Starting phenix.real_space_refine on Sat Jan 25 18:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uty_42553/01_2025/8uty_42553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uty_42553/01_2025/8uty_42553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uty_42553/01_2025/8uty_42553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uty_42553/01_2025/8uty_42553.map" model { file = "/net/cci-nas-00/data/ceres_data/8uty_42553/01_2025/8uty_42553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uty_42553/01_2025/8uty_42553.cif" } resolution = 3.3 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= 0.001 sd= 0.005 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 152 5.16 5 C 14846 2.51 5 N 4067 2.21 5 O 4677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23765 Number of models: 1 Model: "" Number of chains: 16 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: "K" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3039 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain: "S" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3503 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 20, 'TRANS': 428} Chain: "N" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3048 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 12, 'TRANS': 375} 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: "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: "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} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.49 residue: pdb=" N AALA B 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.49 residue: pdb=" N AASP B 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.49 residue: pdb=" N AGLU B 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.49 residue: pdb=" N ATHR I 429 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.49 residue: pdb=" N AALA I 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.49 residue: pdb=" N AASP I 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.49 residue: pdb=" N AGLU I 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.49 residue: pdb=" N AGLN I 433 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.49 Time building chain proxies: 17.27, per 1000 atoms: 0.73 Number of scatterers: 23765 At special positions: 0 Unit cell: (104, 115.7, 240.5, 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 152 16.00 P 19 15.00 Mg 4 11.99 O 4677 8.00 N 4067 7.00 C 14846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 4.3 seconds 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 23 sheets defined 49.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.384A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.349A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 4.639A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 113 through 129 removed outlier: 4.148A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.101A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.539A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.569A 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 258 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.953A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.931A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 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: 3.747A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.118A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.330A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.701A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.147A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (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 126 removed outlier: 3.858A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.596A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.001A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 removed outlier: 3.609A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.835A 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: 3.657A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 424 removed outlier: 3.653A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.724A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.577A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.569A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.587A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.585A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.017A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.822A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.823A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.033A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.142A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 3.825A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.660A pdb=" N GLN I 43 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.120A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.539A pdb=" N ILE I 84 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' 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: 3.842A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 180 through 195 removed outlier: 3.958A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.537A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 4.099A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 282 removed outlier: 4.167A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG I 282 " --> pdb=" O GLN I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 295 Processing helix chain 'I' and resid 296 through 299 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.644A 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: 3.529A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 424 removed outlier: 3.922A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 88 removed outlier: 4.251A pdb=" N GLU K 79 " --> pdb=" O ARG K 75 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 removed outlier: 3.558A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 296 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 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 353 removed outlier: 4.007A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 removed outlier: 4.667A pdb=" N ILE K 369 " --> pdb=" O ASN K 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 3.676A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 80 removed outlier: 3.922A 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 129 Processing helix chain 'S' and resid 144 through 161 removed outlier: 5.612A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 190 Processing helix chain 'S' and resid 190 through 197 Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.541A 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: 3.575A pdb=" N VAL S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.037A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 296 removed outlier: 3.654A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 301 removed outlier: 3.626A pdb=" N GLN S 301 " --> pdb=" O PRO S 298 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 338 removed outlier: 3.588A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 4.004A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 412 removed outlier: 3.720A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 415 through 437 removed outlier: 4.176A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL S 437 " --> pdb=" O GLU S 433 " (cutoff:3.500A) 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 Processing helix chain 'N' and resid 117 through 134 Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.688A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 295 removed outlier: 3.785A pdb=" N ASP N 289 " --> pdb=" O LEU N 285 " (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 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 349 Processing helix chain 'N' and resid 363 through 386 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.709A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.525A 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: 6.288A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.155A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.933A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.618A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AA9, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.094A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU I 3 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY I 132 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER I 138 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE I 163 " --> pdb=" O CYS I 129 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 14.020A pdb=" N ASP I 203 " --> pdb=" O PHE I 270 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 57 removed outlier: 3.535A pdb=" N TYR K 54 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 54 through 57 removed outlier: 3.535A pdb=" N TYR K 54 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AB7, first strand: chain 'S' and resid 65 through 68 removed outlier: 7.805A pdb=" N GLU S 3 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE S 135 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE S 5 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL S 137 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE S 7 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N HIS S 139 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL S 9 " --> pdb=" O HIS S 139 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N HIS S 139 " --> pdb=" O ILE S 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'S' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.320A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.320A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AC5, first strand: chain 'N' and resid 205 through 206 1185 hydrogen bonds defined for protein. 3417 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: 8.49 Time building geometry restraints manager: 7.26 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: 4419 1.33 - 1.45: 6156 1.45 - 1.57: 13402 1.57 - 1.70: 43 1.70 - 1.82: 242 Bond restraints: 24262 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" N LYS K 297 " pdb=" CA LYS K 297 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.29e-02 6.01e+03 3.03e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 24257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 32491 3.37 - 6.74: 412 6.74 - 10.11: 21 10.11 - 13.48: 5 13.48 - 16.85: 3 Bond angle restraints: 32932 Sorted by residual: angle pdb=" O ALA I 428 " pdb=" C ALA I 428 " pdb=" N BTHR I 429 " ideal model delta sigma weight residual 122.59 106.09 16.50 1.33e+00 5.65e-01 1.54e+02 angle pdb=" N ILE S 114 " pdb=" CA ILE S 114 " pdb=" C ILE S 114 " ideal model delta sigma weight residual 112.96 107.20 5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" PB ANP N 501 " pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 126.95 110.10 16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 110.94 16.01 3.00e+00 1.11e-01 2.85e+01 angle pdb=" N AASP B 431 " pdb=" CA AASP B 431 " pdb=" C AASP B 431 " ideal model delta sigma weight residual 110.80 121.69 -10.89 2.13e+00 2.20e-01 2.61e+01 ... (remaining 32927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 14206 35.34 - 70.69: 444 70.69 - 106.03: 68 106.03 - 141.38: 19 141.38 - 176.72: 7 Dihedral angle restraints: 14744 sinusoidal: 6096 harmonic: 8648 Sorted by residual: dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 84.15 176.72 1 2.00e+01 2.50e-03 4.80e+01 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 -115.37 -175.36 1 2.00e+01 2.50e-03 4.79e+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 -81.01 150.28 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 14741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2807 0.053 - 0.105: 595 0.105 - 0.158: 178 0.158 - 0.210: 29 0.210 - 0.263: 7 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C3' ANP N 501 " pdb=" C2' ANP N 501 " pdb=" C4' ANP N 501 " pdb=" O3' ANP N 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.72e+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 -2.61 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA GLN I 375 " pdb=" N GLN I 375 " pdb=" C GLN I 375 " pdb=" CB GLN I 375 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3613 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 428 " 0.086 2.00e-02 2.50e+03 1.60e-01 2.55e+02 pdb=" C ALA I 428 " -0.276 2.00e-02 2.50e+03 pdb=" O ALA I 428 " 0.099 2.00e-02 2.50e+03 pdb=" N BTHR I 429 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 428 " 0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C ALA I 428 " -0.091 2.00e-02 2.50e+03 pdb=" O ALA I 428 " 0.034 2.00e-02 2.50e+03 pdb=" N ATHR I 429 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 295 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C ASN N 295 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN N 295 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS N 296 " 0.021 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 147 2.53 - 3.12: 18418 3.12 - 3.72: 36689 3.72 - 4.31: 50731 4.31 - 4.90: 86385 Nonbonded interactions: 192370 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.941 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.954 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.964 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.968 2.170 nonbonded pdb=" OG SER K 104 " pdb="MG MG K 501 " model vdw 1.972 2.170 ... (remaining 192365 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 389) selection = (chain 'N' and resid 4 through 389) } 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=0.49 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 58.180 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.006 0.144 24262 Z= 0.360 Angle : 0.883 16.847 32932 Z= 0.496 Chirality : 0.050 0.263 3616 Planarity : 0.006 0.160 4281 Dihedral : 18.432 176.724 9196 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.81 % Allowed : 4.38 % Favored : 94.81 % Rotamer: Outliers : 1.45 % Allowed : 14.19 % Favored : 84.37 % 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: -0.11 (0.15), residues: 2974 helix: 1.09 (0.15), residues: 1238 sheet: -0.29 (0.22), residues: 508 loop : -1.14 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 388 HIS 0.004 0.001 HIS N 59 PHE 0.017 0.001 PHE K 86 TYR 0.045 0.001 TYR E 24 ARG 0.015 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 502 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8944 (m-40) cc_final: 0.8731 (m-40) REVERT: A 254 GLU cc_start: 0.4307 (mm-30) cc_final: 0.3620 (mm-30) REVERT: B 203 ASP cc_start: 0.8114 (t0) cc_final: 0.7714 (t0) REVERT: E 51 THR cc_start: 0.8856 (p) cc_final: 0.8636 (t) REVERT: E 120 ASP cc_start: 0.8302 (t0) cc_final: 0.8095 (m-30) REVERT: E 322 ASP cc_start: 0.8721 (t0) cc_final: 0.8181 (t0) REVERT: I 67 ASP cc_start: 0.8165 (t70) cc_final: 0.7940 (t70) REVERT: I 291 GLN cc_start: 0.8356 (tp40) cc_final: 0.8003 (tp40) REVERT: I 359 ARG cc_start: 0.8844 (tpt-90) cc_final: 0.8586 (mmm-85) REVERT: I 374 ILE cc_start: 0.9172 (tp) cc_final: 0.8876 (tt) REVERT: I 424 GLN cc_start: 0.8677 (tt0) cc_final: 0.8354 (tt0) REVERT: K 26 CYS cc_start: 0.8843 (p) cc_final: 0.8477 (m) REVERT: K 67 TYR cc_start: 0.7897 (t80) cc_final: 0.7224 (t80) REVERT: K 74 TYR cc_start: 0.8462 (t80) cc_final: 0.7955 (t80) REVERT: K 83 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8492 (tp-100) REVERT: K 87 GLU cc_start: 0.8698 (mp0) cc_final: 0.8097 (mp0) REVERT: K 105 TYR cc_start: 0.8516 (t80) cc_final: 0.8113 (t80) REVERT: K 189 TYR cc_start: 0.7750 (t80) cc_final: 0.7268 (t80) REVERT: K 285 LEU cc_start: 0.7735 (mp) cc_final: 0.7398 (mm) REVERT: K 290 SER cc_start: 0.7322 (OUTLIER) cc_final: 0.7004 (p) REVERT: K 301 THR cc_start: 0.6461 (OUTLIER) cc_final: 0.6139 (p) REVERT: K 367 LYS cc_start: 0.9572 (ttpp) cc_final: 0.9313 (pttm) REVERT: S 166 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8518 (mtpp) REVERT: S 228 ASN cc_start: 0.9030 (m-40) cc_final: 0.8731 (m-40) REVERT: S 326 LYS cc_start: 0.8882 (pptt) cc_final: 0.8635 (pttm) REVERT: N 20 MET cc_start: 0.8427 (mtm) cc_final: 0.7930 (mtm) REVERT: N 148 GLU cc_start: 0.8226 (pt0) cc_final: 0.8019 (tt0) REVERT: N 180 ASP cc_start: 0.7576 (t0) cc_final: 0.7095 (t0) REVERT: N 217 SER cc_start: 0.9201 (p) cc_final: 0.8740 (p) REVERT: N 248 ASP cc_start: 0.8031 (t0) cc_final: 0.7685 (t0) outliers start: 30 outliers final: 5 residues processed: 529 average time/residue: 0.3857 time to fit residues: 311.2864 Evaluate side-chains 469 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 462 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 299 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain S residue 447 GLU Chi-restraints excluded: chain N residue 44 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 140 optimal weight: 0.0670 chunk 172 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN E 31 GLN E 107 HIS E 128 GLN E 358 GLN I 131 GLN I 423 GLN S 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.119314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091734 restraints weight = 48701.429| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.90 r_work: 0.3207 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24262 Z= 0.168 Angle : 0.597 10.455 32932 Z= 0.297 Chirality : 0.044 0.349 3616 Planarity : 0.004 0.048 4281 Dihedral : 12.822 178.517 3616 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.10 % Favored : 96.63 % Rotamer: Outliers : 2.07 % Allowed : 13.95 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.49 (0.15), residues: 2974 helix: 1.71 (0.15), residues: 1250 sheet: -0.11 (0.22), residues: 546 loop : -0.96 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 21 HIS 0.004 0.001 HIS K 84 PHE 0.012 0.001 PHE K 94 TYR 0.033 0.001 TYR E 24 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 485 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ASP cc_start: 0.8082 (t0) cc_final: 0.7758 (t0) REVERT: B 288 GLU cc_start: 0.8256 (mp0) cc_final: 0.7863 (mp0) REVERT: B 291 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7892 (tp-100) REVERT: E 117 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7695 (tt) REVERT: E 123 ARG cc_start: 0.8710 (ttp-110) cc_final: 0.8244 (ttm-80) REVERT: I 131 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: I 155 ILE cc_start: 0.9034 (mt) cc_final: 0.8699 (mm) REVERT: I 267 MET cc_start: 0.8816 (mtp) cc_final: 0.8521 (mtp) REVERT: I 374 ILE cc_start: 0.9350 (tp) cc_final: 0.8987 (tt) REVERT: I 424 GLN cc_start: 0.8827 (tt0) cc_final: 0.8622 (tt0) REVERT: K 26 CYS cc_start: 0.8960 (p) cc_final: 0.8502 (m) REVERT: K 74 TYR cc_start: 0.8517 (t80) cc_final: 0.8060 (t80) REVERT: K 83 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8487 (tp-100) REVERT: K 193 GLN cc_start: 0.8223 (tp40) cc_final: 0.7978 (tm-30) REVERT: K 327 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7795 (tpp) REVERT: S 1 MET cc_start: 0.6486 (pmm) cc_final: 0.6126 (pmm) REVERT: S 27 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8240 (mt-10) REVERT: S 69 ASP cc_start: 0.7860 (t0) cc_final: 0.7445 (t0) REVERT: S 120 ASP cc_start: 0.8413 (t0) cc_final: 0.8160 (t0) REVERT: S 121 ARG cc_start: 0.6594 (ttt-90) cc_final: 0.5902 (tpt-90) REVERT: S 154 MET cc_start: 0.9131 (mmm) cc_final: 0.8867 (mmm) REVERT: S 220 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8408 (tp30) REVERT: S 259 LEU cc_start: 0.8807 (mp) cc_final: 0.8602 (mp) REVERT: S 326 LYS cc_start: 0.8829 (pptt) cc_final: 0.8537 (pttp) REVERT: S 411 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7587 (mm-30) REVERT: N 20 MET cc_start: 0.8607 (mtm) cc_final: 0.8099 (mtm) REVERT: N 217 SER cc_start: 0.8935 (p) cc_final: 0.8659 (p) REVERT: N 248 ASP cc_start: 0.8304 (t0) cc_final: 0.7693 (t0) REVERT: N 295 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6954 (p0) REVERT: N 346 ARG cc_start: 0.8897 (mtp85) cc_final: 0.8583 (mtp85) outliers start: 46 outliers final: 23 residues processed: 509 average time/residue: 0.4159 time to fit residues: 329.6243 Evaluate side-chains 476 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 449 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 291 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 245 GLN E 128 GLN I 100 ASN I 131 GLN I 384 GLN K 116 GLN ** K 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 HIS N 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.115720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088805 restraints weight = 37900.111| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.49 r_work: 0.3242 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24262 Z= 0.170 Angle : 0.557 8.735 32932 Z= 0.278 Chirality : 0.044 0.460 3616 Planarity : 0.004 0.057 4281 Dihedral : 9.937 176.777 3605 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.24 % Favored : 96.56 % Rotamer: Outliers : 2.66 % Allowed : 14.73 % Favored : 82.61 % 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: 0.70 (0.15), residues: 2974 helix: 1.92 (0.15), residues: 1249 sheet: 0.05 (0.22), residues: 538 loop : -0.91 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.012 0.001 PHE N 15 TYR 0.026 0.001 TYR E 24 ARG 0.006 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 465 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8263 (t0) cc_final: 0.7959 (t0) REVERT: A 215 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.8111 (ttp-110) REVERT: A 284 GLU cc_start: 0.7336 (mp0) cc_final: 0.6993 (mt-10) REVERT: A 396 ASP cc_start: 0.8455 (m-30) cc_final: 0.8204 (m-30) REVERT: B 26 ASP cc_start: 0.8778 (t0) cc_final: 0.8543 (t0) REVERT: B 203 ASP cc_start: 0.8204 (t0) cc_final: 0.7886 (t0) REVERT: B 288 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: B 291 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8058 (tp-100) REVERT: E 24 TYR cc_start: 0.8372 (m-80) cc_final: 0.7456 (m-80) REVERT: E 123 ARG cc_start: 0.8909 (ttp-110) cc_final: 0.8412 (ttm-80) REVERT: E 413 MET cc_start: 0.7939 (mtm) cc_final: 0.7680 (mtp) REVERT: I 31 ASP cc_start: 0.8384 (t70) cc_final: 0.8068 (t0) REVERT: I 131 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: I 155 ILE cc_start: 0.9111 (mt) cc_final: 0.8816 (mm) REVERT: I 226 ASN cc_start: 0.8844 (m-40) cc_final: 0.8396 (m110) REVERT: I 267 MET cc_start: 0.8969 (mtp) cc_final: 0.8706 (mtp) REVERT: I 374 ILE cc_start: 0.9401 (tp) cc_final: 0.9060 (tt) REVERT: K 19 GLU cc_start: 0.8476 (mp0) cc_final: 0.7686 (mt-10) REVERT: K 26 CYS cc_start: 0.8964 (p) cc_final: 0.8513 (m) REVERT: K 74 TYR cc_start: 0.8528 (t80) cc_final: 0.8099 (t80) REVERT: K 83 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8445 (tp-100) REVERT: K 183 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8742 (ttpp) REVERT: K 193 GLN cc_start: 0.8350 (tp40) cc_final: 0.7619 (tm-30) REVERT: K 197 ASP cc_start: 0.8395 (t0) cc_final: 0.8111 (m-30) REVERT: K 266 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8816 (mmmm) REVERT: K 317 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7708 (tp30) REVERT: K 324 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.8242 (mtt180) REVERT: K 327 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7975 (tpp) REVERT: S 1 MET cc_start: 0.6580 (pmm) cc_final: 0.6369 (pmm) REVERT: S 27 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8369 (mt-10) REVERT: S 69 ASP cc_start: 0.8034 (t0) cc_final: 0.7563 (t0) REVERT: S 98 ASP cc_start: 0.8375 (p0) cc_final: 0.8164 (p0) REVERT: S 121 ARG cc_start: 0.6680 (ttt-90) cc_final: 0.6166 (tpt-90) REVERT: S 154 MET cc_start: 0.9174 (mmm) cc_final: 0.8958 (mmm) REVERT: S 220 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8526 (tp30) REVERT: S 228 ASN cc_start: 0.9150 (m-40) cc_final: 0.8862 (m-40) REVERT: S 259 LEU cc_start: 0.8907 (mp) cc_final: 0.8694 (mp) REVERT: S 279 GLU cc_start: 0.8744 (tp30) cc_final: 0.8489 (tp30) REVERT: S 326 LYS cc_start: 0.8900 (pptt) cc_final: 0.8626 (pttp) REVERT: S 411 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7861 (mm-30) REVERT: S 414 GLU cc_start: 0.7124 (pt0) cc_final: 0.6915 (mt-10) REVERT: S 417 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8191 (mt-10) REVERT: N 20 MET cc_start: 0.8623 (mtm) cc_final: 0.8119 (mtm) REVERT: N 148 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: N 217 SER cc_start: 0.8971 (p) cc_final: 0.8430 (p) REVERT: N 248 ASP cc_start: 0.8446 (t0) cc_final: 0.7760 (t0) REVERT: N 282 ILE cc_start: 0.8811 (pt) cc_final: 0.8350 (mt) REVERT: N 295 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7243 (p0) REVERT: N 346 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8267 (mtp85) outliers start: 60 outliers final: 34 residues processed: 502 average time/residue: 0.3782 time to fit residues: 294.0888 Evaluate side-chains 484 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 445 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 283 SER Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 52 PHE Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 244 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 101 optimal weight: 0.0030 chunk 110 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 157 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 100 ASN I 184 ASN K 83 GLN K 366 ASN S 31 GLN S 197 HIS N 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.121564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094293 restraints weight = 41257.545| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.64 r_work: 0.3254 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24262 Z= 0.140 Angle : 0.536 8.631 32932 Z= 0.266 Chirality : 0.043 0.319 3616 Planarity : 0.004 0.046 4281 Dihedral : 9.309 177.311 3605 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.96 % Rotamer: Outliers : 2.42 % Allowed : 15.47 % Favored : 82.10 % 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: 0.84 (0.15), residues: 2974 helix: 2.03 (0.15), residues: 1252 sheet: 0.23 (0.22), residues: 524 loop : -0.88 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 344 HIS 0.002 0.001 HIS K 84 PHE 0.018 0.001 PHE B 367 TYR 0.021 0.001 TYR E 24 ARG 0.007 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 479 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7864 (pm20) cc_final: 0.7253 (pm20) REVERT: A 215 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7898 (ttp-110) REVERT: A 284 GLU cc_start: 0.7080 (mp0) cc_final: 0.6773 (mt-10) REVERT: A 396 ASP cc_start: 0.8289 (m-30) cc_final: 0.7958 (m-30) REVERT: B 203 ASP cc_start: 0.7966 (t0) cc_final: 0.7651 (t0) REVERT: B 288 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: B 291 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7836 (tp-100) REVERT: B 295 ASP cc_start: 0.8471 (t0) cc_final: 0.8157 (t0) REVERT: E 24 TYR cc_start: 0.8215 (m-80) cc_final: 0.7431 (m-80) REVERT: E 123 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8193 (ttm-80) REVERT: E 322 ASP cc_start: 0.8726 (t0) cc_final: 0.8309 (t0) REVERT: I 31 ASP cc_start: 0.8160 (t70) cc_final: 0.7809 (t0) REVERT: I 131 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: I 155 ILE cc_start: 0.9025 (mt) cc_final: 0.8730 (mm) REVERT: I 226 ASN cc_start: 0.8735 (m-40) cc_final: 0.8514 (m110) REVERT: I 230 SER cc_start: 0.8858 (m) cc_final: 0.8525 (t) REVERT: I 267 MET cc_start: 0.8788 (mtp) cc_final: 0.8534 (mtp) REVERT: I 374 ILE cc_start: 0.9319 (tp) cc_final: 0.9005 (tt) REVERT: I 424 GLN cc_start: 0.8869 (tt0) cc_final: 0.8569 (tt0) REVERT: K 19 GLU cc_start: 0.8204 (mp0) cc_final: 0.7593 (mt-10) REVERT: K 26 CYS cc_start: 0.8852 (p) cc_final: 0.8455 (m) REVERT: K 54 TYR cc_start: 0.8332 (m-80) cc_final: 0.8002 (m-10) REVERT: K 74 TYR cc_start: 0.8472 (t80) cc_final: 0.8038 (t80) REVERT: K 83 GLN cc_start: 0.8623 (tp40) cc_final: 0.8295 (tp-100) REVERT: K 112 GLU cc_start: 0.8151 (mp0) cc_final: 0.7832 (mp0) REVERT: K 124 GLU cc_start: 0.8132 (tp30) cc_final: 0.7774 (tm-30) REVERT: K 147 MET cc_start: 0.8653 (ppp) cc_final: 0.8107 (ppp) REVERT: K 183 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8572 (ttpp) REVERT: K 193 GLN cc_start: 0.8274 (tp40) cc_final: 0.7537 (tm-30) REVERT: K 197 ASP cc_start: 0.8286 (t0) cc_final: 0.8082 (m-30) REVERT: K 266 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8756 (mmmm) REVERT: K 285 LEU cc_start: 0.8854 (mm) cc_final: 0.8579 (mt) REVERT: K 317 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7562 (tp30) REVERT: K 324 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8202 (mtt180) REVERT: K 327 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7891 (tpp) REVERT: K 353 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: S 18 ASN cc_start: 0.7068 (m-40) cc_final: 0.6855 (m-40) REVERT: S 27 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8193 (mt-10) REVERT: S 69 ASP cc_start: 0.7806 (t0) cc_final: 0.7328 (t0) REVERT: S 129 CYS cc_start: 0.8714 (p) cc_final: 0.8512 (p) REVERT: S 203 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7795 (mtt) REVERT: S 228 ASN cc_start: 0.9129 (m-40) cc_final: 0.8865 (m-40) REVERT: S 251 ASP cc_start: 0.6574 (t0) cc_final: 0.6336 (t0) REVERT: S 259 LEU cc_start: 0.8805 (mp) cc_final: 0.8582 (mp) REVERT: S 326 LYS cc_start: 0.8768 (pptt) cc_final: 0.8492 (pttp) REVERT: S 411 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7788 (mm-30) REVERT: S 413 MET cc_start: 0.8327 (mmm) cc_final: 0.7582 (mmm) REVERT: S 414 GLU cc_start: 0.7093 (pt0) cc_final: 0.6628 (mt-10) REVERT: S 417 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7914 (mt-10) REVERT: S 447 GLU cc_start: 0.1990 (OUTLIER) cc_final: 0.1677 (pp20) REVERT: N 15 PHE cc_start: 0.7719 (m-80) cc_final: 0.7476 (m-80) REVERT: N 20 MET cc_start: 0.8594 (mtm) cc_final: 0.8060 (mtm) REVERT: N 148 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: N 201 LYS cc_start: 0.9123 (tttt) cc_final: 0.8913 (tppp) REVERT: N 217 SER cc_start: 0.8869 (p) cc_final: 0.8226 (p) REVERT: N 248 ASP cc_start: 0.8289 (t0) cc_final: 0.7499 (t0) REVERT: N 285 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8966 (mp) REVERT: N 346 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8096 (mtp85) outliers start: 54 outliers final: 36 residues processed: 505 average time/residue: 0.3764 time to fit residues: 294.2164 Evaluate side-chains 498 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 454 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 447 GLU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.0570 chunk 157 optimal weight: 0.0980 chunk 195 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 100 ASN I 131 GLN K 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091976 restraints weight = 41727.321| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.64 r_work: 0.3234 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24262 Z= 0.173 Angle : 0.537 7.232 32932 Z= 0.268 Chirality : 0.043 0.270 3616 Planarity : 0.004 0.047 4281 Dihedral : 9.126 178.351 3605 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.10 % Favored : 96.76 % Rotamer: Outliers : 2.89 % Allowed : 15.71 % Favored : 81.40 % 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: 0.91 (0.15), residues: 2974 helix: 2.11 (0.15), residues: 1252 sheet: 0.25 (0.22), residues: 526 loop : -0.87 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.017 0.001 PHE B 367 TYR 0.018 0.001 TYR K 189 ARG 0.006 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 473 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8108 (t0) cc_final: 0.7714 (t0) REVERT: A 196 GLU cc_start: 0.8683 (tp30) cc_final: 0.8341 (tt0) REVERT: A 215 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7911 (ttp-110) REVERT: A 284 GLU cc_start: 0.7094 (mp0) cc_final: 0.6868 (mt-10) REVERT: B 203 ASP cc_start: 0.7976 (t0) cc_final: 0.7688 (t0) REVERT: B 288 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: B 291 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7861 (tp-100) REVERT: E 24 TYR cc_start: 0.8196 (m-80) cc_final: 0.7436 (m-80) REVERT: E 33 ASP cc_start: 0.8744 (t0) cc_final: 0.8529 (t0) REVERT: E 123 ARG cc_start: 0.8742 (ttp-110) cc_final: 0.8184 (ttm-80) REVERT: E 322 ASP cc_start: 0.8719 (t0) cc_final: 0.8295 (t0) REVERT: E 398 MET cc_start: 0.7954 (tpp) cc_final: 0.7710 (tpp) REVERT: I 31 ASP cc_start: 0.8158 (t70) cc_final: 0.7852 (t0) REVERT: I 155 ILE cc_start: 0.9002 (mt) cc_final: 0.8737 (mm) REVERT: I 230 SER cc_start: 0.8866 (m) cc_final: 0.8543 (t) REVERT: I 267 MET cc_start: 0.8850 (mtp) cc_final: 0.8626 (mtp) REVERT: I 374 ILE cc_start: 0.9310 (tp) cc_final: 0.8996 (tt) REVERT: I 424 GLN cc_start: 0.8818 (tt0) cc_final: 0.8536 (tt0) REVERT: K 19 GLU cc_start: 0.8119 (mp0) cc_final: 0.7221 (mt-10) REVERT: K 26 CYS cc_start: 0.8858 (p) cc_final: 0.8507 (m) REVERT: K 55 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8451 (t) REVERT: K 74 TYR cc_start: 0.8516 (t80) cc_final: 0.7997 (t80) REVERT: K 83 GLN cc_start: 0.8739 (tp40) cc_final: 0.8293 (tp-100) REVERT: K 87 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: K 124 GLU cc_start: 0.8275 (tp30) cc_final: 0.7838 (tm-30) REVERT: K 147 MET cc_start: 0.8636 (ppp) cc_final: 0.8072 (ppp) REVERT: K 193 GLN cc_start: 0.8236 (tp40) cc_final: 0.7380 (tm-30) REVERT: K 266 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8756 (mmmm) REVERT: K 285 LEU cc_start: 0.8986 (mm) cc_final: 0.8739 (mt) REVERT: K 287 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8604 (tp30) REVERT: K 317 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7595 (tp30) REVERT: K 327 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7985 (tpp) REVERT: S 27 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8220 (mt-10) REVERT: S 69 ASP cc_start: 0.7832 (t0) cc_final: 0.7325 (t0) REVERT: S 203 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7861 (mtt) REVERT: S 228 ASN cc_start: 0.9138 (m-40) cc_final: 0.8875 (m-40) REVERT: S 251 ASP cc_start: 0.6699 (t0) cc_final: 0.6491 (t0) REVERT: S 259 LEU cc_start: 0.8795 (mp) cc_final: 0.8578 (mp) REVERT: S 279 GLU cc_start: 0.8330 (tp30) cc_final: 0.7849 (tp30) REVERT: S 326 LYS cc_start: 0.8800 (pptt) cc_final: 0.8515 (pttp) REVERT: S 411 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7776 (mm-30) REVERT: S 413 MET cc_start: 0.8387 (mmm) cc_final: 0.7434 (mmm) REVERT: S 414 GLU cc_start: 0.7027 (pt0) cc_final: 0.6549 (mt-10) REVERT: S 417 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7892 (mt-10) REVERT: S 447 GLU cc_start: 0.2159 (OUTLIER) cc_final: 0.1942 (pp20) REVERT: N 15 PHE cc_start: 0.7817 (m-80) cc_final: 0.7589 (m-80) REVERT: N 20 MET cc_start: 0.8619 (mtm) cc_final: 0.8276 (mtm) REVERT: N 148 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: N 180 ASP cc_start: 0.7966 (t0) cc_final: 0.7745 (t0) REVERT: N 217 SER cc_start: 0.8874 (p) cc_final: 0.8243 (p) REVERT: N 248 ASP cc_start: 0.8277 (t0) cc_final: 0.7468 (t0) REVERT: N 285 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8950 (mp) REVERT: N 346 ARG cc_start: 0.8746 (mtp85) cc_final: 0.7956 (mtp85) outliers start: 66 outliers final: 39 residues processed: 506 average time/residue: 0.3780 time to fit residues: 295.1300 Evaluate side-chains 503 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 456 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain S residue 447 GLU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 34 optimal weight: 0.0980 chunk 204 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 282 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 100 ASN I 226 ASN K 115 GLN ** K 121 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 = 0.3885 r_free = 0.3885 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092402 restraints weight = 58990.208| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.28 r_work: 0.3198 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24262 Z= 0.152 Angle : 0.532 8.447 32932 Z= 0.265 Chirality : 0.042 0.236 3616 Planarity : 0.004 0.046 4281 Dihedral : 8.925 178.981 3605 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.86 % Rotamer: Outliers : 2.77 % Allowed : 16.26 % Favored : 80.97 % 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: 0.99 (0.16), residues: 2974 helix: 2.19 (0.15), residues: 1252 sheet: 0.35 (0.22), residues: 537 loop : -0.89 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.003 0.001 HIS N 59 PHE 0.024 0.001 PHE S 395 TYR 0.019 0.001 TYR K 189 ARG 0.007 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 481 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 196 GLU cc_start: 0.8786 (tp30) cc_final: 0.8423 (tt0) REVERT: A 284 GLU cc_start: 0.7185 (mp0) cc_final: 0.6948 (mt-10) REVERT: A 396 ASP cc_start: 0.8325 (m-30) cc_final: 0.7968 (m-30) REVERT: B 170 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: B 203 ASP cc_start: 0.8044 (t0) cc_final: 0.7731 (t0) REVERT: B 288 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: B 291 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7922 (tp-100) REVERT: B 323 MET cc_start: 0.8376 (mmm) cc_final: 0.8072 (mmt) REVERT: E 24 TYR cc_start: 0.8213 (m-80) cc_final: 0.7479 (m-80) REVERT: E 33 ASP cc_start: 0.8752 (t0) cc_final: 0.8495 (t0) REVERT: E 123 ARG cc_start: 0.8777 (ttp-110) cc_final: 0.8186 (ttm-80) REVERT: E 322 ASP cc_start: 0.8787 (t0) cc_final: 0.8390 (t0) REVERT: E 398 MET cc_start: 0.8047 (tpp) cc_final: 0.7736 (tpp) REVERT: I 31 ASP cc_start: 0.8250 (t70) cc_final: 0.7924 (t0) REVERT: I 131 GLN cc_start: 0.8188 (tt0) cc_final: 0.7786 (tp40) REVERT: I 155 ILE cc_start: 0.9013 (mt) cc_final: 0.8767 (mm) REVERT: I 230 SER cc_start: 0.8892 (m) cc_final: 0.8580 (t) REVERT: I 267 MET cc_start: 0.8915 (mtp) cc_final: 0.8692 (mtp) REVERT: I 424 GLN cc_start: 0.8862 (tt0) cc_final: 0.8577 (tt0) REVERT: K 19 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: K 26 CYS cc_start: 0.8878 (p) cc_final: 0.8563 (m) REVERT: K 54 TYR cc_start: 0.8344 (m-80) cc_final: 0.8070 (m-10) REVERT: K 74 TYR cc_start: 0.8576 (t80) cc_final: 0.8085 (t80) REVERT: K 83 GLN cc_start: 0.8772 (tp40) cc_final: 0.8331 (tp-100) REVERT: K 87 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: K 112 GLU cc_start: 0.8197 (mp0) cc_final: 0.7813 (mp0) REVERT: K 124 GLU cc_start: 0.8270 (tp30) cc_final: 0.7858 (tm-30) REVERT: K 147 MET cc_start: 0.8668 (ppp) cc_final: 0.8144 (ppp) REVERT: K 193 GLN cc_start: 0.7877 (tp40) cc_final: 0.7659 (tp40) REVERT: K 266 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8776 (mmmm) REVERT: K 287 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8621 (tp30) REVERT: K 288 MET cc_start: 0.8654 (tmm) cc_final: 0.8331 (ttp) REVERT: K 317 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7856 (tp30) REVERT: K 327 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8025 (tpp) REVERT: S 27 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8231 (mt-10) REVERT: S 120 ASP cc_start: 0.8567 (t0) cc_final: 0.8129 (t0) REVERT: S 121 ARG cc_start: 0.6068 (tpt-90) cc_final: 0.5749 (tpt-90) REVERT: S 203 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: S 251 ASP cc_start: 0.6798 (t0) cc_final: 0.6551 (t0) REVERT: S 259 LEU cc_start: 0.8801 (mp) cc_final: 0.8580 (mp) REVERT: S 279 GLU cc_start: 0.8420 (tp30) cc_final: 0.7931 (tp30) REVERT: S 326 LYS cc_start: 0.8826 (pptt) cc_final: 0.8549 (pttp) REVERT: S 378 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8441 (mm) REVERT: S 392 ASP cc_start: 0.8758 (m-30) cc_final: 0.8485 (m-30) REVERT: S 411 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7836 (mm-30) REVERT: S 413 MET cc_start: 0.8358 (mmm) cc_final: 0.7583 (mmm) REVERT: S 417 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7862 (tt0) REVERT: N 16 ASN cc_start: 0.8517 (p0) cc_final: 0.8275 (p0) REVERT: N 20 MET cc_start: 0.8593 (mtm) cc_final: 0.8222 (mtm) REVERT: N 148 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: N 180 ASP cc_start: 0.8030 (t0) cc_final: 0.7790 (t0) REVERT: N 217 SER cc_start: 0.8885 (p) cc_final: 0.8246 (p) REVERT: N 248 ASP cc_start: 0.8328 (t0) cc_final: 0.7436 (t0) REVERT: N 285 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8985 (mp) REVERT: N 319 LEU cc_start: 0.9185 (mt) cc_final: 0.8951 (mm) REVERT: N 346 ARG cc_start: 0.8734 (mtp85) cc_final: 0.7997 (mtp85) outliers start: 63 outliers final: 40 residues processed: 510 average time/residue: 0.3781 time to fit residues: 298.3466 Evaluate side-chains 503 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 453 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 357 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 378 LEU Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 38 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 282 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 27 optimal weight: 0.0060 chunk 105 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS E 128 GLN I 100 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 HIS N 29 GLN N 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090718 restraints weight = 58064.703| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.26 r_work: 0.3184 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24262 Z= 0.175 Angle : 0.546 8.063 32932 Z= 0.273 Chirality : 0.042 0.232 3616 Planarity : 0.004 0.046 4281 Dihedral : 8.852 179.634 3605 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 2.58 % Allowed : 17.19 % Favored : 80.23 % 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: 1.01 (0.16), residues: 2974 helix: 2.21 (0.15), residues: 1251 sheet: 0.38 (0.22), residues: 539 loop : -0.91 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.003 0.001 HIS N 59 PHE 0.019 0.001 PHE S 395 TYR 0.020 0.001 TYR E 172 ARG 0.013 0.000 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 480 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8276 (t0) cc_final: 0.7924 (t0) REVERT: A 196 GLU cc_start: 0.8796 (tp30) cc_final: 0.8441 (tt0) REVERT: A 215 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7981 (ttp-110) REVERT: A 284 GLU cc_start: 0.7169 (mp0) cc_final: 0.6773 (mt-10) REVERT: A 396 ASP cc_start: 0.8361 (m-30) cc_final: 0.8002 (m-30) REVERT: B 74 ASP cc_start: 0.8610 (m-30) cc_final: 0.8259 (m-30) REVERT: B 170 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: B 203 ASP cc_start: 0.8060 (t0) cc_final: 0.7757 (t0) REVERT: B 288 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: B 291 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7899 (tp-100) REVERT: B 293 MET cc_start: 0.8993 (ttm) cc_final: 0.8758 (mtp) REVERT: B 323 MET cc_start: 0.8415 (mmm) cc_final: 0.8108 (mmt) REVERT: E 24 TYR cc_start: 0.8297 (m-80) cc_final: 0.7378 (m-80) REVERT: E 123 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8184 (ttm-80) REVERT: E 276 ILE cc_start: 0.9223 (tt) cc_final: 0.8982 (tt) REVERT: E 322 ASP cc_start: 0.8798 (t0) cc_final: 0.8405 (t0) REVERT: I 31 ASP cc_start: 0.8259 (t70) cc_final: 0.7926 (t0) REVERT: I 131 GLN cc_start: 0.8180 (tt0) cc_final: 0.7615 (tp40) REVERT: I 155 ILE cc_start: 0.9000 (mt) cc_final: 0.8787 (mm) REVERT: I 164 MET cc_start: 0.8569 (tpp) cc_final: 0.8292 (tpt) REVERT: I 230 SER cc_start: 0.8887 (m) cc_final: 0.8588 (t) REVERT: I 267 MET cc_start: 0.8922 (mtp) cc_final: 0.8698 (mtp) REVERT: I 424 GLN cc_start: 0.8869 (tt0) cc_final: 0.8563 (tt0) REVERT: K 19 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: K 26 CYS cc_start: 0.8931 (p) cc_final: 0.8564 (m) REVERT: K 74 TYR cc_start: 0.8517 (t80) cc_final: 0.8170 (t80) REVERT: K 83 GLN cc_start: 0.8770 (tp40) cc_final: 0.8326 (tp-100) REVERT: K 87 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: K 124 GLU cc_start: 0.8289 (tp30) cc_final: 0.7933 (tm-30) REVERT: K 147 MET cc_start: 0.8667 (ppp) cc_final: 0.8118 (ppp) REVERT: K 266 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8780 (mmmm) REVERT: K 287 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8524 (tp30) REVERT: K 288 MET cc_start: 0.8721 (tmm) cc_final: 0.8460 (ttp) REVERT: K 317 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7884 (tp30) REVERT: K 327 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8025 (tpp) REVERT: K 340 GLU cc_start: 0.8241 (mp0) cc_final: 0.7880 (mp0) REVERT: S 27 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8244 (mt-10) REVERT: S 69 ASP cc_start: 0.7895 (t0) cc_final: 0.7342 (t0) REVERT: S 98 ASP cc_start: 0.8226 (p0) cc_final: 0.7753 (t0) REVERT: S 251 ASP cc_start: 0.6976 (t0) cc_final: 0.6635 (t0) REVERT: S 259 LEU cc_start: 0.8842 (mp) cc_final: 0.8637 (mp) REVERT: S 279 GLU cc_start: 0.8451 (tp30) cc_final: 0.7953 (tp30) REVERT: S 326 LYS cc_start: 0.8859 (pptt) cc_final: 0.8589 (pttp) REVERT: S 390 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7794 (mtp180) REVERT: S 392 ASP cc_start: 0.8754 (m-30) cc_final: 0.8455 (m-30) REVERT: S 411 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7872 (mm-30) REVERT: S 413 MET cc_start: 0.8404 (mmm) cc_final: 0.7855 (mmm) REVERT: S 417 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7941 (tt0) REVERT: N 20 MET cc_start: 0.8613 (mtm) cc_final: 0.8238 (mtm) REVERT: N 72 GLN cc_start: 0.7206 (tp40) cc_final: 0.6932 (tp40) REVERT: N 148 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: N 152 GLU cc_start: 0.8826 (mp0) cc_final: 0.8347 (mp0) REVERT: N 180 ASP cc_start: 0.8027 (t0) cc_final: 0.7773 (t0) REVERT: N 217 SER cc_start: 0.8882 (p) cc_final: 0.8257 (p) REVERT: N 248 ASP cc_start: 0.8298 (t0) cc_final: 0.7399 (t0) REVERT: N 285 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8966 (mp) REVERT: N 319 LEU cc_start: 0.9175 (mt) cc_final: 0.8943 (mm) REVERT: N 346 ARG cc_start: 0.8725 (mtp85) cc_final: 0.7986 (mtp85) outliers start: 58 outliers final: 38 residues processed: 506 average time/residue: 0.3741 time to fit residues: 295.6815 Evaluate side-chains 507 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 0.2980 chunk 201 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS E 128 GLN I 100 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN S 101 ASN S 176 GLN S 216 ASN S 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089402 restraints weight = 60232.100| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.25 r_work: 0.3158 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24262 Z= 0.226 Angle : 0.574 11.082 32932 Z= 0.287 Chirality : 0.044 0.237 3616 Planarity : 0.004 0.046 4281 Dihedral : 8.844 179.255 3601 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 2.62 % Allowed : 17.31 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2974 helix: 2.22 (0.15), residues: 1244 sheet: 0.34 (0.22), residues: 543 loop : -0.89 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.022 0.001 PHE K 52 TYR 0.027 0.001 TYR K 189 ARG 0.010 0.000 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 480 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8339 (t0) cc_final: 0.8006 (t0) REVERT: A 154 MET cc_start: 0.8873 (mmm) cc_final: 0.8539 (mmm) REVERT: A 196 GLU cc_start: 0.8833 (tp30) cc_final: 0.8487 (tt0) REVERT: A 215 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.8023 (ttp-110) REVERT: A 254 GLU cc_start: 0.4367 (mm-30) cc_final: 0.2603 (mm-30) REVERT: A 284 GLU cc_start: 0.7152 (mp0) cc_final: 0.6805 (mt-10) REVERT: A 388 TRP cc_start: 0.9011 (m-10) cc_final: 0.8320 (m-10) REVERT: B 170 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: B 203 ASP cc_start: 0.8106 (t0) cc_final: 0.7842 (t0) REVERT: B 288 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: B 291 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7966 (tp-100) REVERT: B 293 MET cc_start: 0.9044 (ttm) cc_final: 0.8809 (mtp) REVERT: B 323 MET cc_start: 0.8482 (mmm) cc_final: 0.8160 (mmt) REVERT: E 24 TYR cc_start: 0.8321 (m-80) cc_final: 0.7406 (m-80) REVERT: E 123 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8249 (ttm-80) REVERT: E 276 ILE cc_start: 0.9242 (tt) cc_final: 0.8976 (tt) REVERT: E 339 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8598 (ttm-80) REVERT: I 31 ASP cc_start: 0.8306 (t70) cc_final: 0.7980 (t0) REVERT: I 131 GLN cc_start: 0.8209 (tt0) cc_final: 0.7624 (tp40) REVERT: I 147 MET cc_start: 0.8751 (mtp) cc_final: 0.8518 (mtp) REVERT: I 155 ILE cc_start: 0.9020 (mt) cc_final: 0.8757 (mm) REVERT: I 194 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7922 (tm-30) REVERT: I 230 SER cc_start: 0.8910 (m) cc_final: 0.8623 (t) REVERT: I 267 MET cc_start: 0.8913 (mtp) cc_final: 0.8712 (mtp) REVERT: I 424 GLN cc_start: 0.8886 (tt0) cc_final: 0.8577 (tt0) REVERT: K 19 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: K 26 CYS cc_start: 0.8975 (p) cc_final: 0.8559 (m) REVERT: K 54 TYR cc_start: 0.8378 (m-80) cc_final: 0.8175 (m-10) REVERT: K 74 TYR cc_start: 0.8568 (t80) cc_final: 0.8193 (t80) REVERT: K 124 GLU cc_start: 0.8319 (tp30) cc_final: 0.8019 (tm-30) REVERT: K 266 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8781 (mmmm) REVERT: K 287 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8560 (tp30) REVERT: K 288 MET cc_start: 0.8725 (tmm) cc_final: 0.8494 (ttp) REVERT: K 317 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7912 (tp30) REVERT: K 327 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8025 (tpp) REVERT: S 27 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8266 (mt-10) REVERT: S 69 ASP cc_start: 0.7923 (t0) cc_final: 0.7520 (t0) REVERT: S 154 MET cc_start: 0.9073 (mmm) cc_final: 0.8829 (mmm) REVERT: S 220 GLU cc_start: 0.8836 (tp30) cc_final: 0.8527 (mm-30) REVERT: S 251 ASP cc_start: 0.7169 (t0) cc_final: 0.6871 (t0) REVERT: S 259 LEU cc_start: 0.8838 (mp) cc_final: 0.8628 (mp) REVERT: S 279 GLU cc_start: 0.8571 (tp30) cc_final: 0.8096 (tp30) REVERT: S 326 LYS cc_start: 0.8880 (pptt) cc_final: 0.8619 (pttp) REVERT: S 392 ASP cc_start: 0.8737 (m-30) cc_final: 0.8446 (m-30) REVERT: S 411 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7814 (mm-30) REVERT: S 413 MET cc_start: 0.8440 (mmm) cc_final: 0.7908 (mmm) REVERT: S 417 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7963 (tt0) REVERT: N 20 MET cc_start: 0.8587 (mtm) cc_final: 0.8210 (mtm) REVERT: N 72 GLN cc_start: 0.7326 (tp40) cc_final: 0.7026 (tp40) REVERT: N 112 GLU cc_start: 0.8292 (pm20) cc_final: 0.7902 (pm20) REVERT: N 115 GLN cc_start: 0.7906 (pm20) cc_final: 0.6502 (pm20) REVERT: N 148 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: N 152 GLU cc_start: 0.8842 (mp0) cc_final: 0.8450 (mp0) REVERT: N 180 ASP cc_start: 0.8027 (t0) cc_final: 0.7771 (t0) REVERT: N 217 SER cc_start: 0.8875 (p) cc_final: 0.8219 (p) REVERT: N 248 ASP cc_start: 0.8325 (t0) cc_final: 0.7482 (t0) REVERT: N 285 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (mp) REVERT: N 319 LEU cc_start: 0.9192 (mt) cc_final: 0.8966 (mm) REVERT: N 346 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8058 (mtp85) outliers start: 59 outliers final: 47 residues processed: 507 average time/residue: 0.3694 time to fit residues: 291.3543 Evaluate side-chains 510 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 457 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 176 GLN Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 93 optimal weight: 0.4980 chunk 261 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS I 100 ASN K 83 GLN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN S 176 GLN S 216 ASN S 226 ASN N 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.118845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091909 restraints weight = 43421.590| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.70 r_work: 0.3244 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24262 Z= 0.162 Angle : 0.567 10.999 32932 Z= 0.283 Chirality : 0.042 0.221 3616 Planarity : 0.004 0.046 4281 Dihedral : 8.714 178.974 3601 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 2.19 % Allowed : 17.82 % Favored : 79.99 % 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: 2974 helix: 2.21 (0.15), residues: 1246 sheet: 0.40 (0.22), residues: 534 loop : -0.90 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.017 0.001 PHE S 395 TYR 0.027 0.001 TYR K 189 ARG 0.009 0.000 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 476 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8289 (t0) cc_final: 0.7912 (t0) REVERT: A 196 GLU cc_start: 0.8749 (tp30) cc_final: 0.8398 (tt0) REVERT: A 254 GLU cc_start: 0.4223 (mm-30) cc_final: 0.2521 (mm-30) REVERT: A 284 GLU cc_start: 0.7067 (mp0) cc_final: 0.6719 (mt-10) REVERT: A 388 TRP cc_start: 0.8995 (m-10) cc_final: 0.8354 (m-10) REVERT: A 396 ASP cc_start: 0.8257 (m-30) cc_final: 0.7922 (m-30) REVERT: B 74 ASP cc_start: 0.8496 (m-30) cc_final: 0.7697 (m-30) REVERT: B 170 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: B 203 ASP cc_start: 0.7953 (t0) cc_final: 0.7729 (t0) REVERT: B 288 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 291 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7861 (tp-100) REVERT: B 293 MET cc_start: 0.8984 (ttm) cc_final: 0.8759 (mtp) REVERT: B 323 MET cc_start: 0.8370 (mmm) cc_final: 0.8062 (mmt) REVERT: E 24 TYR cc_start: 0.8284 (m-80) cc_final: 0.7197 (m-80) REVERT: E 123 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8178 (ttm-80) REVERT: E 239 THR cc_start: 0.8880 (m) cc_final: 0.8566 (t) REVERT: E 276 ILE cc_start: 0.9224 (tt) cc_final: 0.8965 (tt) REVERT: E 322 ASP cc_start: 0.8744 (t0) cc_final: 0.8345 (t0) REVERT: E 339 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8499 (ttm-80) REVERT: I 31 ASP cc_start: 0.8235 (t70) cc_final: 0.7919 (t0) REVERT: I 131 GLN cc_start: 0.8101 (tt0) cc_final: 0.7464 (tp40) REVERT: I 147 MET cc_start: 0.8631 (mtp) cc_final: 0.8393 (mtp) REVERT: I 155 ILE cc_start: 0.8984 (mt) cc_final: 0.8755 (mm) REVERT: I 164 MET cc_start: 0.8494 (tpp) cc_final: 0.8210 (tpt) REVERT: I 194 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7828 (tm-30) REVERT: I 230 SER cc_start: 0.8841 (m) cc_final: 0.8555 (t) REVERT: I 267 MET cc_start: 0.8839 (mtp) cc_final: 0.8625 (mtp) REVERT: I 424 GLN cc_start: 0.8846 (tt0) cc_final: 0.8513 (tt0) REVERT: K 26 CYS cc_start: 0.8949 (p) cc_final: 0.8546 (m) REVERT: K 74 TYR cc_start: 0.8540 (t80) cc_final: 0.8162 (t80) REVERT: K 112 GLU cc_start: 0.8346 (mp0) cc_final: 0.8040 (mp0) REVERT: K 124 GLU cc_start: 0.8280 (tp30) cc_final: 0.8047 (tm-30) REVERT: K 147 MET cc_start: 0.8699 (ppp) cc_final: 0.8142 (ppp) REVERT: K 266 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8740 (mmmm) REVERT: K 287 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8478 (tp30) REVERT: K 288 MET cc_start: 0.8718 (tmm) cc_final: 0.8467 (ttp) REVERT: K 317 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7851 (tp30) REVERT: K 327 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7983 (tpp) REVERT: K 339 ASP cc_start: 0.7378 (p0) cc_final: 0.6645 (p0) REVERT: K 340 GLU cc_start: 0.8233 (mp0) cc_final: 0.7978 (mp0) REVERT: S 27 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8177 (mt-10) REVERT: S 98 ASP cc_start: 0.7911 (p0) cc_final: 0.7695 (t0) REVERT: S 154 MET cc_start: 0.9042 (mmm) cc_final: 0.8797 (mmm) REVERT: S 220 GLU cc_start: 0.8798 (tp30) cc_final: 0.8544 (mm-30) REVERT: S 259 LEU cc_start: 0.8791 (mp) cc_final: 0.8570 (mp) REVERT: S 279 GLU cc_start: 0.8517 (tp30) cc_final: 0.8113 (tp30) REVERT: S 326 LYS cc_start: 0.8795 (pptt) cc_final: 0.8521 (pttp) REVERT: S 392 ASP cc_start: 0.8692 (m-30) cc_final: 0.8388 (m-30) REVERT: S 411 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7755 (mm-30) REVERT: S 413 MET cc_start: 0.8325 (mmm) cc_final: 0.7853 (mmm) REVERT: S 417 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7918 (tt0) REVERT: N 16 ASN cc_start: 0.8605 (p0) cc_final: 0.8404 (p0) REVERT: N 20 MET cc_start: 0.8550 (mtm) cc_final: 0.8171 (mtm) REVERT: N 148 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: N 152 GLU cc_start: 0.8772 (mp0) cc_final: 0.8373 (mp0) REVERT: N 180 ASP cc_start: 0.7960 (t0) cc_final: 0.7679 (t0) REVERT: N 217 SER cc_start: 0.8838 (p) cc_final: 0.8125 (p) REVERT: N 248 ASP cc_start: 0.8270 (t0) cc_final: 0.7399 (t0) REVERT: N 285 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8955 (mp) REVERT: N 319 LEU cc_start: 0.9160 (mt) cc_final: 0.8940 (mm) REVERT: N 346 ARG cc_start: 0.8597 (mtp85) cc_final: 0.7995 (mtp85) outliers start: 48 outliers final: 39 residues processed: 499 average time/residue: 0.3609 time to fit residues: 279.7342 Evaluate side-chains 498 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 454 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 176 GLN Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 108 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 47 optimal weight: 0.0070 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 ASN S 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.119152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092396 restraints weight = 42255.906| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.63 r_work: 0.3224 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 24262 Z= 0.287 Angle : 0.747 59.189 32932 Z= 0.418 Chirality : 0.044 0.373 3616 Planarity : 0.005 0.156 4281 Dihedral : 8.713 178.987 3601 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 2.19 % Allowed : 18.09 % Favored : 79.72 % Cbeta Deviations : 0.04 % 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: 0.98 (0.16), residues: 2974 helix: 2.18 (0.15), residues: 1247 sheet: 0.39 (0.22), residues: 537 loop : -0.90 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.016 0.001 PHE S 395 TYR 0.064 0.001 TYR B 425 ARG 0.008 0.000 ARG I 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 463 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8275 (t0) cc_final: 0.7899 (t0) REVERT: A 196 GLU cc_start: 0.8738 (tp30) cc_final: 0.8391 (tt0) REVERT: A 254 GLU cc_start: 0.4245 (mm-30) cc_final: 0.2551 (mm-30) REVERT: A 284 GLU cc_start: 0.7072 (mp0) cc_final: 0.6723 (mt-10) REVERT: A 388 TRP cc_start: 0.8997 (m-10) cc_final: 0.8333 (m-10) REVERT: A 396 ASP cc_start: 0.8244 (m-30) cc_final: 0.7898 (m-30) REVERT: A 432 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.6836 (t80) REVERT: B 170 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: B 203 ASP cc_start: 0.7953 (t0) cc_final: 0.7735 (t0) REVERT: B 288 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: B 291 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7870 (tp-100) REVERT: B 293 MET cc_start: 0.8987 (ttm) cc_final: 0.8764 (mtp) REVERT: B 323 MET cc_start: 0.8371 (mmm) cc_final: 0.8063 (mmt) REVERT: B 424 GLN cc_start: 0.8599 (tt0) cc_final: 0.8309 (tt0) REVERT: E 24 TYR cc_start: 0.8278 (m-80) cc_final: 0.7199 (m-80) REVERT: E 123 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8192 (ttm-80) REVERT: E 239 THR cc_start: 0.8879 (m) cc_final: 0.8574 (t) REVERT: E 276 ILE cc_start: 0.9228 (tt) cc_final: 0.8969 (tt) REVERT: E 322 ASP cc_start: 0.8746 (t0) cc_final: 0.8347 (t0) REVERT: E 339 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8502 (ttm-80) REVERT: I 31 ASP cc_start: 0.8230 (t70) cc_final: 0.7918 (t0) REVERT: I 100 ASN cc_start: 0.8982 (m-40) cc_final: 0.8781 (m-40) REVERT: I 131 GLN cc_start: 0.8085 (tt0) cc_final: 0.7457 (tp40) REVERT: I 147 MET cc_start: 0.8611 (mtp) cc_final: 0.8375 (mtp) REVERT: I 155 ILE cc_start: 0.8987 (mt) cc_final: 0.8739 (mm) REVERT: I 164 MET cc_start: 0.8492 (tpp) cc_final: 0.8211 (tpt) REVERT: I 194 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7824 (tm-30) REVERT: I 230 SER cc_start: 0.8839 (m) cc_final: 0.8553 (t) REVERT: I 267 MET cc_start: 0.8826 (mtp) cc_final: 0.8613 (mtp) REVERT: I 424 GLN cc_start: 0.8836 (tt0) cc_final: 0.8506 (tt0) REVERT: K 26 CYS cc_start: 0.8929 (p) cc_final: 0.8539 (m) REVERT: K 74 TYR cc_start: 0.8537 (t80) cc_final: 0.8166 (t80) REVERT: K 112 GLU cc_start: 0.8336 (mp0) cc_final: 0.8033 (mp0) REVERT: K 124 GLU cc_start: 0.8285 (tp30) cc_final: 0.8050 (tm-30) REVERT: K 147 MET cc_start: 0.8703 (ppp) cc_final: 0.8155 (ppp) REVERT: K 266 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8745 (mmmm) REVERT: K 287 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8489 (tp30) REVERT: K 288 MET cc_start: 0.8713 (tmm) cc_final: 0.8465 (ttp) REVERT: K 317 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7856 (tp30) REVERT: K 327 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7969 (tpp) REVERT: S 27 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8196 (mt-10) REVERT: S 69 ASP cc_start: 0.7804 (t0) cc_final: 0.7413 (t0) REVERT: S 98 ASP cc_start: 0.7905 (p0) cc_final: 0.7702 (t0) REVERT: S 154 MET cc_start: 0.9032 (mmm) cc_final: 0.8788 (mmm) REVERT: S 220 GLU cc_start: 0.8791 (tp30) cc_final: 0.8538 (mm-30) REVERT: S 259 LEU cc_start: 0.8796 (mp) cc_final: 0.8576 (mp) REVERT: S 279 GLU cc_start: 0.8527 (tp30) cc_final: 0.8117 (tp30) REVERT: S 326 LYS cc_start: 0.8800 (pptt) cc_final: 0.8530 (pttp) REVERT: S 392 ASP cc_start: 0.8678 (m-30) cc_final: 0.8377 (m-30) REVERT: S 411 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7754 (mm-30) REVERT: S 413 MET cc_start: 0.8321 (mmm) cc_final: 0.7851 (mmm) REVERT: S 417 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7914 (tt0) REVERT: N 20 MET cc_start: 0.8551 (mtm) cc_final: 0.8171 (mtm) REVERT: N 148 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: N 152 GLU cc_start: 0.8786 (mp0) cc_final: 0.8370 (mp0) REVERT: N 180 ASP cc_start: 0.7952 (t0) cc_final: 0.7674 (t0) REVERT: N 217 SER cc_start: 0.8832 (p) cc_final: 0.8137 (p) REVERT: N 248 ASP cc_start: 0.8263 (t0) cc_final: 0.7426 (t70) REVERT: N 285 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8958 (mp) REVERT: N 288 MET cc_start: 0.8553 (tpp) cc_final: 0.8030 (tpt) REVERT: N 319 LEU cc_start: 0.9169 (mt) cc_final: 0.8950 (mm) REVERT: N 346 ARG cc_start: 0.8579 (mtp85) cc_final: 0.7983 (mtp85) outliers start: 48 outliers final: 39 residues processed: 487 average time/residue: 0.3667 time to fit residues: 277.4565 Evaluate side-chains 498 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 453 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain I residue 282 ARG Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 191 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 241 optimal weight: 0.0870 chunk 230 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 275 optimal weight: 4.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.118894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091567 restraints weight = 49730.040| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.92 r_work: 0.3203 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 24262 Z= 0.287 Angle : 0.747 59.189 32932 Z= 0.418 Chirality : 0.044 0.373 3616 Planarity : 0.005 0.156 4281 Dihedral : 8.713 178.987 3601 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 2.07 % Allowed : 18.21 % Favored : 79.72 % Cbeta Deviations : 0.04 % 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: 0.98 (0.16), residues: 2974 helix: 2.18 (0.15), residues: 1247 sheet: 0.39 (0.22), residues: 537 loop : -0.90 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.004 0.001 HIS N 59 PHE 0.016 0.001 PHE S 395 TYR 0.064 0.001 TYR B 425 ARG 0.008 0.000 ARG I 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12732.85 seconds wall clock time: 227 minutes 41.03 seconds (13661.03 seconds total)