Starting phenix.real_space_refine on Sun Aug 24 04:01:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utq_42546/08_2025/8utq_42546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utq_42546/08_2025/8utq_42546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8utq_42546/08_2025/8utq_42546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utq_42546/08_2025/8utq_42546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8utq_42546/08_2025/8utq_42546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utq_42546/08_2025/8utq_42546.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 3 5.21 5 S 114 5.16 5 C 10539 2.51 5 N 2871 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16825 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2911 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} 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: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3381 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "E" 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: "I" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3381 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} 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: "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} Time building chain proxies: 4.13, per 1000 atoms: 0.25 Number of scatterers: 16825 At special positions: 0 Unit cell: (72.584, 111.408, 198.34, 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 114 16.00 P 13 15.00 Mg 3 11.99 O 3285 8.00 N 2871 7.00 C 10539 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: 1.60 Conformation dependent library (CDL) restraints added in 778.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 50.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.761A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 86 Processing helix chain 'K' and resid 102 through 108 removed outlier: 4.029A pdb=" N THR K 106 " --> pdb=" O GLY K 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.580A 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 removed outlier: 3.696A pdb=" N ALA K 286 " --> pdb=" O ILE K 282 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU K 287 " --> pdb=" O SER K 283 " (cutoff:3.500A) Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.881A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 350 Processing helix chain 'K' and resid 363 through 373 removed outlier: 3.526A pdb=" N ILE K 369 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG K 370 " --> pdb=" O ASN K 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.195A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.593A 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 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.662A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.587A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (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: 3.681A 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: 3.651A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.040A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.848A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.940A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.012A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.113A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.228A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.582A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 127 removed outlier: 4.182A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.735A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.634A 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: 3.584A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.636A 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 removed outlier: 3.582A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 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: 3.692A 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: 4.205A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.045A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.738A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.850A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.260A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.531A 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: 3.571A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.154A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.890A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.851A 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 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.078A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.804A 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: 3.564A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.057A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.829A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.358A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.275A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.530A 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 127 removed outlier: 3.682A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.625A pdb=" N SER I 145 " --> pdb=" O GLY I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.594A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.540A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 280 removed outlier: 3.528A pdb=" N SER I 278 " --> pdb=" O SER I 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 295 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.568A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.292A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.091A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 424 removed outlier: 3.782A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 56 through 57 removed outlier: 5.436A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 56 through 57 removed outlier: 5.436A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.356A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.137A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.684A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'I' and resid 90 through 92 removed outlier: 5.948A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS I 137 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 51 through 53 812 hydrogen bonds defined for protein. 2316 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: 3.11 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2997 1.32 - 1.45: 4536 1.45 - 1.57: 9451 1.57 - 1.70: 28 1.70 - 1.82: 183 Bond restraints: 17195 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP K 502 " pdb=" PA ANP K 502 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" N VAL K 247 " pdb=" CA VAL K 247 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 9.98e+00 bond pdb=" N VAL B 23 " pdb=" CA VAL B 23 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.21e+00 ... (remaining 17190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 23088 3.34 - 6.68: 253 6.68 - 10.03: 11 10.03 - 13.37: 4 13.37 - 16.71: 1 Bond angle restraints: 23357 Sorted by residual: angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 110.24 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C ALA K 358 " pdb=" N VAL K 359 " pdb=" CA VAL K 359 " ideal model delta sigma weight residual 121.97 131.56 -9.59 1.80e+00 3.09e-01 2.84e+01 angle pdb=" CA GLN I 426 " pdb=" CB GLN I 426 " pdb=" CG GLN I 426 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C19 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C20 TA1 B 502 " ideal model delta sigma weight residual 112.17 100.71 11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O1B ANP K 502 " pdb=" PB ANP K 502 " pdb=" O2B ANP K 502 " ideal model delta sigma weight residual 120.08 108.74 11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 23352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 10080 35.29 - 70.58: 293 70.58 - 105.87: 56 105.87 - 141.15: 19 141.15 - 176.44: 6 Dihedral angle restraints: 10454 sinusoidal: 4348 harmonic: 6106 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -107.17 176.44 1 2.00e+01 2.50e-03 4.80e+01 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 -43.61 148.20 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -33.38 137.97 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 10451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2424 0.105 - 0.210: 133 0.210 - 0.315: 2 0.315 - 0.420: 0 0.420 - 0.526: 1 Chirality restraints: 2560 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 -2.64 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C02 TA1 B 502 " pdb=" C01 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" O02 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2557 not shown) Planarity restraints: 3030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.065 5.00e-02 4.00e+02 9.73e-02 1.52e+01 pdb=" N PRO K 292 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 21 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C TRP B 21 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 21 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 22 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN K 39 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO K 40 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO K 40 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 40 " -0.035 5.00e-02 4.00e+02 ... (remaining 3027 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 94 2.49 - 3.09: 12325 3.09 - 3.70: 25001 3.70 - 4.30: 36346 4.30 - 4.90: 62751 Nonbonded interactions: 136517 Sorted by model distance: nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.891 2.170 nonbonded pdb=" O1A GTP A 501 " pdb="MG MG A 502 " model vdw 1.927 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.928 2.170 nonbonded pdb="MG MG K 501 " pdb=" O2B ANP K 502 " model vdw 1.967 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.995 2.170 ... (remaining 136512 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' } ncs_group { reference = chain 'B' selection = chain 'I' } 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=1.00 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: 6.450 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.141 17195 Z= 0.235 Angle : 0.808 16.710 23357 Z= 0.422 Chirality : 0.048 0.526 2560 Planarity : 0.006 0.097 3030 Dihedral : 18.598 176.442 6536 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 0.22 % Allowed : 12.43 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.18), residues: 2100 helix: 1.19 (0.18), residues: 870 sheet: -0.28 (0.27), residues: 357 loop : -0.89 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 308 TYR 0.022 0.001 TYR I 422 PHE 0.015 0.001 PHE E 255 TRP 0.013 0.001 TRP K 57 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00488 (17195) covalent geometry : angle 0.80825 (23357) hydrogen bonds : bond 0.16283 ( 787) hydrogen bonds : angle 6.27500 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 297 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.7031 (ptt-90) REVERT: K 50 PHE cc_start: 0.7233 (m-80) cc_final: 0.6660 (m-80) REVERT: K 138 MET cc_start: 0.5055 (mtp) cc_final: 0.4839 (pmm) REVERT: B 291 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7860 (tp-100) REVERT: I 31 ASP cc_start: 0.8155 (t70) cc_final: 0.7703 (t70) outliers start: 4 outliers final: 3 residues processed: 300 average time/residue: 0.1387 time to fit residues: 62.4653 Evaluate side-chains 280 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 386 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 90 ASN A 107 HIS B 37 HIS B 204 ASN E 61 HIS E 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070967 restraints weight = 31896.249| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.83 r_work: 0.3019 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17195 Z= 0.194 Angle : 0.635 11.007 23357 Z= 0.315 Chirality : 0.046 0.365 2560 Planarity : 0.005 0.092 3030 Dihedral : 13.460 174.458 2600 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.48 % Favored : 96.38 % Rotamer: Outliers : 1.60 % Allowed : 11.77 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 2100 helix: 1.74 (0.18), residues: 883 sheet: 0.07 (0.27), residues: 353 loop : -0.76 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 380 TYR 0.014 0.001 TYR B 50 PHE 0.027 0.001 PHE K 225 TRP 0.015 0.002 TRP A 21 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00445 (17195) covalent geometry : angle 0.63533 (23357) hydrogen bonds : bond 0.05042 ( 787) hydrogen bonds : angle 4.57921 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 PHE cc_start: 0.7908 (m-80) cc_final: 0.7176 (m-80) REVERT: K 359 VAL cc_start: 0.1972 (OUTLIER) cc_final: 0.1410 (p) REVERT: A 1 MET cc_start: 0.7221 (ppp) cc_final: 0.6949 (tmm) REVERT: A 3 GLU cc_start: 0.7812 (pt0) cc_final: 0.7199 (pt0) REVERT: A 218 ASP cc_start: 0.9105 (t0) cc_final: 0.8738 (t70) REVERT: A 308 ARG cc_start: 0.9038 (mtm-85) cc_final: 0.8801 (mtm-85) REVERT: A 338 LYS cc_start: 0.9158 (tttt) cc_final: 0.8921 (tppt) REVERT: B 257 MET cc_start: 0.8755 (mmm) cc_final: 0.8480 (mtm) REVERT: E 62 VAL cc_start: 0.9285 (t) cc_final: 0.9033 (m) REVERT: E 322 ASP cc_start: 0.8778 (t0) cc_final: 0.8415 (t0) REVERT: E 339 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8459 (tpp80) REVERT: I 31 ASP cc_start: 0.8572 (t70) cc_final: 0.8143 (t70) REVERT: I 67 ASP cc_start: 0.8744 (t0) cc_final: 0.8471 (t0) REVERT: I 295 ASP cc_start: 0.8886 (t0) cc_final: 0.8473 (t0) REVERT: I 297 LYS cc_start: 0.9144 (mtmm) cc_final: 0.8937 (mtmm) REVERT: I 304 ASP cc_start: 0.8424 (t0) cc_final: 0.8176 (t0) REVERT: I 426 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8339 (tm-30) outliers start: 29 outliers final: 13 residues processed: 312 average time/residue: 0.1339 time to fit residues: 64.0060 Evaluate side-chains 285 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 271 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain E residue 334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 145 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.095439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073520 restraints weight = 31788.736| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.86 r_work: 0.3073 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17195 Z= 0.113 Angle : 0.552 9.018 23357 Z= 0.273 Chirality : 0.044 0.444 2560 Planarity : 0.004 0.085 3030 Dihedral : 9.500 172.423 2595 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.43 % Favored : 96.43 % Rotamer: Outliers : 1.71 % Allowed : 12.10 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.19), residues: 2100 helix: 1.94 (0.18), residues: 906 sheet: 0.16 (0.28), residues: 365 loop : -0.63 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 13 TYR 0.011 0.001 TYR K 140 PHE 0.019 0.001 PHE K 225 TRP 0.012 0.001 TRP E 388 HIS 0.003 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00243 (17195) covalent geometry : angle 0.55189 (23357) hydrogen bonds : bond 0.03967 ( 787) hydrogen bonds : angle 4.18084 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7204 (tmm) cc_final: 0.6626 (ptp) REVERT: K 98 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7903 (pp30) REVERT: K 105 TYR cc_start: 0.7760 (t80) cc_final: 0.7251 (t80) REVERT: K 248 ASP cc_start: 0.7905 (t0) cc_final: 0.7685 (t0) REVERT: K 253 GLU cc_start: 0.8584 (tp30) cc_final: 0.8360 (tp30) REVERT: K 359 VAL cc_start: 0.1592 (OUTLIER) cc_final: 0.0896 (p) REVERT: A 218 ASP cc_start: 0.9092 (t0) cc_final: 0.8727 (t70) REVERT: A 338 LYS cc_start: 0.9134 (tttt) cc_final: 0.8895 (tppt) REVERT: B 136 THR cc_start: 0.9150 (m) cc_final: 0.8944 (p) REVERT: B 213 ARG cc_start: 0.8818 (tpp80) cc_final: 0.8413 (mtm-85) REVERT: B 291 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8217 (tp-100) REVERT: B 295 ASP cc_start: 0.8948 (t0) cc_final: 0.8680 (t0) REVERT: E 127 ASP cc_start: 0.8983 (m-30) cc_final: 0.8779 (m-30) REVERT: E 322 ASP cc_start: 0.8742 (t0) cc_final: 0.8412 (t0) REVERT: E 339 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8487 (tpp80) REVERT: E 434 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7735 (mm-30) REVERT: I 31 ASP cc_start: 0.8562 (t70) cc_final: 0.8078 (t70) REVERT: I 67 ASP cc_start: 0.8788 (t0) cc_final: 0.8443 (t0) REVERT: I 118 ASP cc_start: 0.8976 (t0) cc_final: 0.8565 (m-30) REVERT: I 295 ASP cc_start: 0.8881 (t0) cc_final: 0.8368 (t0) REVERT: I 297 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8894 (mtmm) REVERT: I 376 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8226 (mm-30) REVERT: I 426 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8277 (tm-30) outliers start: 31 outliers final: 11 residues processed: 341 average time/residue: 0.1255 time to fit residues: 66.3494 Evaluate side-chains 304 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 292 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 144 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 98 optimal weight: 0.0980 chunk 165 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.072058 restraints weight = 31867.536| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.86 r_work: 0.3035 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17195 Z= 0.146 Angle : 0.561 8.520 23357 Z= 0.280 Chirality : 0.044 0.335 2560 Planarity : 0.004 0.084 3030 Dihedral : 9.073 172.496 2595 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 1.49 % Allowed : 13.76 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 2100 helix: 1.97 (0.18), residues: 906 sheet: 0.24 (0.28), residues: 363 loop : -0.65 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 308 TYR 0.023 0.001 TYR K 56 PHE 0.023 0.001 PHE K 225 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00333 (17195) covalent geometry : angle 0.56130 (23357) hydrogen bonds : bond 0.04209 ( 787) hydrogen bonds : angle 4.15551 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7422 (tmm) cc_final: 0.6757 (ptp) REVERT: K 98 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7852 (pp30) REVERT: K 105 TYR cc_start: 0.7877 (t80) cc_final: 0.7349 (t80) REVERT: K 138 MET cc_start: 0.5091 (mpp) cc_final: 0.4864 (mpp) REVERT: K 209 ASN cc_start: 0.8454 (t0) cc_final: 0.8101 (t0) REVERT: K 240 LYS cc_start: 0.7763 (ptmm) cc_final: 0.7340 (tptt) REVERT: K 248 ASP cc_start: 0.7983 (t0) cc_final: 0.7693 (t0) REVERT: K 327 MET cc_start: 0.7725 (ttp) cc_final: 0.7511 (ttm) REVERT: A 218 ASP cc_start: 0.9111 (t0) cc_final: 0.8885 (t0) REVERT: A 338 LYS cc_start: 0.9110 (tttt) cc_final: 0.8876 (tppt) REVERT: B 213 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8320 (mtm-85) REVERT: B 257 MET cc_start: 0.8696 (mmm) cc_final: 0.8350 (mmm) REVERT: B 291 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8081 (tp-100) REVERT: E 127 ASP cc_start: 0.9014 (m-30) cc_final: 0.8764 (m-30) REVERT: E 322 ASP cc_start: 0.8772 (t0) cc_final: 0.8490 (t0) REVERT: E 339 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8549 (tpp80) REVERT: E 434 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7786 (mm-30) REVERT: I 31 ASP cc_start: 0.8583 (t70) cc_final: 0.8110 (t70) REVERT: I 67 ASP cc_start: 0.8869 (t0) cc_final: 0.8513 (t0) REVERT: I 118 ASP cc_start: 0.8994 (t0) cc_final: 0.8581 (m-30) REVERT: I 295 ASP cc_start: 0.8894 (t0) cc_final: 0.8364 (t0) REVERT: I 297 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8917 (mtmm) REVERT: I 304 ASP cc_start: 0.8502 (t0) cc_final: 0.8269 (t0) REVERT: I 376 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8270 (mm-30) REVERT: I 426 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8292 (tm-30) outliers start: 27 outliers final: 18 residues processed: 311 average time/residue: 0.1293 time to fit residues: 61.9636 Evaluate side-chains 299 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 281 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain I residue 188 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068011 restraints weight = 32289.958| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.83 r_work: 0.2950 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17195 Z= 0.293 Angle : 0.651 8.162 23357 Z= 0.331 Chirality : 0.048 0.293 2560 Planarity : 0.005 0.082 3030 Dihedral : 9.350 176.109 2595 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 2.04 % Allowed : 14.09 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.19), residues: 2100 helix: 1.78 (0.17), residues: 899 sheet: 0.13 (0.28), residues: 363 loop : -0.79 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 13 TYR 0.025 0.002 TYR K 56 PHE 0.033 0.002 PHE K 225 TRP 0.013 0.002 TRP A 21 HIS 0.006 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00682 (17195) covalent geometry : angle 0.65103 (23357) hydrogen bonds : bond 0.05430 ( 787) hydrogen bonds : angle 4.46677 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 PHE cc_start: 0.8138 (m-80) cc_final: 0.7308 (m-80) REVERT: K 107 MET cc_start: 0.7633 (mmp) cc_final: 0.7216 (mmp) REVERT: K 138 MET cc_start: 0.5159 (mpp) cc_final: 0.4852 (mpp) REVERT: K 248 ASP cc_start: 0.8140 (t0) cc_final: 0.7898 (t0) REVERT: K 327 MET cc_start: 0.8021 (ttp) cc_final: 0.7806 (ttm) REVERT: A 102 ASN cc_start: 0.8803 (t0) cc_final: 0.8392 (t0) REVERT: A 121 ARG cc_start: 0.6920 (tpt-90) cc_final: 0.6581 (tpt-90) REVERT: A 218 ASP cc_start: 0.9097 (t0) cc_final: 0.8824 (t0) REVERT: A 254 GLU cc_start: 0.4402 (tp30) cc_final: 0.2370 (tp30) REVERT: A 338 LYS cc_start: 0.9136 (tttt) cc_final: 0.8870 (tppt) REVERT: B 3 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 291 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8110 (tp-100) REVERT: B 295 ASP cc_start: 0.9031 (t0) cc_final: 0.8787 (t0) REVERT: E 1 MET cc_start: 0.7634 (pmm) cc_final: 0.7390 (ptt) REVERT: E 127 ASP cc_start: 0.9046 (m-30) cc_final: 0.8794 (m-30) REVERT: E 168 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8375 (mm-30) REVERT: E 245 ASP cc_start: 0.8632 (p0) cc_final: 0.8352 (p0) REVERT: E 322 ASP cc_start: 0.8821 (t0) cc_final: 0.8485 (t0) REVERT: E 339 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8527 (tpp80) REVERT: I 31 ASP cc_start: 0.8655 (t70) cc_final: 0.8229 (t70) REVERT: I 67 ASP cc_start: 0.8962 (t0) cc_final: 0.8571 (t0) REVERT: I 118 ASP cc_start: 0.9012 (t0) cc_final: 0.8627 (m-30) REVERT: I 170 MET cc_start: 0.8627 (mtt) cc_final: 0.8394 (mtt) REVERT: I 295 ASP cc_start: 0.8916 (t0) cc_final: 0.8456 (t0) REVERT: I 297 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8989 (mtmm) REVERT: I 304 ASP cc_start: 0.8600 (t0) cc_final: 0.8394 (t0) REVERT: I 347 ASN cc_start: 0.8828 (t0) cc_final: 0.8550 (t0) REVERT: I 376 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8402 (mm-30) outliers start: 37 outliers final: 23 residues processed: 300 average time/residue: 0.1381 time to fit residues: 63.0154 Evaluate side-chains 295 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 188 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.070532 restraints weight = 31910.391| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.84 r_work: 0.3002 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17195 Z= 0.155 Angle : 0.575 8.838 23357 Z= 0.287 Chirality : 0.044 0.265 2560 Planarity : 0.004 0.079 3030 Dihedral : 9.113 174.739 2595 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 1.66 % Allowed : 14.53 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 2100 helix: 1.95 (0.18), residues: 901 sheet: 0.09 (0.28), residues: 369 loop : -0.73 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 13 TYR 0.016 0.001 TYR K 56 PHE 0.030 0.001 PHE K 225 TRP 0.012 0.001 TRP E 21 HIS 0.004 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00357 (17195) covalent geometry : angle 0.57544 (23357) hydrogen bonds : bond 0.04387 ( 787) hydrogen bonds : angle 4.24604 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7446 (tmm) cc_final: 0.6172 (mtt) REVERT: K 50 PHE cc_start: 0.8076 (m-80) cc_final: 0.7258 (m-80) REVERT: K 107 MET cc_start: 0.7628 (mmp) cc_final: 0.7221 (mmp) REVERT: K 138 MET cc_start: 0.5163 (mpp) cc_final: 0.4483 (mpp) REVERT: K 209 ASN cc_start: 0.8635 (t0) cc_final: 0.8360 (t0) REVERT: K 248 ASP cc_start: 0.8096 (t0) cc_final: 0.7860 (t0) REVERT: A 1 MET cc_start: 0.7288 (tmm) cc_final: 0.7068 (tmm) REVERT: A 121 ARG cc_start: 0.6759 (tpt-90) cc_final: 0.6452 (tpt-90) REVERT: A 218 ASP cc_start: 0.9081 (t0) cc_final: 0.8802 (t0) REVERT: A 338 LYS cc_start: 0.9104 (tttt) cc_final: 0.8833 (tppt) REVERT: B 213 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8161 (mtm-85) REVERT: B 257 MET cc_start: 0.8712 (mmm) cc_final: 0.8407 (mmm) REVERT: B 291 GLN cc_start: 0.8495 (tp-100) cc_final: 0.8099 (tp-100) REVERT: B 295 ASP cc_start: 0.8925 (t0) cc_final: 0.8646 (t0) REVERT: E 127 ASP cc_start: 0.9001 (m-30) cc_final: 0.8787 (m-30) REVERT: E 154 MET cc_start: 0.9212 (mmm) cc_final: 0.8875 (mmm) REVERT: E 168 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8306 (mm-30) REVERT: E 245 ASP cc_start: 0.8609 (p0) cc_final: 0.8299 (p0) REVERT: E 322 ASP cc_start: 0.8796 (t0) cc_final: 0.8494 (t0) REVERT: E 339 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8543 (tpp80) REVERT: E 434 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7857 (mm-30) REVERT: I 31 ASP cc_start: 0.8635 (t70) cc_final: 0.8193 (t70) REVERT: I 67 ASP cc_start: 0.8929 (t0) cc_final: 0.8518 (t0) REVERT: I 118 ASP cc_start: 0.8999 (t0) cc_final: 0.8593 (m-30) REVERT: I 295 ASP cc_start: 0.8899 (t0) cc_final: 0.8362 (t0) REVERT: I 297 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8920 (mtmm) REVERT: I 304 ASP cc_start: 0.8567 (t0) cc_final: 0.8348 (t0) REVERT: I 347 ASN cc_start: 0.8769 (t0) cc_final: 0.8493 (t0) REVERT: I 376 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8349 (mm-30) REVERT: I 426 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8434 (tm-30) outliers start: 30 outliers final: 23 residues processed: 308 average time/residue: 0.1336 time to fit residues: 62.8073 Evaluate side-chains 304 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 308 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 274 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 60 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 GLN K 162 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069309 restraints weight = 31976.785| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.84 r_work: 0.2981 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17195 Z= 0.202 Angle : 0.600 8.986 23357 Z= 0.300 Chirality : 0.045 0.241 2560 Planarity : 0.004 0.078 3030 Dihedral : 9.136 175.502 2595 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 2.38 % Allowed : 14.20 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.19), residues: 2100 helix: 1.92 (0.18), residues: 901 sheet: -0.13 (0.27), residues: 379 loop : -0.72 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 13 TYR 0.014 0.001 TYR K 56 PHE 0.032 0.001 PHE K 225 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00469 (17195) covalent geometry : angle 0.60030 (23357) hydrogen bonds : bond 0.04680 ( 787) hydrogen bonds : angle 4.28073 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7506 (tmm) cc_final: 0.6183 (mtt) REVERT: K 107 MET cc_start: 0.7668 (mmp) cc_final: 0.7377 (mmp) REVERT: K 138 MET cc_start: 0.5211 (mpp) cc_final: 0.4455 (mpp) REVERT: K 209 ASN cc_start: 0.8645 (t0) cc_final: 0.8427 (t0) REVERT: K 248 ASP cc_start: 0.8125 (t0) cc_final: 0.7868 (t0) REVERT: A 121 ARG cc_start: 0.6831 (tpt-90) cc_final: 0.6540 (tpt-90) REVERT: A 218 ASP cc_start: 0.9090 (t0) cc_final: 0.8767 (t70) REVERT: A 254 GLU cc_start: 0.4244 (tp30) cc_final: 0.2103 (tp30) REVERT: A 306 ASP cc_start: 0.8679 (t0) cc_final: 0.8461 (t0) REVERT: A 338 LYS cc_start: 0.9098 (tttt) cc_final: 0.8815 (tppt) REVERT: B 257 MET cc_start: 0.8764 (mmm) cc_final: 0.8419 (mmm) REVERT: B 291 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8124 (tp-100) REVERT: B 295 ASP cc_start: 0.8949 (t0) cc_final: 0.8655 (t0) REVERT: E 49 PHE cc_start: 0.7997 (m-80) cc_final: 0.7638 (m-10) REVERT: E 127 ASP cc_start: 0.8999 (m-30) cc_final: 0.8756 (m-30) REVERT: E 245 ASP cc_start: 0.8632 (p0) cc_final: 0.8334 (p0) REVERT: E 322 ASP cc_start: 0.8825 (t0) cc_final: 0.8526 (t0) REVERT: E 339 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8539 (tpp80) REVERT: E 434 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7908 (mm-30) REVERT: I 31 ASP cc_start: 0.8646 (t70) cc_final: 0.8205 (t70) REVERT: I 67 ASP cc_start: 0.8945 (t0) cc_final: 0.8529 (t0) REVERT: I 118 ASP cc_start: 0.9007 (t0) cc_final: 0.8598 (m-30) REVERT: I 295 ASP cc_start: 0.8905 (t0) cc_final: 0.8375 (t0) REVERT: I 297 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8934 (mtmm) REVERT: I 304 ASP cc_start: 0.8595 (t0) cc_final: 0.8380 (t0) REVERT: I 347 ASN cc_start: 0.8785 (t0) cc_final: 0.8511 (t0) REVERT: I 376 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8368 (mm-30) REVERT: I 426 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8441 (tm-30) outliers start: 43 outliers final: 29 residues processed: 309 average time/residue: 0.1331 time to fit residues: 62.7216 Evaluate side-chains 301 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 274 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 147 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 197 HIS A 256 GLN I 334 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072791 restraints weight = 31513.427| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.86 r_work: 0.3048 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17195 Z= 0.113 Angle : 0.568 9.170 23357 Z= 0.280 Chirality : 0.043 0.212 2560 Planarity : 0.004 0.077 3030 Dihedral : 8.841 172.925 2595 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.33 % Allowed : 15.30 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 2100 helix: 2.12 (0.18), residues: 898 sheet: -0.01 (0.27), residues: 379 loop : -0.67 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 308 TYR 0.013 0.001 TYR K 89 PHE 0.023 0.001 PHE K 225 TRP 0.021 0.001 TRP E 388 HIS 0.002 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00245 (17195) covalent geometry : angle 0.56783 (23357) hydrogen bonds : bond 0.03732 ( 787) hydrogen bonds : angle 4.09581 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 316 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7530 (tmm) cc_final: 0.6091 (mtt) REVERT: K 107 MET cc_start: 0.7628 (mmp) cc_final: 0.7373 (mmp) REVERT: K 138 MET cc_start: 0.5182 (mpp) cc_final: 0.4332 (mpp) REVERT: K 248 ASP cc_start: 0.8106 (t0) cc_final: 0.7797 (t0) REVERT: A 218 ASP cc_start: 0.9014 (t0) cc_final: 0.8721 (t70) REVERT: A 306 ASP cc_start: 0.8610 (t0) cc_final: 0.8385 (t0) REVERT: A 338 LYS cc_start: 0.9021 (tttt) cc_final: 0.8740 (tppt) REVERT: A 392 ASP cc_start: 0.9044 (m-30) cc_final: 0.8778 (t0) REVERT: B 1 MET cc_start: 0.7976 (mpp) cc_final: 0.7230 (pmm) REVERT: B 136 THR cc_start: 0.9238 (m) cc_final: 0.8983 (p) REVERT: B 213 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8401 (mtm-85) REVERT: B 257 MET cc_start: 0.8565 (mmm) cc_final: 0.8281 (mmm) REVERT: B 291 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8106 (tp-100) REVERT: B 295 ASP cc_start: 0.8874 (t0) cc_final: 0.8564 (t0) REVERT: E 49 PHE cc_start: 0.7607 (m-80) cc_final: 0.7294 (m-10) REVERT: E 154 MET cc_start: 0.9203 (mmm) cc_final: 0.8930 (mmm) REVERT: E 168 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: E 245 ASP cc_start: 0.8608 (p0) cc_final: 0.8039 (p0) REVERT: E 322 ASP cc_start: 0.8793 (t0) cc_final: 0.8537 (t0) REVERT: E 339 ARG cc_start: 0.8792 (tpp80) cc_final: 0.8573 (tpp80) REVERT: E 434 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7845 (mm-30) REVERT: I 31 ASP cc_start: 0.8613 (t70) cc_final: 0.8158 (t70) REVERT: I 67 ASP cc_start: 0.8875 (t0) cc_final: 0.8428 (t0) REVERT: I 118 ASP cc_start: 0.8972 (t0) cc_final: 0.8566 (m-30) REVERT: I 288 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8637 (mm-30) REVERT: I 295 ASP cc_start: 0.8906 (t0) cc_final: 0.8352 (t0) REVERT: I 297 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8941 (mtmm) REVERT: I 304 ASP cc_start: 0.8553 (t0) cc_final: 0.8326 (t0) REVERT: I 376 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8165 (mm-30) REVERT: I 407 GLU cc_start: 0.8448 (tt0) cc_final: 0.8194 (mt-10) REVERT: I 426 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8438 (tm-30) outliers start: 24 outliers final: 18 residues processed: 333 average time/residue: 0.1376 time to fit residues: 69.1372 Evaluate side-chains 317 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 298 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 274 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 10 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072842 restraints weight = 31450.208| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.85 r_work: 0.3050 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17195 Z= 0.117 Angle : 0.574 9.168 23357 Z= 0.282 Chirality : 0.043 0.205 2560 Planarity : 0.004 0.077 3030 Dihedral : 8.733 171.852 2595 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.44 % Allowed : 15.52 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.19), residues: 2100 helix: 2.17 (0.18), residues: 901 sheet: 0.07 (0.28), residues: 379 loop : -0.63 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 308 TYR 0.028 0.001 TYR K 56 PHE 0.026 0.001 PHE K 225 TRP 0.013 0.001 TRP K 57 HIS 0.004 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00264 (17195) covalent geometry : angle 0.57411 (23357) hydrogen bonds : bond 0.03731 ( 787) hydrogen bonds : angle 4.01377 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7440 (tmm) cc_final: 0.6036 (mtt) REVERT: K 76 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8200 (p0) REVERT: K 107 MET cc_start: 0.7679 (mmp) cc_final: 0.7309 (mmp) REVERT: K 138 MET cc_start: 0.5176 (mpp) cc_final: 0.4341 (mpp) REVERT: K 248 ASP cc_start: 0.8104 (t0) cc_final: 0.7786 (t0) REVERT: A 49 PHE cc_start: 0.7383 (m-10) cc_final: 0.7158 (m-80) REVERT: A 218 ASP cc_start: 0.8998 (t0) cc_final: 0.8712 (t70) REVERT: A 254 GLU cc_start: 0.4206 (tp30) cc_final: 0.2144 (tp30) REVERT: A 306 ASP cc_start: 0.8556 (t0) cc_final: 0.8332 (t0) REVERT: A 338 LYS cc_start: 0.9008 (tttt) cc_final: 0.8770 (tppt) REVERT: A 392 ASP cc_start: 0.9069 (m-30) cc_final: 0.8778 (t0) REVERT: B 1 MET cc_start: 0.8061 (mpp) cc_final: 0.7291 (pmm) REVERT: B 136 THR cc_start: 0.9218 (m) cc_final: 0.9007 (p) REVERT: B 213 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8381 (mtm-85) REVERT: B 257 MET cc_start: 0.8576 (mmm) cc_final: 0.8298 (mmm) REVERT: B 291 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8092 (tp-100) REVERT: B 295 ASP cc_start: 0.8862 (t0) cc_final: 0.8542 (t0) REVERT: B 409 THR cc_start: 0.8959 (m) cc_final: 0.8659 (p) REVERT: E 154 MET cc_start: 0.9206 (mmm) cc_final: 0.8850 (mmm) REVERT: E 168 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: E 245 ASP cc_start: 0.8485 (p0) cc_final: 0.8207 (p0) REVERT: E 322 ASP cc_start: 0.8779 (t0) cc_final: 0.8544 (t0) REVERT: E 339 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8565 (tpp80) REVERT: E 434 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7838 (mm-30) REVERT: I 31 ASP cc_start: 0.8627 (t70) cc_final: 0.8173 (t70) REVERT: I 67 ASP cc_start: 0.8871 (t0) cc_final: 0.8448 (t0) REVERT: I 118 ASP cc_start: 0.8964 (t0) cc_final: 0.8555 (m-30) REVERT: I 288 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8623 (mm-30) REVERT: I 295 ASP cc_start: 0.8872 (t0) cc_final: 0.8289 (t0) REVERT: I 297 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8915 (mtmm) REVERT: I 304 ASP cc_start: 0.8534 (t0) cc_final: 0.8287 (t0) REVERT: I 376 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8126 (mm-30) REVERT: I 407 GLU cc_start: 0.8432 (tt0) cc_final: 0.8188 (mt-10) REVERT: I 426 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 26 outliers final: 22 residues processed: 325 average time/residue: 0.1394 time to fit residues: 68.7505 Evaluate side-chains 321 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 308 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 104 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 131 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 207 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.095788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073981 restraints weight = 31265.654| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.85 r_work: 0.3072 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17195 Z= 0.110 Angle : 0.581 9.617 23357 Z= 0.286 Chirality : 0.043 0.200 2560 Planarity : 0.004 0.077 3030 Dihedral : 8.641 170.465 2595 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.22 % Allowed : 15.91 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 2100 helix: 2.18 (0.18), residues: 900 sheet: 0.15 (0.28), residues: 377 loop : -0.68 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 308 TYR 0.057 0.001 TYR K 56 PHE 0.021 0.001 PHE K 225 TRP 0.011 0.001 TRP I 344 HIS 0.012 0.001 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00245 (17195) covalent geometry : angle 0.58130 (23357) hydrogen bonds : bond 0.03542 ( 787) hydrogen bonds : angle 4.00474 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 325 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7320 (tmm) cc_final: 0.5888 (mtm) REVERT: K 50 PHE cc_start: 0.7955 (m-80) cc_final: 0.7065 (m-80) REVERT: K 76 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (p0) REVERT: K 107 MET cc_start: 0.7706 (mmp) cc_final: 0.7371 (mmp) REVERT: K 138 MET cc_start: 0.5166 (mpp) cc_final: 0.4176 (mpp) REVERT: K 248 ASP cc_start: 0.8108 (t0) cc_final: 0.7778 (t0) REVERT: A 127 ASP cc_start: 0.8845 (m-30) cc_final: 0.8632 (m-30) REVERT: A 218 ASP cc_start: 0.8993 (t0) cc_final: 0.8720 (t70) REVERT: A 254 GLU cc_start: 0.4325 (tp30) cc_final: 0.2671 (tp30) REVERT: A 306 ASP cc_start: 0.8507 (t0) cc_final: 0.8263 (t0) REVERT: A 338 LYS cc_start: 0.9040 (tttt) cc_final: 0.8815 (tppt) REVERT: A 392 ASP cc_start: 0.9074 (m-30) cc_final: 0.8787 (t0) REVERT: B 1 MET cc_start: 0.8020 (mpp) cc_final: 0.7318 (pmm) REVERT: B 67 ASP cc_start: 0.8214 (t0) cc_final: 0.7996 (t0) REVERT: B 213 ARG cc_start: 0.8783 (tpp80) cc_final: 0.8446 (mtm-85) REVERT: B 257 MET cc_start: 0.8506 (mmm) cc_final: 0.8270 (mmm) REVERT: B 291 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8043 (tp-100) REVERT: B 295 ASP cc_start: 0.8858 (t0) cc_final: 0.8536 (t0) REVERT: B 409 THR cc_start: 0.8960 (m) cc_final: 0.8679 (p) REVERT: E 245 ASP cc_start: 0.8447 (p0) cc_final: 0.8185 (p0) REVERT: E 322 ASP cc_start: 0.8782 (t0) cc_final: 0.8507 (t0) REVERT: E 339 ARG cc_start: 0.8792 (tpp80) cc_final: 0.8580 (tpp80) REVERT: E 434 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7811 (mm-30) REVERT: E 437 VAL cc_start: 0.8712 (t) cc_final: 0.8506 (p) REVERT: I 3 GLU cc_start: 0.8168 (mp0) cc_final: 0.7728 (mp0) REVERT: I 31 ASP cc_start: 0.8627 (t70) cc_final: 0.8169 (t70) REVERT: I 67 ASP cc_start: 0.8876 (t0) cc_final: 0.8414 (t0) REVERT: I 118 ASP cc_start: 0.8950 (t0) cc_final: 0.8547 (m-30) REVERT: I 195 ASN cc_start: 0.8974 (m-40) cc_final: 0.8762 (m-40) REVERT: I 288 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8582 (mm-30) REVERT: I 295 ASP cc_start: 0.8848 (t0) cc_final: 0.8224 (t0) REVERT: I 297 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8895 (mtmm) REVERT: I 304 ASP cc_start: 0.8522 (t0) cc_final: 0.8261 (t0) REVERT: I 376 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8134 (mm-30) REVERT: I 407 GLU cc_start: 0.8424 (tt0) cc_final: 0.8153 (mt-10) REVERT: I 426 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8409 (tm-30) outliers start: 22 outliers final: 16 residues processed: 336 average time/residue: 0.1338 time to fit residues: 67.8446 Evaluate side-chains 326 residues out of total 1810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 309 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 71 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 160 optimal weight: 0.0670 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072962 restraints weight = 31299.106| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.83 r_work: 0.3050 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17195 Z= 0.128 Angle : 0.592 10.330 23357 Z= 0.291 Chirality : 0.044 0.196 2560 Planarity : 0.004 0.077 3030 Dihedral : 8.648 169.481 2595 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.49 % Allowed : 16.19 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.19), residues: 2100 helix: 2.19 (0.18), residues: 900 sheet: 0.11 (0.28), residues: 379 loop : -0.64 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 308 TYR 0.031 0.001 TYR K 56 PHE 0.023 0.001 PHE K 225 TRP 0.016 0.001 TRP K 57 HIS 0.012 0.001 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00292 (17195) covalent geometry : angle 0.59195 (23357) hydrogen bonds : bond 0.03769 ( 787) hydrogen bonds : angle 4.02507 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.32 seconds wall clock time: 61 minutes 54.85 seconds (3714.85 seconds total)