Starting phenix.real_space_refine on Sat Jan 25 06:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypt_39493/01_2025/8ypt_39493_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypt_39493/01_2025/8ypt_39493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ypt_39493/01_2025/8ypt_39493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypt_39493/01_2025/8ypt_39493.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypt_39493/01_2025/8ypt_39493_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypt_39493/01_2025/8ypt_39493_neut.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.283 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 14633 2.51 5 N 3936 2.21 5 O 4439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23068 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3377 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 20, 'TRANS': 402} Chain: "B" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3377 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 20, 'TRANS': 402} Chain: "C" Number of atoms: 7850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7850 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 38, 'TRANS': 947} Chain: "D" Number of atoms: 7850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7850 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 38, 'TRANS': 947} Chain: "E" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 614 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 46 residue: pdb=" N ASN A 67 " occ=0.74 ... (6 atoms not shown) pdb=" ND2 ASN A 67 " occ=0.71 residue: pdb=" N ASP A 72 " occ=0.47 ... (6 atoms not shown) pdb=" OD2 ASP A 72 " occ=0.29 residue: pdb=" N SER A 158 " occ=0.95 ... (4 atoms not shown) pdb=" OG SER A 158 " occ=0.49 residue: pdb=" N ASP A 215 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP A 215 " occ=0.20 residue: pdb=" N GLY A 226 " occ=0.44 ... (2 atoms not shown) pdb=" O GLY A 226 " occ=0.44 residue: pdb=" N SER A 234 " occ=0.28 ... (4 atoms not shown) pdb=" OG SER A 234 " occ=0.33 residue: pdb=" N ALA A 235 " occ=0.55 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.80 residue: pdb=" N MET A 248 " occ=0.43 ... (6 atoms not shown) pdb=" CE MET A 248 " occ=0.89 residue: pdb=" N THR A 266 " occ=0.29 ... (5 atoms not shown) pdb=" CG2 THR A 266 " occ=0.46 residue: pdb=" N LEU A 289 " occ=0.72 ... (6 atoms not shown) pdb=" CD2 LEU A 289 " occ=0.74 residue: pdb=" N TYR A 290 " occ=0.40 ... (10 atoms not shown) pdb=" OH TYR A 290 " occ=0.23 residue: pdb=" N GLY A 308 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY A 308 " occ=0.78 ... (remaining 34 not shown) Time building chain proxies: 12.30, per 1000 atoms: 0.53 Number of scatterers: 23068 At special positions: 0 Unit cell: (127.44, 129.8, 147.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 4439 8.00 N 3936 7.00 C 14633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 70 " - pdb=" SG CYS E 76 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 3.0 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 26 sheets defined 31.5% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.441A pdb=" N LEU A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.793A pdb=" N SER A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 120 through 147 removed outlier: 3.598A pdb=" N GLN A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 210 through 226 Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 283 through 290 removed outlier: 3.590A pdb=" N TYR A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 4.060A pdb=" N ALA A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.743A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.622A pdb=" N THR A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.609A pdb=" N ASP B 24 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.660A pdb=" N ALA B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 Processing helix chain 'B' and resid 69 through 81 removed outlier: 4.061A pdb=" N SER B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.975A pdb=" N ILE B 116 " --> pdb=" O GLN B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 120 through 147 Processing helix chain 'B' and resid 178 through 196 Processing helix chain 'B' and resid 210 through 226 Processing helix chain 'B' and resid 227 through 242 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.511A pdb=" N PHE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.674A pdb=" N SER B 321 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.710A pdb=" N MET B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.597A pdb=" N LYS B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 371 Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 395 through 404 removed outlier: 3.742A pdb=" N THR B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.705A pdb=" N THR B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.908A pdb=" N VAL C 213 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 216 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 243 through 248 removed outlier: 6.928A pdb=" N ALA C 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 248 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 4.229A pdb=" N ARG C 283 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.912A pdb=" N TYR C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.862A pdb=" N LYS C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.813A pdb=" N ASP C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 530 through 540 removed outlier: 3.643A pdb=" N ILE C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 632 Processing helix chain 'C' and resid 694 through 704 Proline residue: C 697 - end of helix removed outlier: 3.543A pdb=" N GLN C 700 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY C 701 " --> pdb=" O PHE C 698 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 703 " --> pdb=" O GLN C 700 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS C 704 " --> pdb=" O GLY C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 980 through 986 removed outlier: 3.583A pdb=" N LEU C 984 " --> pdb=" O SER C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1015 Processing helix chain 'C' and resid 1016 through 1021 removed outlier: 3.612A pdb=" N LYS C1020 " --> pdb=" O SER C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1022 through 1024 No H-bonds generated for 'chain 'C' and resid 1022 through 1024' Processing helix chain 'C' and resid 1044 through 1052 Processing helix chain 'C' and resid 1077 through 1081 removed outlier: 3.692A pdb=" N MET C1081 " --> pdb=" O PRO C1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 209 through 213 removed outlier: 4.259A pdb=" N VAL D 213 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 243 through 248 removed outlier: 6.860A pdb=" N ALA D 246 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.101A pdb=" N ARG D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.508A pdb=" N TYR D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 331 through 334 Processing helix chain 'D' and resid 335 through 348 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 476 through 483 Processing helix chain 'D' and resid 530 through 540 Processing helix chain 'D' and resid 676 through 680 Processing helix chain 'D' and resid 694 through 703 Proline residue: D 697 - end of helix removed outlier: 4.744A pdb=" N GLY D 701 " --> pdb=" O PHE D 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 703 " --> pdb=" O GLN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 803 Processing helix chain 'D' and resid 895 through 901 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 980 through 986 removed outlier: 3.794A pdb=" N ILE D 983 " --> pdb=" O ASN D 980 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 984 " --> pdb=" O SER D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1015 removed outlier: 3.617A pdb=" N GLN D1014 " --> pdb=" O TYR D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1021 removed outlier: 3.697A pdb=" N LYS D1020 " --> pdb=" O SER D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1024 No H-bonds generated for 'chain 'D' and resid 1022 through 1024' Processing helix chain 'D' and resid 1044 through 1051 Processing helix chain 'D' and resid 1077 through 1081 removed outlier: 3.962A pdb=" N MET D1081 " --> pdb=" O PRO D1078 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 removed outlier: 5.883A pdb=" N ASN A 176 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 264 through 266 removed outlier: 6.478A pdb=" N PHE A 324 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 412 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.115A pdb=" N ASN B 176 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 266 removed outlier: 6.536A pdb=" N PHE B 324 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 408 through 412 Processing sheet with id=AA9, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 138 removed outlier: 6.178A pdb=" N LEU C 191 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE C 255 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 193 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR C 257 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AB3, first strand: chain 'C' and resid 847 through 850 removed outlier: 5.175A pdb=" N VAL C 848 " --> pdb=" O VAL C 815 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 815 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 850 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER C 806 " --> pdb=" O MET C 797 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET C 797 " --> pdb=" O SER C 806 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN C 808 " --> pdb=" O LYS C 795 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS C 795 " --> pdb=" O ASN C 808 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN C 810 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 793 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA C 812 " --> pdb=" O ASP C 791 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY C 558 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN C 388 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE C 361 " --> pdb=" O ASN C 388 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY C 372 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LYS C 264 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 847 through 850 removed outlier: 5.175A pdb=" N VAL C 848 " --> pdb=" O VAL C 815 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 815 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 850 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TRP C 835 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 829 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER C 955 " --> pdb=" O LEU C1034 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C1034 " --> pdb=" O SER C 955 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASN C 957 " --> pdb=" O PHE C1032 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE C1032 " --> pdb=" O ASN C 957 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY C 959 " --> pdb=" O ASN C1030 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN C1030 " --> pdb=" O GLY C 959 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR C 961 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS C1028 " --> pdb=" O TYR C 961 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG C 963 " --> pdb=" O VAL C1026 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C1026 " --> pdb=" O ARG C 963 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 541 through 544 removed outlier: 3.678A pdb=" N SER C 549 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 730 through 736 removed outlier: 6.861A pdb=" N LEU C 730 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 869 through 872 removed outlier: 6.810A pdb=" N ILE C 870 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 875 through 878 removed outlier: 7.795A pdb=" N THR C 875 " --> pdb=" O TYR C 887 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR C 887 " --> pdb=" O THR C 875 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 877 " --> pdb=" O LEU C 885 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AC1, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.578A pdb=" N ASN D 231 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU D 191 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE D 255 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 193 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR D 257 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 161 through 165 Processing sheet with id=AC3, first strand: chain 'D' and resid 1067 through 1069 removed outlier: 4.994A pdb=" N LYS D 264 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY D 372 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE D 361 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN D 388 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY D 558 " --> pdb=" O GLY D 610 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA D 812 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 793 " --> pdb=" O ASN D 810 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN D 810 " --> pdb=" O ILE D 793 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS D 795 " --> pdb=" O ASN D 808 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN D 808 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET D 797 " --> pdb=" O SER D 806 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER D 806 " --> pdb=" O MET D 797 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER D 813 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP D 835 " --> pdb=" O ASN D 827 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA D 829 " --> pdb=" O PHE D 833 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER D 955 " --> pdb=" O LEU D1034 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU D1034 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN D 957 " --> pdb=" O PHE D1032 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE D1032 " --> pdb=" O ASN D 957 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 959 " --> pdb=" O ASN D1030 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN D1030 " --> pdb=" O GLY D 959 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR D 961 " --> pdb=" O LYS D1028 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS D1028 " --> pdb=" O TYR D 961 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG D 963 " --> pdb=" O VAL D1026 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D1026 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 541 through 544 Processing sheet with id=AC5, first strand: chain 'D' and resid 730 through 734 removed outlier: 6.661A pdb=" N LEU D 730 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 869 through 872 removed outlier: 6.764A pdb=" N ILE D 870 " --> pdb=" O ILE D 928 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 875 through 878 removed outlier: 7.813A pdb=" N THR D 875 " --> pdb=" O TYR D 887 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR D 887 " --> pdb=" O THR D 875 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY D 877 " --> pdb=" O LEU D 885 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 12 through 16 removed outlier: 9.012A pdb=" N ILE E 67 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE E 4 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE E 69 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS E 6 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE E 71 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 48 " --> pdb=" O TYR E 45 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.64 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3884 1.27 - 1.40: 5952 1.40 - 1.54: 13466 1.54 - 1.68: 157 1.68 - 1.81: 110 Bond restraints: 23569 Sorted by residual: bond pdb=" C ILE E 69 " pdb=" O ILE E 69 " ideal model delta sigma weight residual 1.236 1.134 0.102 1.02e-02 9.61e+03 1.00e+02 bond pdb=" CA ILE E 69 " pdb=" C ILE E 69 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.18e-02 7.18e+03 2.15e+01 bond pdb=" N LEU C 739 " pdb=" CA LEU C 739 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.02e+01 bond pdb=" N VAL C 204 " pdb=" CA VAL C 204 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.60e-03 1.73e+04 2.00e+01 bond pdb=" C LEU E 68 " pdb=" N ILE E 69 " ideal model delta sigma weight residual 1.331 1.273 0.057 1.40e-02 5.10e+03 1.68e+01 ... (remaining 23564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 31458 2.00 - 4.00: 413 4.00 - 6.00: 67 6.00 - 8.01: 11 8.01 - 10.01: 7 Bond angle restraints: 31956 Sorted by residual: angle pdb=" N ASN D 467 " pdb=" CA ASN D 467 " pdb=" C ASN D 467 " ideal model delta sigma weight residual 109.62 101.90 7.72 1.50e+00 4.44e-01 2.65e+01 angle pdb=" N LEU D 709 " pdb=" CA LEU D 709 " pdb=" C LEU D 709 " ideal model delta sigma weight residual 107.61 98.74 8.87 1.74e+00 3.30e-01 2.60e+01 angle pdb=" N LEU C 709 " pdb=" CA LEU C 709 " pdb=" C LEU C 709 " ideal model delta sigma weight residual 107.61 98.85 8.76 1.74e+00 3.30e-01 2.53e+01 angle pdb=" N ASP C 472 " pdb=" CA ASP C 472 " pdb=" C ASP C 472 " ideal model delta sigma weight residual 114.62 109.39 5.23 1.14e+00 7.69e-01 2.10e+01 angle pdb=" C LEU D 709 " pdb=" CA LEU D 709 " pdb=" CB LEU D 709 " ideal model delta sigma weight residual 110.79 117.12 -6.33 1.39e+00 5.18e-01 2.07e+01 ... (remaining 31951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12392 17.90 - 35.80: 1338 35.80 - 53.70: 318 53.70 - 71.60: 60 71.60 - 89.50: 19 Dihedral angle restraints: 14127 sinusoidal: 5683 harmonic: 8444 Sorted by residual: dihedral pdb=" C ASP E 73 " pdb=" N ASP E 73 " pdb=" CA ASP E 73 " pdb=" CB ASP E 73 " ideal model delta harmonic sigma weight residual -122.60 -132.58 9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C ASN C 410 " pdb=" N ASN C 410 " pdb=" CA ASN C 410 " pdb=" CB ASN C 410 " ideal model delta harmonic sigma weight residual -122.60 -112.83 -9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C ASN C 215 " pdb=" N ASN C 215 " pdb=" CA ASN C 215 " pdb=" CB ASN C 215 " ideal model delta harmonic sigma weight residual -122.60 -131.01 8.41 0 2.50e+00 1.60e-01 1.13e+01 ... (remaining 14124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3131 0.076 - 0.152: 328 0.152 - 0.228: 20 0.228 - 0.304: 3 0.304 - 0.380: 3 Chirality restraints: 3485 Sorted by residual: chirality pdb=" CA ASN C 215 " pdb=" N ASN C 215 " pdb=" C ASN C 215 " pdb=" CB ASN C 215 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA MET B 340 " pdb=" N MET B 340 " pdb=" C MET B 340 " pdb=" CB MET B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE E 69 " pdb=" CA ILE E 69 " pdb=" CG1 ILE E 69 " pdb=" CG2 ILE E 69 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 3482 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 86 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 87 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 335 " 0.058 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO D 336 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 336 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 336 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 68 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C LEU E 68 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU E 68 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE E 69 " -0.014 2.00e-02 2.50e+03 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 790 2.71 - 3.26: 21493 3.26 - 3.81: 37016 3.81 - 4.35: 49657 4.35 - 4.90: 85942 Nonbonded interactions: 194898 Sorted by model distance: nonbonded pdb=" O GLU C 480 " pdb=" OG1 THR C 484 " model vdw 2.167 3.040 nonbonded pdb=" OG SER A 213 " pdb=" OG1 THR A 266 " model vdw 2.179 3.040 nonbonded pdb=" OH TYR B 290 " pdb=" O ARG B 388 " model vdw 2.185 3.040 nonbonded pdb=" OE1 GLN D 776 " pdb=" ND2 ASN D 779 " model vdw 2.198 3.120 nonbonded pdb=" O LEU A 297 " pdb=" NH1 ARG A 310 " model vdw 2.202 3.120 ... (remaining 194893 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.83 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.120 Set scattering table: 0.230 Process input model: 51.300 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.003 0.102 23569 Z= 0.227 Angle : 0.593 10.007 31956 Z= 0.344 Chirality : 0.047 0.380 3485 Planarity : 0.005 0.103 4158 Dihedral : 15.676 89.505 8726 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.80 % Allowed : 17.70 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2884 helix: 0.54 (0.20), residues: 729 sheet: 0.33 (0.17), residues: 856 loop : -0.02 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 96 HIS 0.004 0.001 HIS D 745 PHE 0.027 0.001 PHE D 503 TYR 0.026 0.001 TYR B 363 ARG 0.014 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 2.867 Fit side-chains revert: symmetry clash REVERT: B 329 LEU cc_start: 0.6053 (mm) cc_final: 0.5452 (mm) REVERT: B 354 MET cc_start: 0.6966 (mmm) cc_final: 0.6762 (mtp) REVERT: B 363 TYR cc_start: 0.3943 (t80) cc_final: 0.3582 (t80) REVERT: D 374 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: D 583 ASN cc_start: 0.8285 (m-40) cc_final: 0.8062 (m110) REVERT: D 1071 SER cc_start: 0.8551 (t) cc_final: 0.8348 (p) REVERT: E 71 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6221 (pt) outliers start: 20 outliers final: 9 residues processed: 338 average time/residue: 0.3963 time to fit residues: 204.1420 Evaluate side-chains 297 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 286 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain E residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 146 optimal weight: 0.0060 chunk 116 optimal weight: 3.9990 chunk 224 optimal weight: 0.0870 chunk 87 optimal weight: 0.0770 chunk 136 optimal weight: 0.0970 chunk 167 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.077259 restraints weight = 27603.399| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 1.41 r_work: 0.2632 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 301 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 335 | |-----------------------------------------------------------------------------| r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23569 Z= 0.155 Angle : 0.487 6.926 31956 Z= 0.263 Chirality : 0.043 0.181 3485 Planarity : 0.004 0.072 4158 Dihedral : 4.536 54.983 3228 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.47 % Allowed : 16.11 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2884 helix: 0.69 (0.20), residues: 747 sheet: 0.34 (0.17), residues: 834 loop : 0.13 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 96 HIS 0.004 0.001 HIS D 745 PHE 0.013 0.001 PHE D1032 TYR 0.022 0.001 TYR A 426 ARG 0.007 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 2.707 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7216 (t80) cc_final: 0.7013 (t80) REVERT: A 356 LYS cc_start: 0.7589 (mptp) cc_final: 0.7212 (mmtt) REVERT: B 329 LEU cc_start: 0.6300 (mm) cc_final: 0.5756 (mm) REVERT: B 363 TYR cc_start: 0.4754 (t80) cc_final: 0.4395 (t80) REVERT: C 316 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8342 (mt) REVERT: C 320 TYR cc_start: 0.8827 (m-10) cc_final: 0.8430 (m-10) REVERT: C 746 MET cc_start: 0.9140 (mtt) cc_final: 0.8888 (mtt) REVERT: D 282 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8125 (t0) REVERT: D 349 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: D 515 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 583 ASN cc_start: 0.8444 (m-40) cc_final: 0.8232 (m110) REVERT: D 704 LYS cc_start: 0.8096 (ptpp) cc_final: 0.7321 (mmtm) REVERT: D 850 ARG cc_start: 0.8343 (mmp-170) cc_final: 0.7657 (mmt180) outliers start: 62 outliers final: 34 residues processed: 355 average time/residue: 0.3729 time to fit residues: 204.2881 Evaluate side-chains 334 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 954 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN C 486 ASN C 524 GLN D 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.071873 restraints weight = 27656.034| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 1.27 r_work: 0.2513 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2414 r_free = 0.2414 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 335 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2391 r_free = 0.2391 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 327 | |-----------------------------------------------------------------------------| r_final: 0.2391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 23569 Z= 0.502 Angle : 0.635 7.447 31956 Z= 0.332 Chirality : 0.049 0.186 3485 Planarity : 0.005 0.060 4158 Dihedral : 4.852 57.043 3210 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.23 % Allowed : 16.11 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2884 helix: 0.32 (0.19), residues: 743 sheet: 0.21 (0.17), residues: 832 loop : -0.05 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 96 HIS 0.007 0.001 HIS D 635 PHE 0.023 0.002 PHE C 970 TYR 0.022 0.002 TYR A 426 ARG 0.009 0.001 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 2.583 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7350 (t80) cc_final: 0.7143 (t80) REVERT: A 272 MET cc_start: 0.8144 (mmt) cc_final: 0.7803 (mmt) REVERT: A 385 GLU cc_start: 0.7800 (tp30) cc_final: 0.7542 (tp30) REVERT: B 363 TYR cc_start: 0.5397 (t80) cc_final: 0.5150 (t80) REVERT: B 407 ARG cc_start: 0.7640 (ttt-90) cc_final: 0.7395 (ttt-90) REVERT: C 298 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: C 320 TYR cc_start: 0.9013 (m-10) cc_final: 0.8549 (m-10) REVERT: C 374 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: C 412 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8530 (mtp) REVERT: C 579 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8131 (mtt90) REVERT: D 282 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8187 (t0) REVERT: D 349 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: D 515 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.8907 (mt) outliers start: 81 outliers final: 57 residues processed: 332 average time/residue: 0.4019 time to fit residues: 202.3342 Evaluate side-chains 338 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 362 ASN Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 30 optimal weight: 0.9980 chunk 279 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN D 745 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.074294 restraints weight = 27600.444| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 1.32 r_work: 0.2532 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 327 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 352 | |-----------------------------------------------------------------------------| r_final: 0.2406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23569 Z= 0.208 Angle : 0.497 6.543 31956 Z= 0.265 Chirality : 0.043 0.186 3485 Planarity : 0.004 0.058 4158 Dihedral : 4.518 58.081 3210 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.35 % Allowed : 16.63 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2884 helix: 0.58 (0.19), residues: 753 sheet: 0.28 (0.17), residues: 816 loop : 0.01 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 96 HIS 0.003 0.001 HIS D 560 PHE 0.015 0.001 PHE C 970 TYR 0.017 0.001 TYR A 100 ARG 0.008 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 295 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8003 (mmt) cc_final: 0.7698 (mmt) REVERT: A 305 ASP cc_start: 0.7127 (t0) cc_final: 0.6904 (t0) REVERT: A 318 ARG cc_start: 0.7971 (tpt90) cc_final: 0.7737 (tpt90) REVERT: A 329 LEU cc_start: 0.8490 (mm) cc_final: 0.8199 (mm) REVERT: A 356 LYS cc_start: 0.7781 (mptp) cc_final: 0.7465 (mmmt) REVERT: A 385 GLU cc_start: 0.7909 (tp30) cc_final: 0.7688 (tp30) REVERT: B 329 LEU cc_start: 0.6676 (mm) cc_final: 0.6315 (mm) REVERT: B 363 TYR cc_start: 0.5759 (t80) cc_final: 0.5554 (t80) REVERT: B 375 LYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4843 (tttm) REVERT: B 389 GLU cc_start: 0.6619 (tp30) cc_final: 0.5682 (tp30) REVERT: B 407 ARG cc_start: 0.7733 (ttt-90) cc_final: 0.7416 (ttt-90) REVERT: C 298 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: C 320 TYR cc_start: 0.8960 (m-10) cc_final: 0.8515 (m-10) REVERT: C 374 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: C 746 MET cc_start: 0.9245 (mtt) cc_final: 0.8997 (mtt) REVERT: C 949 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8437 (tp30) REVERT: D 264 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8083 (mmtt) REVERT: D 282 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8161 (t0) REVERT: D 295 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8855 (tp) REVERT: D 349 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: D 850 ARG cc_start: 0.8558 (mmp-170) cc_final: 0.7943 (mmp-170) REVERT: D 928 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8709 (mm) outliers start: 84 outliers final: 53 residues processed: 346 average time/residue: 0.4000 time to fit residues: 210.4561 Evaluate side-chains 346 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 285 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 132 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN D 832 ASN ** E 49 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 = 0.2968 r_free = 0.2968 target = 0.095291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.069816 restraints weight = 27894.190| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 1.30 r_work: 0.2436 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2344 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 352 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2342 r_free = 0.2342 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 400 | |-----------------------------------------------------------------------------| r_final: 0.2342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 23569 Z= 0.421 Angle : 0.589 6.631 31956 Z= 0.308 Chirality : 0.047 0.188 3485 Planarity : 0.005 0.057 4158 Dihedral : 4.701 53.277 3210 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.07 % Allowed : 16.15 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 2884 helix: 0.39 (0.19), residues: 745 sheet: 0.17 (0.17), residues: 828 loop : -0.09 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 96 HIS 0.012 0.001 HIS D 745 PHE 0.023 0.002 PHE C 970 TYR 0.020 0.002 TYR C 385 ARG 0.009 0.001 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 285 time to evaluate : 2.490 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8012 (mmt) cc_final: 0.7696 (mmt) REVERT: A 305 ASP cc_start: 0.7228 (t0) cc_final: 0.6985 (t0) REVERT: A 310 ARG cc_start: 0.6060 (mtp180) cc_final: 0.5693 (mtp180) REVERT: A 385 GLU cc_start: 0.8045 (tp30) cc_final: 0.7756 (tp30) REVERT: B 329 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6499 (mm) REVERT: B 375 LYS cc_start: 0.5307 (OUTLIER) cc_final: 0.5047 (tttm) REVERT: B 389 GLU cc_start: 0.6823 (tp30) cc_final: 0.6149 (tp30) REVERT: C 320 TYR cc_start: 0.9028 (m-10) cc_final: 0.8520 (m-10) REVERT: C 374 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: C 412 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: C 515 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9115 (mt) REVERT: C 949 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8426 (tp30) REVERT: D 264 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8094 (mmtt) REVERT: D 282 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8189 (t0) REVERT: D 295 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 349 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: D 515 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.8875 (mt) REVERT: D 690 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9337 (tp) REVERT: D 928 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8704 (mm) REVERT: E 5 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8050 (mm) outliers start: 102 outliers final: 71 residues processed: 352 average time/residue: 0.3977 time to fit residues: 214.0364 Evaluate side-chains 363 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 279 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 362 ASN Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 34 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 250 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 6 optimal weight: 0.0000 chunk 249 optimal weight: 0.2980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN C 458 ASN C 524 GLN D 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.073826 restraints weight = 27501.692| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 1.28 r_work: 0.2505 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 400 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2398 r_free = 0.2398 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 473 | |-----------------------------------------------------------------------------| r_final: 0.2398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23569 Z= 0.158 Angle : 0.475 6.415 31956 Z= 0.255 Chirality : 0.042 0.187 3485 Planarity : 0.004 0.054 4158 Dihedral : 4.344 51.686 3210 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.99 % Allowed : 17.07 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2884 helix: 0.68 (0.19), residues: 756 sheet: 0.27 (0.17), residues: 818 loop : 0.06 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 96 HIS 0.002 0.001 HIS D 586 PHE 0.017 0.001 PHE D 503 TYR 0.018 0.001 TYR A 100 ARG 0.011 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 306 time to evaluate : 2.426 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7754 (mmt) cc_final: 0.7412 (mmt) REVERT: A 305 ASP cc_start: 0.7321 (t0) cc_final: 0.7062 (t0) REVERT: A 310 ARG cc_start: 0.6372 (mtp180) cc_final: 0.5938 (mtp180) REVERT: A 329 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8245 (mm) REVERT: A 356 LYS cc_start: 0.7892 (mptp) cc_final: 0.7227 (mmtt) REVERT: A 385 GLU cc_start: 0.8028 (tp30) cc_final: 0.7782 (tp30) REVERT: B 329 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6527 (mm) REVERT: B 375 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4998 (tttm) REVERT: B 389 GLU cc_start: 0.6840 (tp30) cc_final: 0.6074 (tp30) REVERT: C 268 ASN cc_start: 0.8536 (m-40) cc_final: 0.8249 (m-40) REVERT: C 320 TYR cc_start: 0.8921 (m-10) cc_final: 0.8434 (m-10) REVERT: C 374 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: C 386 GLN cc_start: 0.9209 (tp40) cc_final: 0.8949 (tp-100) REVERT: C 472 ASP cc_start: 0.8743 (p0) cc_final: 0.7925 (p0) REVERT: C 515 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9112 (mt) REVERT: C 949 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8427 (tp30) REVERT: D 264 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8046 (mmtt) REVERT: D 282 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8096 (t0) REVERT: D 295 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8834 (tp) REVERT: D 515 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.8812 (mt) REVERT: D 755 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8622 (mttt) REVERT: D 850 ARG cc_start: 0.8465 (mmp-170) cc_final: 0.7880 (mmp-170) REVERT: D 868 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8303 (p0) REVERT: D 928 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8629 (mm) outliers start: 75 outliers final: 46 residues processed: 354 average time/residue: 0.4104 time to fit residues: 221.0798 Evaluate side-chains 352 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 143 optimal weight: 4.9990 chunk 142 optimal weight: 0.1980 chunk 273 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN D 745 HIS D 832 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.097257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.070951 restraints weight = 27802.955| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 1.27 r_work: 0.2471 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 473 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 529 | |-----------------------------------------------------------------------------| r_final: 0.2360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23569 Z= 0.324 Angle : 0.539 6.417 31956 Z= 0.284 Chirality : 0.045 0.190 3485 Planarity : 0.004 0.054 4158 Dihedral : 4.428 51.667 3208 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.67 % Allowed : 16.47 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2884 helix: 0.57 (0.19), residues: 754 sheet: 0.22 (0.17), residues: 828 loop : 0.00 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 96 HIS 0.003 0.001 HIS D 635 PHE 0.020 0.002 PHE C 970 TYR 0.019 0.002 TYR C 385 ARG 0.011 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 291 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: A 272 MET cc_start: 0.7830 (mmt) cc_final: 0.7458 (mmt) REVERT: A 305 ASP cc_start: 0.7452 (t0) cc_final: 0.7197 (t0) REVERT: A 310 ARG cc_start: 0.6736 (mtp180) cc_final: 0.6290 (mtp180) REVERT: A 329 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 385 GLU cc_start: 0.8114 (tp30) cc_final: 0.7774 (tp30) REVERT: B 329 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6652 (mm) REVERT: B 363 TYR cc_start: 0.6539 (t80) cc_final: 0.6242 (t80) REVERT: B 375 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5115 (tttm) REVERT: B 389 GLU cc_start: 0.6825 (tp30) cc_final: 0.5921 (tp30) REVERT: C 320 TYR cc_start: 0.8941 (m-10) cc_final: 0.8384 (m-10) REVERT: C 374 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: C 386 GLN cc_start: 0.9246 (tp40) cc_final: 0.8986 (tp-100) REVERT: C 515 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9124 (mt) REVERT: C 949 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8437 (tp30) REVERT: D 264 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8099 (mmtt) REVERT: D 282 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8148 (t0) REVERT: D 295 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8805 (tp) REVERT: D 515 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8868 (mt) REVERT: D 690 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9255 (tp) REVERT: D 755 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8644 (mttt) REVERT: D 928 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8707 (mm) outliers start: 92 outliers final: 65 residues processed: 350 average time/residue: 0.3964 time to fit residues: 211.9622 Evaluate side-chains 363 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 286 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 103 optimal weight: 0.0470 chunk 236 optimal weight: 0.9980 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN ** E 49 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 = 0.2992 r_free = 0.2992 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.070368 restraints weight = 27663.519| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 1.28 r_work: 0.2452 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2351 r_free = 0.2351 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 529 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 570 | |-----------------------------------------------------------------------------| r_final: 0.2348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23569 Z= 0.316 Angle : 0.540 6.606 31956 Z= 0.285 Chirality : 0.045 0.192 3485 Planarity : 0.004 0.054 4158 Dihedral : 4.454 52.040 3207 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.87 % Allowed : 16.71 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2884 helix: 0.54 (0.19), residues: 755 sheet: 0.18 (0.17), residues: 828 loop : -0.03 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 96 HIS 0.003 0.001 HIS D 635 PHE 0.020 0.002 PHE D 503 TYR 0.018 0.002 TYR C 385 ARG 0.014 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 289 time to evaluate : 2.704 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: A 272 MET cc_start: 0.7872 (mmt) cc_final: 0.7549 (mmt) REVERT: A 305 ASP cc_start: 0.7490 (t0) cc_final: 0.7229 (t0) REVERT: A 310 ARG cc_start: 0.6876 (mtp180) cc_final: 0.6448 (mtp180) REVERT: A 329 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8250 (mm) REVERT: A 385 GLU cc_start: 0.8213 (tp30) cc_final: 0.7872 (tp30) REVERT: B 329 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6722 (mm) REVERT: B 375 LYS cc_start: 0.5438 (OUTLIER) cc_final: 0.5179 (tttm) REVERT: B 389 GLU cc_start: 0.6903 (tp30) cc_final: 0.5940 (tp30) REVERT: C 320 TYR cc_start: 0.8929 (m-10) cc_final: 0.8350 (m-10) REVERT: C 374 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: C 515 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9120 (mt) REVERT: C 949 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8450 (tp30) REVERT: D 264 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8115 (mmtt) REVERT: D 282 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8177 (t0) REVERT: D 295 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8790 (tp) REVERT: D 515 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.8873 (mt) REVERT: D 690 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9275 (tp) REVERT: D 755 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8607 (mttt) REVERT: D 928 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8740 (mm) outliers start: 97 outliers final: 74 residues processed: 352 average time/residue: 0.4090 time to fit residues: 219.2850 Evaluate side-chains 371 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 362 ASN Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 161 optimal weight: 0.0070 chunk 213 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 745 HIS ** E 49 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 = 0.3014 r_free = 0.3014 target = 0.098678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.071610 restraints weight = 27619.468| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 1.26 r_work: 0.2451 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2367 r_free = 0.2367 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 570 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2365 r_free = 0.2365 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 612 | |-----------------------------------------------------------------------------| r_final: 0.2365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23569 Z= 0.281 Angle : 0.525 7.681 31956 Z= 0.277 Chirality : 0.044 0.191 3485 Planarity : 0.004 0.056 4158 Dihedral : 4.403 51.457 3207 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.79 % Allowed : 16.75 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2884 helix: 0.58 (0.19), residues: 755 sheet: 0.19 (0.17), residues: 828 loop : -0.01 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 96 HIS 0.003 0.001 HIS D 635 PHE 0.020 0.002 PHE D 503 TYR 0.017 0.001 TYR C 385 ARG 0.014 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 289 time to evaluate : 2.778 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7673 (t80) cc_final: 0.7438 (t80) REVERT: A 122 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: A 272 MET cc_start: 0.7743 (mmt) cc_final: 0.7435 (mmt) REVERT: A 305 ASP cc_start: 0.7496 (t0) cc_final: 0.7236 (t0) REVERT: A 310 ARG cc_start: 0.6913 (mtp180) cc_final: 0.6489 (mtp180) REVERT: A 329 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 385 GLU cc_start: 0.8186 (tp30) cc_final: 0.7854 (tp30) REVERT: B 329 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6707 (mm) REVERT: B 375 LYS cc_start: 0.5425 (OUTLIER) cc_final: 0.5186 (tttm) REVERT: B 389 GLU cc_start: 0.6937 (tp30) cc_final: 0.5945 (tp30) REVERT: C 268 ASN cc_start: 0.8543 (m-40) cc_final: 0.8286 (m-40) REVERT: C 320 TYR cc_start: 0.8906 (m-10) cc_final: 0.8319 (m-10) REVERT: C 374 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: C 515 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9113 (mt) REVERT: C 949 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8417 (tp30) REVERT: D 264 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8154 (mmtt) REVERT: D 282 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8146 (t0) REVERT: D 295 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 515 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.8860 (mt) REVERT: D 690 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9257 (tp) REVERT: D 755 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8558 (mttt) REVERT: D 850 ARG cc_start: 0.8482 (mmp-170) cc_final: 0.7926 (mmp-170) REVERT: D 928 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8708 (mm) REVERT: E 5 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7952 (mm) outliers start: 95 outliers final: 76 residues processed: 353 average time/residue: 0.4195 time to fit residues: 227.8138 Evaluate side-chains 379 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 362 ASN Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain E residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 157 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN C 458 ASN D 745 HIS E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.099518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.072225 restraints weight = 27522.502| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 1.26 r_work: 0.2466 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2377 r_free = 0.2377 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 612 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2375 r_free = 0.2375 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 644 | |-----------------------------------------------------------------------------| r_final: 0.2375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23569 Z= 0.221 Angle : 0.506 6.477 31956 Z= 0.268 Chirality : 0.043 0.191 3485 Planarity : 0.004 0.063 4158 Dihedral : 4.341 50.749 3207 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.35 % Allowed : 17.15 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2884 helix: 0.65 (0.19), residues: 755 sheet: 0.19 (0.17), residues: 834 loop : 0.03 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 96 HIS 0.012 0.001 HIS D 745 PHE 0.020 0.001 PHE D 503 TYR 0.017 0.001 TYR A 100 ARG 0.015 0.000 ARG D 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 294 time to evaluate : 2.640 Fit side-chains REVERT: A 88 PHE cc_start: 0.7677 (t80) cc_final: 0.7391 (t80) REVERT: A 122 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: A 272 MET cc_start: 0.7604 (mmt) cc_final: 0.7321 (mmt) REVERT: A 305 ASP cc_start: 0.7508 (t0) cc_final: 0.7274 (t0) REVERT: A 310 ARG cc_start: 0.6965 (mtp180) cc_final: 0.6558 (mtp180) REVERT: A 329 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8205 (mm) REVERT: A 356 LYS cc_start: 0.8083 (mptp) cc_final: 0.7294 (mmtt) REVERT: A 385 GLU cc_start: 0.8150 (tp30) cc_final: 0.7824 (tp30) REVERT: B 329 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6715 (mm) REVERT: B 389 GLU cc_start: 0.6954 (tp30) cc_final: 0.5965 (tp30) REVERT: C 268 ASN cc_start: 0.8531 (m-40) cc_final: 0.8273 (m-40) REVERT: C 320 TYR cc_start: 0.8883 (m-10) cc_final: 0.8281 (m-10) REVERT: C 374 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: C 386 GLN cc_start: 0.9233 (tp40) cc_final: 0.8950 (tp-100) REVERT: C 515 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9125 (mt) REVERT: C 949 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8426 (tp30) REVERT: D 264 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8134 (mmtt) REVERT: D 282 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (t0) REVERT: D 295 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8796 (tp) REVERT: D 515 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.8844 (mt) REVERT: D 755 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8560 (mttt) REVERT: D 850 ARG cc_start: 0.8468 (mmp-170) cc_final: 0.7913 (mmp-170) REVERT: E 5 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7958 (mm) outliers start: 84 outliers final: 69 residues processed: 348 average time/residue: 0.4071 time to fit residues: 214.9691 Evaluate side-chains 367 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 851 GLU Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 881 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 362 ASN Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 745 HIS Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 889 LYS Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain E residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 74 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 227 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 250 optimal weight: 0.1980 chunk 64 optimal weight: 0.4980 chunk 276 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 ASN D 745 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.099038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.071713 restraints weight = 27492.355| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 1.22 r_work: 0.2473 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 644 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2395 r_free = 0.2395 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 704 | |-----------------------------------------------------------------------------| r_final: 0.2395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23569 Z= 0.185 Angle : 0.493 8.193 31956 Z= 0.262 Chirality : 0.043 0.197 3485 Planarity : 0.004 0.063 4158 Dihedral : 4.247 49.545 3207 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.15 % Allowed : 17.38 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2884 helix: 0.70 (0.19), residues: 758 sheet: 0.23 (0.17), residues: 832 loop : 0.07 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 96 HIS 0.026 0.001 HIS D 745 PHE 0.020 0.001 PHE D 503 TYR 0.018 0.001 TYR A 100 ARG 0.015 0.000 ARG D 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11544.63 seconds wall clock time: 206 minutes 53.52 seconds (12413.52 seconds total)