7098 (ttp) REVERT: I 417 ASP cc_start: 0.8717 (m-30) cc_final: 0.8477 (m-30) REVERT: I 426 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8144 (tm-30) REVERT: S 1 MET cc_start: 0.6889 (tpp) cc_final: 0.6330 (tpp) REVERT: S 3 GLU cc_start: 0.7732 (pm20) cc_final: 0.6977 (mp0) REVERT: S 6 SER cc_start: 0.9071 (m) cc_final: 0.8713 (t) REVERT: S 15 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7597 (mm-40) REVERT: S 50 ASN cc_start: 0.8209 (t0) cc_final: 0.7284 (t0) REVERT: S 55 GLU cc_start: 0.8121 (tt0) cc_final: 0.7634 (mt-10) REVERT: S 85 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8474 (mm-40) REVERT: S 154 MET cc_start: 0.7984 (mmm) cc_final: 0.7604 (mmm) REVERT: S 182 VAL cc_start: 0.8047 (m) cc_final: 0.7788 (m) REVERT: S 297 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7721 (mm-30) REVERT: S 377 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8290 (ttm) REVERT: S 391 LEU cc_start: 0.9060 (tp) cc_final: 0.8766 (tp) REVERT: S 450 GLU cc_start: 0.3740 (OUTLIER) cc_final: 0.3085 (mm-30) outliers start: 63 outliers final: 38 residues processed: 511 average time/residue: 0.3903 time to fit residues: 317.3951 Evaluate side-chains 500 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 451 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 319 LEU 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 335 ILE 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 60 VAL Chi-restraints excluded: chain B residue 135 LEU 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 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 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 335 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 15 GLN 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 217 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 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 28 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 290 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 135 ASN N 171 HIS A 216 ASN A 226 ASN E 31 GLN S 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.123727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087725 restraints weight = 37727.694| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.37 r_work: 0.3208 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 24243 Z= 0.288 Angle : 0.658 9.392 32906 Z= 0.333 Chirality : 0.048 0.310 3613 Planarity : 0.005 0.146 4276 Dihedral : 9.669 155.075 3598 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.39 % Favored : 95.41 % Rotamer: Outliers : 4.07 % Allowed : 18.69 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2969 helix: 1.71 (0.15), residues: 1244 sheet: 0.35 (0.23), residues: 532 loop : -1.26 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 344 HIS 0.010 0.002 HIS E 88 PHE 0.026 0.002 PHE K 303 TYR 0.015 0.002 TYR N 338 ARG 0.019 0.001 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.05713 ( 1089) hydrogen bonds : angle 4.22529 ( 3309) covalent geometry : bond 0.00702 (24242) covalent geometry : angle 0.65812 (32906) Misc. bond : bond 0.00670 ( 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 556 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 456 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 44 LYS cc_start: 0.8980 (tptm) cc_final: 0.8388 (pptt) REVERT: K 63 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6688 (mt-10) REVERT: K 98 GLN cc_start: 0.7758 (pp30) cc_final: 0.7426 (pp30) REVERT: K 105 TYR cc_start: 0.8483 (t80) cc_final: 0.8112 (t80) REVERT: K 142 VAL cc_start: 0.8492 (t) cc_final: 0.8178 (m) REVERT: K 179 GLU cc_start: 0.8651 (tt0) cc_final: 0.8345 (tm-30) REVERT: K 275 LEU cc_start: 0.9096 (mm) cc_final: 0.8783 (mp) REVERT: K 288 MET cc_start: 0.8430 (tmm) cc_final: 0.8163 (tmm) REVERT: K 316 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7952 (ttp80) REVERT: N 30 MET cc_start: 0.7951 (ppp) cc_final: 0.7684 (ppp) REVERT: N 91 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7860 (t) REVERT: N 115 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.4506 (mm-40) REVERT: N 159 ASN cc_start: 0.9030 (t0) cc_final: 0.8722 (t0) REVERT: N 178 VAL cc_start: 0.8929 (t) cc_final: 0.8663 (p) REVERT: A 24 TYR cc_start: 0.8714 (m-80) cc_final: 0.8414 (m-80) REVERT: A 230 LEU cc_start: 0.8826 (mt) cc_final: 0.8548 (mp) REVERT: A 334 THR cc_start: 0.9109 (m) cc_final: 0.8803 (t) REVERT: A 379 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 31 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7904 (t70) REVERT: B 407 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: E 220 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7708 (tp30) REVERT: E 275 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8824 (m) REVERT: E 297 GLU cc_start: 0.8505 (tp30) cc_final: 0.8117 (tt0) REVERT: E 392 ASP cc_start: 0.8708 (t0) cc_final: 0.8479 (m-30) REVERT: E 434 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8427 (tm-30) REVERT: E 445 GLU cc_start: 0.2954 (OUTLIER) cc_final: 0.2538 (tm-30) REVERT: I 164 MET cc_start: 0.8583 (tpp) cc_final: 0.7983 (tpp) REVERT: I 196 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8428 (p) REVERT: I 209 ASP cc_start: 0.8525 (t70) cc_final: 0.8296 (t0) REVERT: I 213 ARG cc_start: 0.8547 (ttm110) cc_final: 0.8186 (ttm-80) REVERT: I 406 MET cc_start: 0.8032 (ttp) cc_final: 0.7647 (ttp) REVERT: S 6 SER cc_start: 0.9101 (m) cc_final: 0.8693 (t) REVERT: S 16 ILE cc_start: 0.8579 (mt) cc_final: 0.7942 (mp) REVERT: S 20 CYS cc_start: 0.8110 (m) cc_final: 0.7695 (m) REVERT: S 50 ASN cc_start: 0.8126 (t0) cc_final: 0.7512 (t0) REVERT: S 55 GLU cc_start: 0.8061 (tt0) cc_final: 0.7619 (mt-10) REVERT: S 182 VAL cc_start: 0.8228 (m) cc_final: 0.8001 (m) REVERT: S 297 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7842 (mm-30) REVERT: S 377 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8412 (ttm) outliers start: 100 outliers final: 63 residues processed: 513 average time/residue: 0.3448 time to fit residues: 277.0751 Evaluate side-chains 505 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 432 time to evaluate : 2.692 ------------------------------------------------------------------------------- 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 178 VAL Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 316 ARG Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 GLN Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE 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 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 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 68 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU 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 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 130 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 437 VAL Chi-restraints excluded: chain E residue 445 GLU 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 196 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 4 CYS Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 242 LEU 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 362 VAL Chi-restraints excluded: chain S residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 207 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 68 optimal weight: 0.0870 chunk 71 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS A 18 ASN A 61 HIS A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.128667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092090 restraints weight = 37463.431| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.44 r_work: 0.3295 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24243 Z= 0.115 Angle : 0.568 11.153 32906 Z= 0.282 Chirality : 0.043 0.267 3613 Planarity : 0.005 0.143 4276 Dihedral : 9.139 151.842 3595 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 2.66 % Allowed : 20.25 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2969 helix: 1.97 (0.15), residues: 1240 sheet: 0.51 (0.22), residues: 546 loop : -1.12 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.006 0.001 HIS N 171 PHE 0.023 0.001 PHE I 270 TYR 0.031 0.001 TYR S 24 ARG 0.021 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 1089) hydrogen bonds : angle 3.95374 ( 3309) covalent geometry : bond 0.00255 (24242) covalent geometry : angle 0.56816 (32906) Misc. bond : bond 0.00385 ( 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 512 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 448 time to evaluate : 2.788 Fit side-chains revert: symmetry clash REVERT: K 44 LYS cc_start: 0.8947 (tptm) cc_final: 0.8379 (pptt) REVERT: K 46 THR cc_start: 0.5943 (OUTLIER) cc_final: 0.5727 (p) REVERT: K 57 TRP cc_start: 0.7800 (t-100) cc_final: 0.7554 (t-100) REVERT: K 98 GLN cc_start: 0.7685 (pp30) cc_final: 0.7392 (pp30) REVERT: K 105 TYR cc_start: 0.8480 (t80) cc_final: 0.8148 (t80) REVERT: K 142 VAL cc_start: 0.8507 (t) cc_final: 0.8220 (m) REVERT: K 179 GLU cc_start: 0.8617 (tt0) cc_final: 0.8272 (tm-30) REVERT: K 275 LEU cc_start: 0.8990 (mm) cc_final: 0.8669 (mp) REVERT: K 288 MET cc_start: 0.8313 (tmm) cc_final: 0.8065 (tmm) REVERT: N 107 MET cc_start: 0.7456 (mmm) cc_final: 0.7208 (tpp) REVERT: N 178 VAL cc_start: 0.8921 (t) cc_final: 0.8656 (p) REVERT: N 197 ASP cc_start: 0.8599 (t0) cc_final: 0.8303 (t0) REVERT: N 201 LYS cc_start: 0.8704 (tppt) cc_final: 0.8247 (mtmm) REVERT: N 347 TYR cc_start: 0.8390 (t80) cc_final: 0.7860 (t80) REVERT: A 24 TYR cc_start: 0.8644 (m-80) cc_final: 0.8404 (m-80) REVERT: A 230 LEU cc_start: 0.8763 (mt) cc_final: 0.8478 (mp) REVERT: A 254 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7363 (mt-10) REVERT: A 279 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8542 (mp0) REVERT: A 379 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8499 (p) REVERT: B 31 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7852 (t70) REVERT: B 136 THR cc_start: 0.8965 (m) cc_final: 0.8720 (p) REVERT: B 209 ASP cc_start: 0.8553 (t70) cc_final: 0.8194 (t0) REVERT: B 407 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: E 220 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7618 (tp30) REVERT: E 265 ILE cc_start: 0.8507 (pt) cc_final: 0.8072 (mt) REVERT: E 275 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8746 (p) REVERT: E 379 SER cc_start: 0.9038 (t) cc_final: 0.8455 (p) REVERT: E 392 ASP cc_start: 0.8701 (t0) cc_final: 0.8365 (m-30) REVERT: I 186 THR cc_start: 0.8823 (m) cc_final: 0.8521 (p) REVERT: I 209 ASP cc_start: 0.8470 (t70) cc_final: 0.8243 (t0) REVERT: I 213 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8171 (ttm-80) REVERT: I 406 MET cc_start: 0.7741 (ttp) cc_final: 0.7532 (ttp) REVERT: I 426 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8200 (tm-30) REVERT: S 6 SER cc_start: 0.9109 (m) cc_final: 0.8701 (t) REVERT: S 16 ILE cc_start: 0.8580 (mt) cc_final: 0.7874 (mp) REVERT: S 20 CYS cc_start: 0.7993 (m) cc_final: 0.7537 (m) REVERT: S 24 TYR cc_start: 0.8500 (m-80) cc_final: 0.8209 (m-80) REVERT: S 36 MET cc_start: 0.7509 (ttm) cc_final: 0.7256 (ttm) REVERT: S 50 ASN cc_start: 0.8086 (t0) cc_final: 0.7464 (t0) REVERT: S 55 GLU cc_start: 0.8113 (tt0) cc_final: 0.7574 (mt-10) REVERT: S 297 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7760 (mm-30) REVERT: S 377 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8229 (ttm) REVERT: S 420 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8426 (mt-10) REVERT: S 434 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8424 (tm-30) outliers start: 64 outliers final: 40 residues processed: 486 average time/residue: 0.3488 time to fit residues: 266.0770 Evaluate side-chains 485 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 439 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 130 THR 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 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 60 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU 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 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 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 422 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 44 optimal weight: 0.3980 chunk 276 optimal weight: 0.0970 chunk 118 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 272 ASN N 171 HIS N 318 ASN A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.128421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091119 restraints weight = 44737.758| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.73 r_work: 0.3275 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24243 Z= 0.113 Angle : 0.563 11.552 32906 Z= 0.276 Chirality : 0.043 0.344 3613 Planarity : 0.005 0.155 4276 Dihedral : 8.929 152.755 3595 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.38 % Allowed : 20.64 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2969 helix: 2.11 (0.15), residues: 1232 sheet: 0.65 (0.22), residues: 546 loop : -1.03 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.006 0.001 HIS N 171 PHE 0.025 0.001 PHE K 52 TYR 0.025 0.001 TYR S 24 ARG 0.019 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 1089) hydrogen bonds : angle 3.87935 ( 3309) covalent geometry : bond 0.00258 (24242) covalent geometry : angle 0.56302 (32906) Misc. bond : bond 0.00548 ( 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 507 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 450 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 THR cc_start: 0.5862 (OUTLIER) cc_final: 0.5640 (p) REVERT: K 57 TRP cc_start: 0.7762 (t-100) cc_final: 0.7526 (t-100) REVERT: K 98 GLN cc_start: 0.7648 (pp30) cc_final: 0.7362 (pp30) REVERT: K 105 TYR cc_start: 0.8504 (t80) cc_final: 0.8163 (t80) REVERT: K 142 VAL cc_start: 0.8486 (t) cc_final: 0.8203 (m) REVERT: K 179 GLU cc_start: 0.8566 (tt0) cc_final: 0.8205 (tm-30) REVERT: K 275 LEU cc_start: 0.8891 (mm) cc_final: 0.8574 (mp) REVERT: K 331 LEU cc_start: 0.8475 (mt) cc_final: 0.8239 (mp) REVERT: N 107 MET cc_start: 0.7444 (mmm) cc_final: 0.7205 (tpp) REVERT: N 110 LYS cc_start: 0.8187 (tptp) cc_final: 0.7742 (tptp) REVERT: N 159 ASN cc_start: 0.8996 (t0) cc_final: 0.8732 (t0) REVERT: N 178 VAL cc_start: 0.8871 (t) cc_final: 0.8654 (p) REVERT: N 197 ASP cc_start: 0.8573 (t0) cc_final: 0.8263 (t0) REVERT: N 201 LYS cc_start: 0.8695 (tppt) cc_final: 0.8233 (mtmm) REVERT: A 24 TYR cc_start: 0.8577 (m-80) cc_final: 0.8252 (m-80) REVERT: A 49 PHE cc_start: 0.7538 (m-10) cc_final: 0.7314 (m-10) REVERT: A 230 LEU cc_start: 0.8703 (mt) cc_final: 0.8418 (mp) REVERT: A 254 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7280 (mt-10) REVERT: A 279 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8389 (mp0) REVERT: A 379 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 31 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7636 (t70) REVERT: B 209 ASP cc_start: 0.8369 (t70) cc_final: 0.7933 (t0) REVERT: B 407 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: E 322 ASP cc_start: 0.8628 (t0) cc_final: 0.8319 (t70) REVERT: E 379 SER cc_start: 0.8938 (t) cc_final: 0.8358 (p) REVERT: E 392 ASP cc_start: 0.8518 (t0) cc_final: 0.8085 (m-30) REVERT: E 429 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8226 (mt-10) REVERT: I 186 THR cc_start: 0.8735 (m) cc_final: 0.8395 (p) REVERT: I 209 ASP cc_start: 0.8351 (t70) cc_final: 0.8114 (t0) REVERT: I 213 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8154 (ttm-80) REVERT: I 330 MET cc_start: 0.8456 (mmt) cc_final: 0.8022 (mmt) REVERT: S 6 SER cc_start: 0.9084 (m) cc_final: 0.8652 (t) REVERT: S 20 CYS cc_start: 0.7804 (m) cc_final: 0.7422 (m) REVERT: S 24 TYR cc_start: 0.8489 (m-80) cc_final: 0.8228 (m-80) REVERT: S 36 MET cc_start: 0.7433 (ttm) cc_final: 0.7229 (ttm) REVERT: S 50 ASN cc_start: 0.7958 (t0) cc_final: 0.7325 (t0) REVERT: S 55 GLU cc_start: 0.7984 (tt0) cc_final: 0.7476 (mt-10) REVERT: S 297 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7879 (mm-30) REVERT: S 377 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8194 (ttm) REVERT: S 422 ARG cc_start: 0.8299 (tpt90) cc_final: 0.7812 (tpt90) REVERT: S 425 MET cc_start: 0.7875 (tpp) cc_final: 0.7623 (tpt) REVERT: S 434 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8255 (tm-30) outliers start: 57 outliers final: 40 residues processed: 478 average time/residue: 0.3606 time to fit residues: 270.3670 Evaluate side-chains 483 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 438 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 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 B residue 31 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 276 ARG 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 191 THR Chi-restraints excluded: chain E residue 295 CYS 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 74 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 133 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 242 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4072 r_free = 0.4072 target = 0.127438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091144 restraints weight = 35335.498| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.34 r_work: 0.3277 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 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 = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24243 Z= 0.158 Angle : 0.596 11.263 32906 Z= 0.292 Chirality : 0.044 0.362 3613 Planarity : 0.005 0.164 4276 Dihedral : 8.972 152.532 3595 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 2.31 % Allowed : 20.68 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 2969 helix: 2.07 (0.15), residues: 1240 sheet: 0.61 (0.22), residues: 553 loop : -1.06 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 388 HIS 0.006 0.001 HIS N 171 PHE 0.022 0.002 PHE I 270 TYR 0.022 0.001 TYR S 24 ARG 0.018 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1089) hydrogen bonds : angle 3.96930 ( 3309) covalent geometry : bond 0.00382 (24242) covalent geometry : angle 0.59634 (32906) Misc. bond : bond 0.00549 ( 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 515 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 460 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 28 ILE cc_start: 0.9099 (mm) cc_final: 0.8800 (pt) REVERT: K 29 GLN cc_start: 0.7305 (tm-30) cc_final: 0.7098 (tm-30) REVERT: K 46 THR cc_start: 0.5823 (OUTLIER) cc_final: 0.5600 (p) REVERT: K 57 TRP cc_start: 0.7827 (t-100) cc_final: 0.7571 (t-100) REVERT: K 98 GLN cc_start: 0.7795 (pp30) cc_final: 0.7482 (pp30) REVERT: K 105 TYR cc_start: 0.8516 (t80) cc_final: 0.8174 (t80) REVERT: K 142 VAL cc_start: 0.8469 (t) cc_final: 0.8224 (m) REVERT: K 166 LEU cc_start: 0.9087 (mm) cc_final: 0.8824 (mm) REVERT: K 179 GLU cc_start: 0.8619 (tt0) cc_final: 0.8184 (tm-30) REVERT: K 275 LEU cc_start: 0.8985 (mm) cc_final: 0.8644 (mp) REVERT: K 331 LEU cc_start: 0.8565 (mt) cc_final: 0.8342 (mp) REVERT: N 107 MET cc_start: 0.7437 (mmm) cc_final: 0.7187 (tpp) REVERT: N 110 LYS cc_start: 0.8141 (tptp) cc_final: 0.7680 (tptp) REVERT: N 178 VAL cc_start: 0.8888 (t) cc_final: 0.8659 (p) REVERT: N 197 ASP cc_start: 0.8572 (t0) cc_final: 0.8268 (t0) REVERT: N 201 LYS cc_start: 0.8722 (tppt) cc_final: 0.8268 (mtmm) REVERT: N 347 TYR cc_start: 0.8424 (t80) cc_final: 0.7881 (t80) REVERT: A 24 TYR cc_start: 0.8691 (m-80) cc_final: 0.8352 (m-80) REVERT: A 230 LEU cc_start: 0.8782 (mt) cc_final: 0.8493 (mp) REVERT: A 254 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7447 (mt-10) REVERT: A 279 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8538 (mp0) REVERT: A 379 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 31 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7813 (t70) REVERT: B 209 ASP cc_start: 0.8564 (t70) cc_final: 0.8078 (t0) REVERT: B 407 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: E 24 TYR cc_start: 0.8796 (m-10) cc_final: 0.8577 (m-10) REVERT: E 265 ILE cc_start: 0.8621 (pt) cc_final: 0.8249 (mt) REVERT: E 379 SER cc_start: 0.9035 (t) cc_final: 0.8436 (p) REVERT: E 392 ASP cc_start: 0.8673 (t0) cc_final: 0.8366 (m-30) REVERT: I 209 ASP cc_start: 0.8497 (t70) cc_final: 0.8264 (t0) REVERT: I 213 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8249 (ttm-80) REVERT: I 330 MET cc_start: 0.8575 (mmt) cc_final: 0.8219 (mmt) REVERT: I 406 MET cc_start: 0.7478 (ttp) cc_final: 0.7208 (ttp) REVERT: S 6 SER cc_start: 0.9136 (m) cc_final: 0.8690 (t) REVERT: S 20 CYS cc_start: 0.7998 (m) cc_final: 0.7546 (m) REVERT: S 24 TYR cc_start: 0.8564 (m-80) cc_final: 0.8344 (m-80) REVERT: S 35 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7336 (mp10) REVERT: S 36 MET cc_start: 0.7533 (ttm) cc_final: 0.7200 (ttm) REVERT: S 50 ASN cc_start: 0.8015 (t0) cc_final: 0.7406 (t0) REVERT: S 55 GLU cc_start: 0.8103 (tt0) cc_final: 0.7571 (mt-10) REVERT: S 297 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8017 (mm-30) REVERT: S 377 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8274 (ttm) REVERT: S 434 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 55 outliers final: 45 residues processed: 490 average time/residue: 0.3726 time to fit residues: 287.0184 Evaluate side-chains 497 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 447 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 178 VAL 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 38 VAL Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE 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 135 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 284 LEU 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 26 LEU 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 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 74 VAL 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 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 112 optimal weight: 0.9980 chunk 292 optimal weight: 9.9990 chunk 64 optimal weight: 0.0370 chunk 229 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 289 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 250 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.128529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091040 restraints weight = 44761.446| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.73 r_work: 0.3266 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24243 Z= 0.114 Angle : 0.576 12.876 32906 Z= 0.281 Chirality : 0.043 0.352 3613 Planarity : 0.005 0.167 4276 Dihedral : 8.829 153.258 3595 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 2.19 % Allowed : 20.76 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2969 helix: 2.14 (0.15), residues: 1234 sheet: 0.70 (0.22), residues: 551 loop : -0.99 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.005 0.001 HIS N 171 PHE 0.022 0.001 PHE I 270 TYR 0.024 0.001 TYR S 24 ARG 0.023 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1089) hydrogen bonds : angle 3.90619 ( 3309) covalent geometry : bond 0.00260 (24242) covalent geometry : angle 0.57644 (32906) Misc. bond : bond 0.00491 ( 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 502 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 450 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 THR cc_start: 0.5750 (OUTLIER) cc_final: 0.5531 (p) REVERT: K 57 TRP cc_start: 0.7804 (t-100) cc_final: 0.7556 (t-100) REVERT: K 98 GLN cc_start: 0.7637 (pp30) cc_final: 0.7361 (pp30) REVERT: K 105 TYR cc_start: 0.8511 (t80) cc_final: 0.8205 (t80) REVERT: K 120 PRO cc_start: 0.8164 (Cg_exo) cc_final: 0.7927 (Cg_endo) REVERT: K 166 LEU cc_start: 0.9043 (mm) cc_final: 0.8752 (mm) REVERT: K 179 GLU cc_start: 0.8524 (tt0) cc_final: 0.8114 (tm-30) REVERT: K 275 LEU cc_start: 0.8893 (mm) cc_final: 0.8585 (mp) REVERT: N 110 LYS cc_start: 0.8141 (tptp) cc_final: 0.7685 (tptp) REVERT: N 197 ASP cc_start: 0.8549 (t0) cc_final: 0.7979 (t0) REVERT: N 201 LYS cc_start: 0.8669 (tppt) cc_final: 0.8213 (mtmm) REVERT: N 347 TYR cc_start: 0.8412 (t80) cc_final: 0.7796 (t80) REVERT: A 24 TYR cc_start: 0.8568 (m-80) cc_final: 0.8236 (m-80) REVERT: A 49 PHE cc_start: 0.7529 (m-10) cc_final: 0.7209 (m-10) REVERT: A 230 LEU cc_start: 0.8710 (mt) cc_final: 0.8422 (mp) REVERT: A 254 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7307 (mt-10) REVERT: A 279 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8374 (mp0) REVERT: A 379 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 31 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7597 (t70) REVERT: B 209 ASP cc_start: 0.8422 (t70) cc_final: 0.7992 (t0) REVERT: B 328 GLU cc_start: 0.8217 (tt0) cc_final: 0.8005 (tt0) REVERT: B 407 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: E 265 ILE cc_start: 0.8552 (pt) cc_final: 0.8176 (mt) REVERT: E 379 SER cc_start: 0.8931 (t) cc_final: 0.8354 (p) REVERT: E 392 ASP cc_start: 0.8514 (t0) cc_final: 0.8033 (m-30) REVERT: E 429 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8234 (mt-10) REVERT: I 209 ASP cc_start: 0.8333 (t70) cc_final: 0.8092 (t0) REVERT: I 213 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8167 (ttm-80) REVERT: I 274 THR cc_start: 0.8411 (t) cc_final: 0.8208 (t) REVERT: I 330 MET cc_start: 0.8449 (mmt) cc_final: 0.8067 (mmt) REVERT: I 406 MET cc_start: 0.7115 (ttp) cc_final: 0.6838 (ttp) REVERT: S 6 SER cc_start: 0.9091 (m) cc_final: 0.8653 (t) REVERT: S 20 CYS cc_start: 0.7807 (m) cc_final: 0.7387 (m) REVERT: S 24 TYR cc_start: 0.8486 (m-80) cc_final: 0.8254 (m-80) REVERT: S 50 ASN cc_start: 0.7836 (t0) cc_final: 0.7214 (t0) REVERT: S 55 GLU cc_start: 0.7973 (tt0) cc_final: 0.7456 (mt-10) REVERT: S 297 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7864 (mm-30) REVERT: S 377 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8179 (ttm) REVERT: S 434 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 52 outliers final: 40 residues processed: 478 average time/residue: 0.3405 time to fit residues: 253.0780 Evaluate side-chains 480 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 435 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE 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 135 LEU 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 191 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 118 ASP 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 4 CYS 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 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 116 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.127086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090227 restraints weight = 37518.715| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.45 r_work: 0.3259 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 24243 Z= 0.148 Angle : 0.612 13.091 32906 Z= 0.297 Chirality : 0.044 0.307 3613 Planarity : 0.007 0.325 4276 Dihedral : 8.840 153.300 3594 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 2.35 % Allowed : 20.80 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 2969 helix: 2.10 (0.15), residues: 1242 sheet: 0.66 (0.22), residues: 551 loop : -1.05 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 344 HIS 0.006 0.001 HIS N 171 PHE 0.021 0.001 PHE I 270 TYR 0.022 0.001 TYR S 24 ARG 0.035 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 1089) hydrogen bonds : angle 3.96831 ( 3309) covalent geometry : bond 0.00356 (24242) covalent geometry : angle 0.61161 (32906) Misc. bond : bond 0.00808 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16433.24 seconds wall clock time: 283 minutes 18.01 seconds (16998.01 seconds total)