Starting phenix.real_space_refine on Sat Jan 25 19:14:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utp_42545/01_2025/8utp_42545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utp_42545/01_2025/8utp_42545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8utp_42545/01_2025/8utp_42545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utp_42545/01_2025/8utp_42545.map" model { file = "/net/cci-nas-00/data/ceres_data/8utp_42545/01_2025/8utp_42545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utp_42545/01_2025/8utp_42545.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 4 5.21 5 S 153 5.16 5 C 14863 2.51 5 N 4070 2.21 5 O 4683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23792 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3038 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain: "N" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3055 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 13, 'TRANS': 375} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "I" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Conformer: "B" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} bond proxies already assigned to first conformer: 3444 Chain: "S" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.49 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.51 residue: pdb=" N AALA B 430 " occ=0.49 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.51 residue: pdb=" N AASP B 431 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.51 residue: pdb=" N AGLU B 432 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.51 residue: pdb=" N ATHR I 429 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.46 residue: pdb=" N AALA I 430 " occ=0.54 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.46 residue: pdb=" N AASP I 431 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.46 residue: pdb=" N AGLU I 432 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.46 residue: pdb=" N AGLN I 433 " occ=0.54 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.46 Time building chain proxies: 18.40, per 1000 atoms: 0.77 Number of scatterers: 23792 At special positions: 0 Unit cell: (81.024, 114.784, 238.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 153 16.00 P 19 15.00 Mg 4 11.99 O 4683 8.00 N 4070 7.00 C 14863 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: 5.91 Conformation dependent library (CDL) restraints added in 3.7 seconds 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 24 sheets defined 49.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 88 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.659A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP K 132 " --> pdb=" O SER K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.669A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.825A pdb=" N ASP K 308 " --> pdb=" O PRO K 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 337 through 353 removed outlier: 3.772A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 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 108 removed outlier: 3.669A pdb=" N THR N 106 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 133 removed outlier: 3.536A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.614A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 296 Proline residue: N 292 - end of helix Processing helix chain 'N' and resid 305 through 308 removed outlier: 3.806A pdb=" N ASP N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 337 through 350 removed outlier: 3.786A pdb=" N ARG N 350 " --> pdb=" O ARG N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 386 removed outlier: 3.530A pdb=" N GLN N 386 " --> pdb=" O LEU N 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.119A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.575A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 113 through 128 removed outlier: 4.319A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.054A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.599A 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 205 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.772A 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 removed outlier: 3.671A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.905A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.880A 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 removed outlier: 3.549A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.850A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.985A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.209A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.803A pdb=" N GLU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.273A 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: 3.762A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.895A 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 193 removed outlier: 3.604A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.763A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.639A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) 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: 3.946A 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 373 through 390 removed outlier: 4.245A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.205A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.831A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 4.026A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.734A 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: 3.508A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 3.508A pdb=" N SER E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.720A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.785A 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: 3.615A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.008A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.715A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.532A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.852A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.139A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.814A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.715A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 126 removed outlier: 3.693A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.657A 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 193 removed outlier: 3.597A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.564A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.612A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 3.973A 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: 4.277A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 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: 3.612A 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 373 through 390 removed outlier: 4.262A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 424 removed outlier: 4.134A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR I 409 " --> pdb=" O GLU I 405 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 4.128A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.343A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 3.746A 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 removed outlier: 3.506A pdb=" N GLN S 128 " --> pdb=" O LYS S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.170A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 198 removed outlier: 4.482A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER S 198 " --> pdb=" O THR S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.831A 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: 3.811A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 266 removed outlier: 4.123A pdb=" N HIS S 266 " --> pdb=" O PRO S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.092A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.676A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU S 297 " --> pdb=" O ASN S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 301 Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 337 removed outlier: 3.703A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR S 337 " --> pdb=" O ALA S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 3.990A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 4.412A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.284A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.513A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.513A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 208 removed outlier: 5.554A pdb=" N ALA K 206 " --> pdb=" O THR K 213 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR K 213 " --> pdb=" O ALA K 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 56 removed outlier: 8.245A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 54 through 56 removed outlier: 8.245A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'N' and resid 205 through 206 removed outlier: 3.574A pdb=" N ALA N 206 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.496A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.241A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.716A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.120A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'I' and resid 90 through 92 removed outlier: 6.023A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 90 through 92 removed outlier: 6.023A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC4, first strand: chain 'S' and resid 65 through 68 removed outlier: 8.448A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU S 3 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY S 134 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER S 140 " --> pdb=" O VAL S 9 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N HIS S 139 " --> pdb=" O ILE S 171 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'S' and resid 269 through 272 1185 hydrogen bonds defined for protein. 3390 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: 9.10 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4079 1.32 - 1.44: 6441 1.44 - 1.57: 13490 1.57 - 1.70: 38 1.70 - 1.82: 244 Bond restraints: 24292 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CA SER E 277 " pdb=" CB SER E 277 " ideal model delta sigma weight residual 1.529 1.462 0.068 1.64e-02 3.72e+03 1.70e+01 ... (remaining 24287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 32628 3.61 - 7.23: 325 7.23 - 10.84: 12 10.84 - 14.45: 7 14.45 - 18.07: 2 Bond angle restraints: 32974 Sorted by residual: angle pdb=" O ALA B 271 " pdb=" C ALA B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 121.85 116.80 5.05 7.00e-01 2.04e+00 5.20e+01 angle pdb=" O ALA I 271 " pdb=" C ALA I 271 " pdb=" N PRO I 272 " ideal model delta sigma weight residual 121.85 117.47 4.38 7.00e-01 2.04e+00 3.91e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 108.88 18.07 3.00e+00 1.11e-01 3.63e+01 angle pdb=" PB ANP N 501 " pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 126.95 111.67 15.28 3.00e+00 1.11e-01 2.59e+01 angle pdb=" CA ALA B 271 " pdb=" C ALA B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 118.16 123.49 -5.33 1.08e+00 8.57e-01 2.44e+01 ... (remaining 32969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 14012 30.40 - 60.80: 634 60.80 - 91.20: 73 91.20 - 121.60: 20 121.60 - 152.00: 25 Dihedral angle restraints: 14764 sinusoidal: 6106 harmonic: 8658 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -47.40 152.00 1 2.00e+01 2.50e-03 4.52e+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 -144.61 -146.12 1 2.00e+01 2.50e-03 4.39e+01 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 260.87 123.02 137.86 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 14761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3422 0.106 - 0.211: 185 0.211 - 0.317: 8 0.317 - 0.423: 0 0.423 - 0.528: 2 Chirality restraints: 3617 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.63 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" C18 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" C17 TA1 I 502 " pdb=" C20 TA1 I 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.63 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" C02 TA1 I 502 " pdb=" C01 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" O02 TA1 I 502 " both_signs ideal model delta sigma weight residual False 2.56 2.83 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3614 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 I 502 " 0.073 2.00e-02 2.50e+03 6.03e-02 4.54e+01 pdb=" C30 TA1 I 502 " -0.020 2.00e-02 2.50e+03 pdb=" C31 TA1 I 502 " 0.056 2.00e-02 2.50e+03 pdb=" N01 TA1 I 502 " -0.095 2.00e-02 2.50e+03 pdb=" O14 TA1 I 502 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY N 291 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO N 292 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO N 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 292 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO K 292 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.048 5.00e-02 4.00e+02 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 123 2.52 - 3.12: 17570 3.12 - 3.71: 35523 3.71 - 4.31: 49619 4.31 - 4.90: 85633 Nonbonded interactions: 188468 Sorted by model distance: nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.930 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.939 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.939 2.170 nonbonded pdb=" OE2 GLU E 71 " pdb="MG MG E 502 " model vdw 1.945 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 1.945 2.170 ... (remaining 188463 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 58.110 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.005 0.146 24292 Z= 0.340 Angle : 0.849 18.068 32974 Z= 0.459 Chirality : 0.050 0.528 3617 Planarity : 0.006 0.104 4288 Dihedral : 18.534 151.997 9210 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.21 % Favored : 95.35 % Rotamer: Outliers : 0.94 % Allowed : 14.36 % Favored : 84.70 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.59 % 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: -0.04 (0.15), residues: 2977 helix: 1.17 (0.15), residues: 1229 sheet: -0.14 (0.22), residues: 542 loop : -1.19 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS I 137 PHE 0.026 0.002 PHE S 255 TYR 0.040 0.001 TYR S 24 ARG 0.015 0.001 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 529 time to evaluate : 2.644 Fit side-chains revert: symmetry clash REVERT: K 127 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7942 (t80) REVERT: K 153 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8196 (mtp85) REVERT: K 367 LYS cc_start: 0.8990 (tptt) cc_final: 0.8575 (tptt) REVERT: N 94 PHE cc_start: 0.8294 (m-80) cc_final: 0.7942 (m-80) REVERT: N 98 GLN cc_start: 0.5933 (mt0) cc_final: 0.5716 (mt0) REVERT: A 24 TYR cc_start: 0.8560 (m-80) cc_final: 0.8137 (m-80) REVERT: A 254 GLU cc_start: 0.5547 (mm-30) cc_final: 0.5191 (mm-30) REVERT: B 1 MET cc_start: 0.6184 (tmm) cc_final: 0.4857 (tmm) REVERT: B 48 ASN cc_start: 0.8508 (m-40) cc_final: 0.8068 (p0) REVERT: B 147 MET cc_start: 0.8346 (mtp) cc_final: 0.8121 (mtp) REVERT: B 168 SER cc_start: 0.8876 (p) cc_final: 0.8538 (m) REVERT: B 282 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8507 (mtp85) REVERT: S 398 MET cc_start: 0.8378 (mtp) cc_final: 0.8054 (mtp) outliers start: 18 outliers final: 8 residues processed: 536 average time/residue: 0.3661 time to fit residues: 303.5769 Evaluate side-chains 506 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 497 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain N residue 333 PRO Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 424 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 268 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 70 GLN N 16 ASN B 48 ASN B 204 ASN E 197 HIS E 358 GLN I 375 GLN I 426 GLN I 433 GLN A S 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.094034 restraints weight = 52654.836| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.06 r_work: 0.3171 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24292 Z= 0.186 Angle : 0.576 11.222 32974 Z= 0.286 Chirality : 0.044 0.295 3617 Planarity : 0.005 0.094 4288 Dihedral : 12.733 149.135 3621 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 1.56 % Allowed : 14.75 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2977 helix: 1.78 (0.15), residues: 1241 sheet: 0.27 (0.22), residues: 527 loop : -1.03 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS S 266 PHE 0.016 0.001 PHE K 94 TYR 0.049 0.001 TYR S 24 ARG 0.006 0.001 ARG I 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 517 time to evaluate : 2.616 Fit side-chains revert: symmetry clash REVERT: K 74 TYR cc_start: 0.8084 (t80) cc_final: 0.7786 (t80) REVERT: K 86 PHE cc_start: 0.8343 (m-80) cc_final: 0.8057 (m-10) REVERT: K 125 ASP cc_start: 0.7997 (t0) cc_final: 0.7041 (t0) REVERT: K 153 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8086 (mtp85) REVERT: K 367 LYS cc_start: 0.8726 (tptt) cc_final: 0.8425 (tppt) REVERT: N 98 GLN cc_start: 0.6061 (mt0) cc_final: 0.5777 (mt0) REVERT: N 288 MET cc_start: 0.8202 (tmm) cc_final: 0.7858 (tpp) REVERT: N 345 LEU cc_start: 0.9167 (mp) cc_final: 0.8902 (mm) REVERT: A 147 SER cc_start: 0.8080 (t) cc_final: 0.7810 (m) REVERT: A 254 GLU cc_start: 0.5372 (mm-30) cc_final: 0.4616 (mm-30) REVERT: B 1 MET cc_start: 0.6176 (tmm) cc_final: 0.5291 (tmm) REVERT: B 3 GLU cc_start: 0.8147 (mp0) cc_final: 0.7667 (mp0) REVERT: B 48 ASN cc_start: 0.8476 (m110) cc_final: 0.8170 (p0) REVERT: B 279 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: B 423 GLN cc_start: 0.7981 (mt0) cc_final: 0.7666 (tm-30) REVERT: E 260 VAL cc_start: 0.8732 (t) cc_final: 0.8261 (m) REVERT: I 31 ASP cc_start: 0.8064 (t0) cc_final: 0.7702 (t0) REVERT: I 299 MET cc_start: 0.8672 (mmp) cc_final: 0.8273 (mmt) REVERT: S 35 GLN cc_start: 0.7310 (mp10) cc_final: 0.7100 (mp10) REVERT: S 102 ASN cc_start: 0.8336 (t0) cc_final: 0.8015 (t0) REVERT: S 394 LYS cc_start: 0.7676 (mttt) cc_final: 0.7003 (tptt) REVERT: S 398 MET cc_start: 0.8292 (mtp) cc_final: 0.7963 (mtp) outliers start: 34 outliers final: 22 residues processed: 527 average time/residue: 0.3686 time to fit residues: 303.5507 Evaluate side-chains 500 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 477 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 397 LEU Chi-restraints excluded: chain S residue 413 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 193 optimal weight: 0.0040 chunk 69 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 GLN A 301 GLN B 165 ASN E 107 HIS E 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.121502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094681 restraints weight = 40084.795| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.68 r_work: 0.3208 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24292 Z= 0.166 Angle : 0.536 9.610 32974 Z= 0.265 Chirality : 0.044 0.476 3617 Planarity : 0.004 0.088 4288 Dihedral : 10.042 145.225 3606 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 1.83 % Allowed : 15.34 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.86 (0.16), residues: 2977 helix: 2.02 (0.15), residues: 1239 sheet: 0.42 (0.22), residues: 530 loop : -0.91 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 139 PHE 0.030 0.001 PHE K 94 TYR 0.048 0.001 TYR S 24 ARG 0.006 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 522 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 ASP cc_start: 0.7478 (t0) cc_final: 0.6936 (t0) REVERT: K 153 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8103 (mtp85) REVERT: K 367 LYS cc_start: 0.8668 (tptt) cc_final: 0.8371 (tppt) REVERT: N 98 GLN cc_start: 0.6086 (mt0) cc_final: 0.5703 (mt0) REVERT: N 288 MET cc_start: 0.8071 (tmm) cc_final: 0.7800 (tpp) REVERT: N 310 VAL cc_start: 0.9049 (m) cc_final: 0.8810 (p) REVERT: N 319 LEU cc_start: 0.8736 (mm) cc_final: 0.8513 (mt) REVERT: A 123 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7795 (ttt180) REVERT: A 147 SER cc_start: 0.8222 (t) cc_final: 0.7917 (m) REVERT: A 254 GLU cc_start: 0.5467 (mm-30) cc_final: 0.5226 (mm-30) REVERT: A 408 TYR cc_start: 0.8602 (m-80) cc_final: 0.7981 (m-80) REVERT: B 1 MET cc_start: 0.5897 (tmm) cc_final: 0.4889 (tmm) REVERT: B 3 GLU cc_start: 0.8127 (mp0) cc_final: 0.7633 (mp0) REVERT: B 48 ASN cc_start: 0.8411 (m110) cc_final: 0.8163 (p0) REVERT: B 147 MET cc_start: 0.8213 (mtp) cc_final: 0.7921 (mtp) REVERT: B 279 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: B 415 MET cc_start: 0.8397 (tpp) cc_final: 0.8100 (ttt) REVERT: B 423 GLN cc_start: 0.7988 (mt0) cc_final: 0.7679 (tm-30) REVERT: E 3 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7071 (pt0) REVERT: E 392 ASP cc_start: 0.7975 (m-30) cc_final: 0.7549 (m-30) REVERT: I 31 ASP cc_start: 0.8114 (t0) cc_final: 0.7753 (t0) REVERT: I 246 LEU cc_start: 0.8444 (tp) cc_final: 0.8035 (tt) REVERT: I 299 MET cc_start: 0.8661 (mmp) cc_final: 0.8365 (mmt) REVERT: I 342 VAL cc_start: 0.8811 (t) cc_final: 0.8525 (m) REVERT: I 359 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7996 (mtp85) REVERT: I 401 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8193 (mm-30) REVERT: S 35 GLN cc_start: 0.7369 (mp10) cc_final: 0.7107 (mp10) REVERT: S 102 ASN cc_start: 0.8448 (t0) cc_final: 0.8036 (t0) REVERT: S 411 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7313 (tp30) outliers start: 41 outliers final: 24 residues processed: 535 average time/residue: 0.3589 time to fit residues: 299.1105 Evaluate side-chains 510 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 485 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 258 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 293 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN I 195 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.120558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093740 restraints weight = 40157.249| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.68 r_work: 0.3192 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24292 Z= 0.196 Angle : 0.533 10.202 32974 Z= 0.266 Chirality : 0.043 0.350 3617 Planarity : 0.004 0.084 4288 Dihedral : 9.395 147.866 3606 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.38 % Allowed : 16.43 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.94 (0.16), residues: 2977 helix: 2.09 (0.15), residues: 1234 sheet: 0.46 (0.22), residues: 538 loop : -0.86 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS B 137 PHE 0.024 0.001 PHE K 94 TYR 0.042 0.001 TYR S 24 ARG 0.006 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 513 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 113 LYS cc_start: 0.8314 (mmtm) cc_final: 0.7940 (mmtt) REVERT: K 125 ASP cc_start: 0.7426 (t0) cc_final: 0.7062 (t0) REVERT: K 129 ARG cc_start: 0.7561 (ttm170) cc_final: 0.7315 (ttm170) REVERT: K 153 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8087 (mtp85) REVERT: K 367 LYS cc_start: 0.8660 (tptt) cc_final: 0.8357 (tppt) REVERT: N 54 TYR cc_start: 0.7966 (m-10) cc_final: 0.7251 (m-10) REVERT: N 76 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8136 (t0) REVERT: N 98 GLN cc_start: 0.6084 (mt0) cc_final: 0.5768 (mt0) REVERT: N 156 ASP cc_start: 0.7367 (t70) cc_final: 0.7145 (t70) REVERT: N 253 GLU cc_start: 0.8155 (mp0) cc_final: 0.7904 (mp0) REVERT: N 288 MET cc_start: 0.8026 (tmm) cc_final: 0.7768 (tpp) REVERT: N 310 VAL cc_start: 0.9043 (m) cc_final: 0.8806 (p) REVERT: N 319 LEU cc_start: 0.8712 (mm) cc_final: 0.8481 (mt) REVERT: N 345 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 123 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7805 (ttt180) REVERT: A 147 SER cc_start: 0.8290 (t) cc_final: 0.7873 (m) REVERT: A 254 GLU cc_start: 0.5577 (mm-30) cc_final: 0.4672 (mm-30) REVERT: A 301 GLN cc_start: 0.8755 (mm110) cc_final: 0.8373 (mm110) REVERT: A 305 CYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 1 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.4839 (tmm) REVERT: B 3 GLU cc_start: 0.8074 (mp0) cc_final: 0.7521 (mp0) REVERT: B 48 ASN cc_start: 0.8431 (m110) cc_final: 0.8198 (p0) REVERT: B 219 THR cc_start: 0.9249 (m) cc_final: 0.8877 (p) REVERT: B 415 MET cc_start: 0.8462 (tpp) cc_final: 0.8094 (ttm) REVERT: B 423 GLN cc_start: 0.8013 (mt0) cc_final: 0.7708 (tm-30) REVERT: E 147 SER cc_start: 0.8374 (p) cc_final: 0.8168 (m) REVERT: E 392 ASP cc_start: 0.7967 (m-30) cc_final: 0.7587 (m-30) REVERT: I 31 ASP cc_start: 0.8139 (t0) cc_final: 0.7787 (t0) REVERT: I 246 LEU cc_start: 0.8444 (tp) cc_final: 0.8051 (tt) REVERT: I 299 MET cc_start: 0.8787 (mmp) cc_final: 0.8333 (mmt) REVERT: I 342 VAL cc_start: 0.8813 (t) cc_final: 0.8556 (m) REVERT: I 401 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8181 (mm-30) REVERT: S 35 GLN cc_start: 0.7439 (mp10) cc_final: 0.7090 (mp10) REVERT: S 102 ASN cc_start: 0.8436 (t0) cc_final: 0.7961 (t0) REVERT: S 242 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8561 (pp) REVERT: S 394 LYS cc_start: 0.7835 (mttt) cc_final: 0.7192 (tptt) REVERT: S 411 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7318 (tp30) outliers start: 55 outliers final: 36 residues processed: 534 average time/residue: 0.3696 time to fit residues: 305.2362 Evaluate side-chains 534 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 493 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 140 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 287 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 249 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 HIS S 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.115935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089426 restraints weight = 38233.541| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.58 r_work: 0.3144 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24292 Z= 0.336 Angle : 0.584 9.321 32974 Z= 0.295 Chirality : 0.045 0.285 3617 Planarity : 0.005 0.083 4288 Dihedral : 9.395 149.424 3604 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.54 % Favored : 96.29 % Rotamer: Outliers : 2.97 % Allowed : 16.47 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.81 (0.16), residues: 2977 helix: 2.01 (0.15), residues: 1228 sheet: 0.52 (0.22), residues: 521 loop : -1.00 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.008 0.001 HIS A 88 PHE 0.026 0.002 PHE K 94 TYR 0.030 0.001 TYR S 24 ARG 0.005 0.001 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 521 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 113 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7916 (mmtm) REVERT: K 125 ASP cc_start: 0.7647 (t0) cc_final: 0.7147 (t0) REVERT: K 138 MET cc_start: 0.7402 (tpt) cc_final: 0.5935 (tpp) REVERT: K 153 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8225 (mtp85) REVERT: K 201 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8398 (tptp) REVERT: K 229 ARG cc_start: 0.8654 (mmt90) cc_final: 0.8008 (mmp-170) REVERT: K 367 LYS cc_start: 0.8624 (tptt) cc_final: 0.8315 (tppt) REVERT: N 76 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8188 (t0) REVERT: N 98 GLN cc_start: 0.6307 (mt0) cc_final: 0.5986 (mt0) REVERT: N 253 GLU cc_start: 0.8257 (mp0) cc_final: 0.7989 (mp0) REVERT: N 288 MET cc_start: 0.8137 (tmm) cc_final: 0.7871 (tpp) REVERT: N 319 LEU cc_start: 0.8814 (mm) cc_final: 0.8535 (mt) REVERT: A 70 LEU cc_start: 0.8298 (mt) cc_final: 0.8068 (mp) REVERT: A 147 SER cc_start: 0.8422 (t) cc_final: 0.7968 (m) REVERT: A 150 THR cc_start: 0.8485 (m) cc_final: 0.8244 (m) REVERT: A 254 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5417 (mm-30) REVERT: A 408 TYR cc_start: 0.8647 (m-80) cc_final: 0.8217 (m-80) REVERT: B 1 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.4987 (tmm) REVERT: B 3 GLU cc_start: 0.8384 (mp0) cc_final: 0.7727 (mp0) REVERT: B 48 ASN cc_start: 0.8617 (m110) cc_final: 0.8233 (p0) REVERT: B 219 THR cc_start: 0.9262 (m) cc_final: 0.8996 (p) REVERT: B 423 GLN cc_start: 0.8176 (mt0) cc_final: 0.7823 (tm-30) REVERT: E 242 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8856 (pp) REVERT: E 260 VAL cc_start: 0.8852 (t) cc_final: 0.8440 (m) REVERT: E 265 ILE cc_start: 0.8793 (pt) cc_final: 0.8413 (mt) REVERT: E 392 ASP cc_start: 0.8209 (m-30) cc_final: 0.7883 (m-30) REVERT: I 31 ASP cc_start: 0.8313 (t0) cc_final: 0.7953 (t0) REVERT: I 147 MET cc_start: 0.8624 (mtp) cc_final: 0.8288 (ttm) REVERT: I 401 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8348 (mm-30) REVERT: S 35 GLN cc_start: 0.7584 (mp-120) cc_final: 0.7254 (mp10) REVERT: S 102 ASN cc_start: 0.8562 (t0) cc_final: 0.8050 (t0) REVERT: S 203 MET cc_start: 0.8437 (mmt) cc_final: 0.8005 (mmm) REVERT: S 242 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8746 (pp) REVERT: S 297 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7998 (mm-30) REVERT: S 411 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7499 (tp30) outliers start: 70 outliers final: 46 residues processed: 553 average time/residue: 0.3743 time to fit residues: 321.8274 Evaluate side-chains 548 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 497 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 292 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 252 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 GLN ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 ASN S 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.091489 restraints weight = 34853.171| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.47 r_work: 0.3184 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24292 Z= 0.215 Angle : 0.543 8.833 32974 Z= 0.273 Chirality : 0.043 0.259 3617 Planarity : 0.004 0.081 4288 Dihedral : 9.205 152.609 3604 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.58 % Allowed : 17.68 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.87 (0.16), residues: 2977 helix: 2.04 (0.15), residues: 1234 sheet: 0.49 (0.22), residues: 527 loop : -0.95 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.009 0.001 HIS B 137 PHE 0.023 0.001 PHE K 94 TYR 0.020 0.001 TYR S 24 ARG 0.006 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 506 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 66 ASN cc_start: 0.8772 (m110) cc_final: 0.8518 (m-40) REVERT: K 125 ASP cc_start: 0.7594 (t0) cc_final: 0.6996 (t0) REVERT: K 126 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7985 (tp) REVERT: K 129 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7095 (ttp80) REVERT: K 138 MET cc_start: 0.7467 (tpt) cc_final: 0.5863 (tpp) REVERT: K 153 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8198 (mtp85) REVERT: K 201 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8379 (tptp) REVERT: K 203 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8274 (ttt-90) REVERT: K 229 ARG cc_start: 0.8620 (mmt90) cc_final: 0.8027 (mmp-170) REVERT: K 367 LYS cc_start: 0.8638 (tptt) cc_final: 0.8315 (tppt) REVERT: N 76 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8179 (t0) REVERT: N 98 GLN cc_start: 0.6164 (mt0) cc_final: 0.5825 (mt0) REVERT: N 116 GLN cc_start: 0.6828 (mm-40) cc_final: 0.6616 (mm-40) REVERT: N 156 ASP cc_start: 0.7621 (t70) cc_final: 0.7408 (t70) REVERT: N 253 GLU cc_start: 0.8257 (mp0) cc_final: 0.7982 (mp0) REVERT: N 288 MET cc_start: 0.8114 (tmm) cc_final: 0.7863 (tpp) REVERT: N 310 VAL cc_start: 0.9123 (m) cc_final: 0.8858 (p) REVERT: N 319 LEU cc_start: 0.8808 (mm) cc_final: 0.8524 (mt) REVERT: A 3 GLU cc_start: 0.7862 (pm20) cc_final: 0.7465 (pm20) REVERT: A 147 SER cc_start: 0.8371 (t) cc_final: 0.7924 (m) REVERT: A 150 THR cc_start: 0.8450 (m) cc_final: 0.8209 (m) REVERT: A 254 GLU cc_start: 0.5761 (mm-30) cc_final: 0.5342 (mm-30) REVERT: A 408 TYR cc_start: 0.8619 (m-80) cc_final: 0.8234 (m-80) REVERT: B 1 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.4944 (tmm) REVERT: B 3 GLU cc_start: 0.8336 (mp0) cc_final: 0.7738 (mp0) REVERT: B 48 ASN cc_start: 0.8595 (m110) cc_final: 0.8253 (p0) REVERT: B 219 THR cc_start: 0.9295 (m) cc_final: 0.8994 (p) REVERT: B 233 MET cc_start: 0.8934 (mtp) cc_final: 0.8687 (mtp) REVERT: B 282 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8455 (mtp85) REVERT: B 423 GLN cc_start: 0.8146 (mt0) cc_final: 0.7813 (tm-30) REVERT: E 147 SER cc_start: 0.8472 (p) cc_final: 0.8241 (m) REVERT: E 242 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8809 (pp) REVERT: E 265 ILE cc_start: 0.8731 (pt) cc_final: 0.8288 (mt) REVERT: E 392 ASP cc_start: 0.8265 (m-30) cc_final: 0.7874 (m-30) REVERT: I 26 ASP cc_start: 0.8951 (t0) cc_final: 0.8717 (t0) REVERT: I 31 ASP cc_start: 0.8307 (t0) cc_final: 0.7951 (t0) REVERT: I 147 MET cc_start: 0.8592 (mtp) cc_final: 0.8241 (ttm) REVERT: I 368 ILE cc_start: 0.8778 (mt) cc_final: 0.8540 (mt) REVERT: I 401 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8356 (mm-30) REVERT: S 102 ASN cc_start: 0.8526 (t0) cc_final: 0.8004 (t0) REVERT: S 203 MET cc_start: 0.8390 (mmt) cc_final: 0.7921 (mmm) REVERT: S 242 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8743 (pp) REVERT: S 411 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7451 (tp30) outliers start: 60 outliers final: 46 residues processed: 536 average time/residue: 0.3757 time to fit residues: 312.2234 Evaluate side-chains 545 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 493 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 232 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 184 optimal weight: 0.5980 chunk 252 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 295 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN I 433 GLN A S 18 ASN S 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.120685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093723 restraints weight = 44568.833| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.85 r_work: 0.3176 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24292 Z= 0.167 Angle : 0.530 11.371 32974 Z= 0.265 Chirality : 0.042 0.227 3617 Planarity : 0.004 0.078 4288 Dihedral : 8.994 155.672 3604 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.37 % Favored : 96.46 % Rotamer: Outliers : 3.04 % Allowed : 17.33 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2977 helix: 2.12 (0.15), residues: 1241 sheet: 0.52 (0.22), residues: 528 loop : -0.91 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.008 0.001 HIS B 137 PHE 0.022 0.001 PHE K 94 TYR 0.017 0.001 TYR S 24 ARG 0.006 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 509 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 66 ASN cc_start: 0.8714 (m110) cc_final: 0.8508 (m-40) REVERT: K 80 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7643 (tm-30) REVERT: K 125 ASP cc_start: 0.7488 (t0) cc_final: 0.6926 (t0) REVERT: K 126 LEU cc_start: 0.8264 (tt) cc_final: 0.7973 (tp) REVERT: K 129 ARG cc_start: 0.7519 (ttm170) cc_final: 0.7042 (ttp80) REVERT: K 153 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8072 (mtp85) REVERT: K 193 GLN cc_start: 0.8220 (tp40) cc_final: 0.7925 (tp40) REVERT: K 277 THR cc_start: 0.9189 (m) cc_final: 0.8864 (t) REVERT: K 367 LYS cc_start: 0.8589 (tptt) cc_final: 0.8275 (tppt) REVERT: N 76 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8150 (t0) REVERT: N 98 GLN cc_start: 0.6018 (mt0) cc_final: 0.5696 (mt0) REVERT: N 116 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6549 (mm-40) REVERT: N 156 ASP cc_start: 0.7518 (t70) cc_final: 0.7301 (t70) REVERT: N 193 GLN cc_start: 0.6366 (mt0) cc_final: 0.6024 (mp10) REVERT: N 243 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7704 (mtpp) REVERT: N 288 MET cc_start: 0.8011 (tmm) cc_final: 0.7772 (tpp) REVERT: N 310 VAL cc_start: 0.9044 (m) cc_final: 0.8795 (p) REVERT: N 319 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 3 GLU cc_start: 0.7645 (pm20) cc_final: 0.7316 (pm20) REVERT: A 127 ASP cc_start: 0.8080 (m-30) cc_final: 0.7873 (m-30) REVERT: A 147 SER cc_start: 0.8297 (t) cc_final: 0.7858 (m) REVERT: A 150 THR cc_start: 0.8336 (m) cc_final: 0.8075 (m) REVERT: A 408 TYR cc_start: 0.8551 (m-80) cc_final: 0.8166 (m-80) REVERT: B 1 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.4830 (tmm) REVERT: B 3 GLU cc_start: 0.8072 (mp0) cc_final: 0.7712 (mp0) REVERT: B 48 ASN cc_start: 0.8410 (m110) cc_final: 0.8195 (p0) REVERT: B 170 MET cc_start: 0.8207 (mtt) cc_final: 0.7929 (mtt) REVERT: B 219 THR cc_start: 0.9273 (m) cc_final: 0.8967 (p) REVERT: B 233 MET cc_start: 0.8855 (mtp) cc_final: 0.8572 (mtp) REVERT: B 415 MET cc_start: 0.8454 (tpp) cc_final: 0.7949 (ttp) REVERT: B 423 GLN cc_start: 0.8016 (mt0) cc_final: 0.7741 (tm-30) REVERT: E 3 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7069 (pt0) REVERT: E 242 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8726 (pp) REVERT: E 392 ASP cc_start: 0.8099 (m-30) cc_final: 0.7700 (m-30) REVERT: I 31 ASP cc_start: 0.8169 (t0) cc_final: 0.7796 (t0) REVERT: I 147 MET cc_start: 0.8477 (mtp) cc_final: 0.8130 (ttm) REVERT: I 299 MET cc_start: 0.8806 (mmp) cc_final: 0.8376 (mmt) REVERT: I 368 ILE cc_start: 0.8665 (mt) cc_final: 0.8409 (mt) REVERT: I 401 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8178 (mm-30) REVERT: S 35 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: S 102 ASN cc_start: 0.8511 (t0) cc_final: 0.8014 (t0) REVERT: S 242 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (pp) REVERT: S 322 ASP cc_start: 0.8660 (t0) cc_final: 0.8433 (t0) REVERT: S 411 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7322 (tp30) outliers start: 72 outliers final: 55 residues processed: 545 average time/residue: 0.3769 time to fit residues: 319.3640 Evaluate side-chains 553 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 492 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain K residue 331 LEU Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 35 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 396 ASP Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 241 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 295 optimal weight: 0.0000 chunk 202 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 212 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 121 GLN B 165 ASN E 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.119775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093147 restraints weight = 35161.662| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.51 r_work: 0.3217 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24292 Z= 0.164 Angle : 0.534 11.873 32974 Z= 0.267 Chirality : 0.042 0.216 3617 Planarity : 0.004 0.073 4288 Dihedral : 8.924 157.476 3604 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 2.89 % Allowed : 17.60 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 2977 helix: 2.13 (0.15), residues: 1241 sheet: 0.51 (0.22), residues: 533 loop : -0.88 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.008 0.001 HIS B 137 PHE 0.033 0.001 PHE K 94 TYR 0.031 0.001 TYR K 56 ARG 0.008 0.000 ARG N 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 511 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 80 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7725 (tm-30) REVERT: K 125 ASP cc_start: 0.7684 (t0) cc_final: 0.7153 (t0) REVERT: K 126 LEU cc_start: 0.8280 (tt) cc_final: 0.7995 (tp) REVERT: K 129 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7105 (ttp80) REVERT: K 277 THR cc_start: 0.9228 (m) cc_final: 0.8939 (t) REVERT: K 301 THR cc_start: 0.4541 (OUTLIER) cc_final: 0.4018 (p) REVERT: N 76 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8196 (t0) REVERT: N 98 GLN cc_start: 0.6122 (mt0) cc_final: 0.5731 (mt0) REVERT: N 116 GLN cc_start: 0.6756 (mm-40) cc_final: 0.6471 (mm-40) REVERT: N 156 ASP cc_start: 0.7615 (t70) cc_final: 0.7390 (t70) REVERT: N 243 LYS cc_start: 0.8501 (mtpp) cc_final: 0.7731 (mtpp) REVERT: N 288 MET cc_start: 0.8040 (tmm) cc_final: 0.7787 (tpp) REVERT: N 319 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 3 GLU cc_start: 0.7847 (pm20) cc_final: 0.7488 (pm20) REVERT: A 123 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8055 (ttt180) REVERT: A 127 ASP cc_start: 0.8209 (m-30) cc_final: 0.7992 (m-30) REVERT: A 147 SER cc_start: 0.8356 (t) cc_final: 0.7909 (m) REVERT: A 150 THR cc_start: 0.8395 (m) cc_final: 0.8141 (m) REVERT: A 254 GLU cc_start: 0.5549 (mm-30) cc_final: 0.5316 (mm-30) REVERT: A 408 TYR cc_start: 0.8598 (m-80) cc_final: 0.8201 (m-80) REVERT: A 432 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.7603 (t80) REVERT: B 1 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.4960 (tmm) REVERT: B 3 GLU cc_start: 0.8279 (mp0) cc_final: 0.7656 (mp0) REVERT: B 48 ASN cc_start: 0.8563 (m110) cc_final: 0.8269 (p0) REVERT: B 170 MET cc_start: 0.8490 (mtt) cc_final: 0.8202 (mtt) REVERT: B 219 THR cc_start: 0.9273 (m) cc_final: 0.8988 (p) REVERT: B 233 MET cc_start: 0.8931 (mtp) cc_final: 0.8666 (mtp) REVERT: B 282 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8531 (mtp85) REVERT: B 299 MET cc_start: 0.9138 (mmm) cc_final: 0.8898 (mmt) REVERT: B 415 MET cc_start: 0.8616 (tpp) cc_final: 0.8058 (ttp) REVERT: B 423 GLN cc_start: 0.8103 (mt0) cc_final: 0.7781 (tm-30) REVERT: E 3 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7270 (pt0) REVERT: E 242 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8794 (pp) REVERT: E 265 ILE cc_start: 0.8632 (pt) cc_final: 0.8234 (mt) REVERT: E 392 ASP cc_start: 0.8276 (m-30) cc_final: 0.7874 (m-30) REVERT: I 31 ASP cc_start: 0.8285 (t0) cc_final: 0.7927 (t0) REVERT: I 147 MET cc_start: 0.8597 (mtp) cc_final: 0.8260 (ttm) REVERT: I 299 MET cc_start: 0.8799 (mmp) cc_final: 0.8411 (mmt) REVERT: I 368 ILE cc_start: 0.8717 (mt) cc_final: 0.8338 (tt) REVERT: I 401 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8307 (mm-30) REVERT: S 7 ILE cc_start: 0.8554 (mm) cc_final: 0.8352 (mt) REVERT: S 35 GLN cc_start: 0.8058 (mp10) cc_final: 0.7776 (pm20) REVERT: S 102 ASN cc_start: 0.8540 (t0) cc_final: 0.8040 (t0) REVERT: S 242 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8750 (pp) REVERT: S 322 ASP cc_start: 0.8835 (t0) cc_final: 0.8601 (t0) REVERT: S 411 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7451 (tp30) outliers start: 68 outliers final: 52 residues processed: 547 average time/residue: 0.3607 time to fit residues: 307.1045 Evaluate side-chains 553 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 494 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 36 MET Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 121 GLN A 256 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN E 101 ASN I 204 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.117093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090911 restraints weight = 35043.120| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.45 r_work: 0.3156 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24292 Z= 0.330 Angle : 0.595 11.179 32974 Z= 0.301 Chirality : 0.045 0.219 3617 Planarity : 0.004 0.073 4288 Dihedral : 9.090 158.868 3604 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 2.85 % Allowed : 17.88 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.83 (0.16), residues: 2977 helix: 1.96 (0.15), residues: 1239 sheet: 0.47 (0.22), residues: 527 loop : -0.91 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 57 HIS 0.010 0.001 HIS B 137 PHE 0.035 0.002 PHE K 94 TYR 0.027 0.001 TYR K 56 ARG 0.009 0.001 ARG N 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 522 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8118 (mm-40) REVERT: K 80 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7742 (tm-30) REVERT: K 113 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7993 (tppt) REVERT: K 125 ASP cc_start: 0.7676 (t0) cc_final: 0.7131 (t0) REVERT: K 126 LEU cc_start: 0.8259 (tt) cc_final: 0.7972 (tp) REVERT: K 129 ARG cc_start: 0.7559 (ttm170) cc_final: 0.7252 (ttm170) REVERT: K 153 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8203 (mtp85) REVERT: K 277 THR cc_start: 0.9260 (m) cc_final: 0.9009 (t) REVERT: K 301 THR cc_start: 0.4330 (OUTLIER) cc_final: 0.3805 (p) REVERT: N 76 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8167 (t0) REVERT: N 98 GLN cc_start: 0.6323 (mt0) cc_final: 0.5960 (mt0) REVERT: N 116 GLN cc_start: 0.6752 (mm-40) cc_final: 0.6438 (mm-40) REVERT: N 156 ASP cc_start: 0.7639 (t70) cc_final: 0.7409 (t70) REVERT: N 288 MET cc_start: 0.8080 (tmm) cc_final: 0.7840 (tpp) REVERT: N 319 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8537 (mt) REVERT: A 3 GLU cc_start: 0.7970 (pm20) cc_final: 0.7612 (pm20) REVERT: A 147 SER cc_start: 0.8421 (t) cc_final: 0.8042 (m) REVERT: A 150 THR cc_start: 0.8460 (m) cc_final: 0.8199 (m) REVERT: A 254 GLU cc_start: 0.5761 (mm-30) cc_final: 0.4654 (mm-30) REVERT: A 408 TYR cc_start: 0.8628 (m-80) cc_final: 0.8264 (m-80) REVERT: B 1 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.4974 (tmm) REVERT: B 3 GLU cc_start: 0.8268 (mp0) cc_final: 0.7541 (mp0) REVERT: B 48 ASN cc_start: 0.8624 (m110) cc_final: 0.8322 (p0) REVERT: B 170 MET cc_start: 0.8567 (mtt) cc_final: 0.8264 (mtt) REVERT: B 219 THR cc_start: 0.9294 (m) cc_final: 0.9011 (p) REVERT: B 233 MET cc_start: 0.8966 (mtp) cc_final: 0.8713 (mtp) REVERT: B 413 SER cc_start: 0.8850 (m) cc_final: 0.8635 (p) REVERT: B 415 MET cc_start: 0.8666 (tpp) cc_final: 0.8374 (ttm) REVERT: B 423 GLN cc_start: 0.8220 (mt0) cc_final: 0.7895 (tm-30) REVERT: E 242 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8862 (pp) REVERT: E 260 VAL cc_start: 0.8850 (t) cc_final: 0.8463 (m) REVERT: E 265 ILE cc_start: 0.8781 (pt) cc_final: 0.8434 (mt) REVERT: E 302 MET cc_start: 0.8687 (mtp) cc_final: 0.8471 (mtt) REVERT: E 392 ASP cc_start: 0.8233 (m-30) cc_final: 0.7878 (m-30) REVERT: I 31 ASP cc_start: 0.8349 (t0) cc_final: 0.7981 (t0) REVERT: I 368 ILE cc_start: 0.8810 (mt) cc_final: 0.8588 (mt) REVERT: I 401 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8315 (mm-30) REVERT: S 35 GLN cc_start: 0.7885 (mp10) cc_final: 0.7543 (pm20) REVERT: S 97 GLU cc_start: 0.8436 (mp0) cc_final: 0.7894 (mt-10) REVERT: S 102 ASN cc_start: 0.8577 (t0) cc_final: 0.8069 (t0) REVERT: S 203 MET cc_start: 0.8408 (mmt) cc_final: 0.7963 (mmm) REVERT: S 242 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8804 (pp) REVERT: S 322 ASP cc_start: 0.8850 (t0) cc_final: 0.8624 (t0) REVERT: S 411 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7467 (tp30) outliers start: 67 outliers final: 51 residues processed: 553 average time/residue: 0.3713 time to fit residues: 319.4731 Evaluate side-chains 560 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 503 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 321 MET Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 396 ASP Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 13 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 188 optimal weight: 0.1980 chunk 198 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS K 121 GLN A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN S 18 ASN S 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092291 restraints weight = 44785.677| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.90 r_work: 0.3185 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24292 Z= 0.157 Angle : 0.544 9.971 32974 Z= 0.271 Chirality : 0.042 0.201 3617 Planarity : 0.004 0.072 4288 Dihedral : 8.875 163.255 3604 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 2.46 % Allowed : 18.50 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.95 (0.16), residues: 2977 helix: 2.07 (0.15), residues: 1243 sheet: 0.52 (0.22), residues: 523 loop : -0.86 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.008 0.001 HIS B 137 PHE 0.032 0.001 PHE K 94 TYR 0.034 0.001 TYR S 24 ARG 0.007 0.000 ARG E 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 507 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8011 (mm110) REVERT: K 80 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7687 (tm-30) REVERT: K 113 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8066 (tppt) REVERT: K 125 ASP cc_start: 0.7579 (t0) cc_final: 0.7078 (t0) REVERT: K 126 LEU cc_start: 0.8192 (tt) cc_final: 0.7900 (tp) REVERT: K 127 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7888 (t80) REVERT: K 129 ARG cc_start: 0.7498 (ttm170) cc_final: 0.7051 (ttp80) REVERT: K 153 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8072 (mtp85) REVERT: K 229 ARG cc_start: 0.8600 (mmt90) cc_final: 0.8038 (mmp-170) REVERT: K 301 THR cc_start: 0.4170 (OUTLIER) cc_final: 0.3660 (p) REVERT: K 355 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8032 (ptp-170) REVERT: N 76 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8179 (t0) REVERT: N 98 GLN cc_start: 0.6038 (mt0) cc_final: 0.5666 (mt0) REVERT: N 116 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6426 (mm-40) REVERT: N 156 ASP cc_start: 0.7508 (t70) cc_final: 0.7290 (t70) REVERT: N 288 MET cc_start: 0.7983 (tmm) cc_final: 0.7716 (tpp) REVERT: N 319 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 2 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6530 (mtm-85) REVERT: A 123 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7929 (ttt180) REVERT: A 147 SER cc_start: 0.8307 (t) cc_final: 0.7901 (m) REVERT: A 254 GLU cc_start: 0.5452 (mm-30) cc_final: 0.4557 (mm-30) REVERT: A 408 TYR cc_start: 0.8543 (m-80) cc_final: 0.8172 (m-80) REVERT: A 432 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 1 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.4791 (tmm) REVERT: B 3 GLU cc_start: 0.8043 (mp0) cc_final: 0.7620 (mp0) REVERT: B 48 ASN cc_start: 0.8435 (m110) cc_final: 0.8204 (p0) REVERT: B 170 MET cc_start: 0.8220 (mtt) cc_final: 0.7948 (mtt) REVERT: B 219 THR cc_start: 0.9261 (m) cc_final: 0.8969 (p) REVERT: B 233 MET cc_start: 0.8823 (mtp) cc_final: 0.8523 (mtp) REVERT: B 413 SER cc_start: 0.8724 (m) cc_final: 0.8489 (p) REVERT: B 415 MET cc_start: 0.8472 (tpp) cc_final: 0.8145 (ttt) REVERT: B 423 GLN cc_start: 0.8062 (mt0) cc_final: 0.7779 (tm-30) REVERT: B 424 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8286 (pt0) REVERT: E 3 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7069 (pt0) REVERT: E 242 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8776 (pp) REVERT: E 265 ILE cc_start: 0.8571 (pt) cc_final: 0.8230 (mt) REVERT: E 302 MET cc_start: 0.8516 (mtp) cc_final: 0.8269 (mtt) REVERT: E 392 ASP cc_start: 0.8095 (m-30) cc_final: 0.7676 (m-30) REVERT: I 31 ASP cc_start: 0.8203 (t0) cc_final: 0.7833 (t0) REVERT: I 299 MET cc_start: 0.8748 (mmp) cc_final: 0.8348 (mmt) REVERT: I 368 ILE cc_start: 0.8617 (mt) cc_final: 0.8291 (tt) REVERT: I 401 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8186 (mm-30) REVERT: S 35 GLN cc_start: 0.7638 (mp-120) cc_final: 0.7360 (pm20) REVERT: S 75 ILE cc_start: 0.8621 (mm) cc_final: 0.8367 (mm) REVERT: S 97 GLU cc_start: 0.8302 (mp0) cc_final: 0.7786 (mt-10) REVERT: S 102 ASN cc_start: 0.8461 (t0) cc_final: 0.7922 (t0) REVERT: S 242 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8706 (pp) REVERT: S 322 ASP cc_start: 0.8714 (t0) cc_final: 0.8501 (t0) outliers start: 57 outliers final: 42 residues processed: 534 average time/residue: 0.3754 time to fit residues: 312.0604 Evaluate side-chains 543 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 492 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 396 ASP Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS K 121 GLN A 256 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090089 restraints weight = 37892.419| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.57 r_work: 0.3137 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24292 Z= 0.382 Angle : 0.618 10.130 32974 Z= 0.312 Chirality : 0.046 0.218 3617 Planarity : 0.005 0.072 4288 Dihedral : 9.056 162.770 3604 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.82 % Rotamer: Outliers : 2.54 % Allowed : 19.09 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.80 (0.16), residues: 2977 helix: 1.96 (0.15), residues: 1231 sheet: 0.43 (0.22), residues: 524 loop : -0.92 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.010 0.001 HIS B 137 PHE 0.035 0.002 PHE K 94 TYR 0.031 0.002 TYR S 24 ARG 0.008 0.001 ARG N 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13463.63 seconds wall clock time: 240 minutes 44.44 seconds (14444.44 seconds total)