Starting phenix.real_space_refine on Thu Jun 19 22:24:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypt_39493/06_2025/8ypt_39493_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypt_39493/06_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_39493/06_2025/8ypt_39493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypt_39493/06_2025/8ypt_39493.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypt_39493/06_2025/8ypt_39493_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypt_39493/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.14, per 1000 atoms: 0.57 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: 5.85 Conformation dependent library (CDL) restraints added in 2.8 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: 4.68 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: 14.24 Time building geometry restraints manager: 6.65 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: 1.910 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: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.190 Process input model: 55.840 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- 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 23570 Z= 0.207 Angle : 0.593 10.007 31958 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 Details of bonding type rmsd hydrogen bonds : bond 0.12505 ( 1131) hydrogen bonds : angle 5.97952 ( 3171) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.93319 ( 2) covalent geometry : bond 0.00349 (23569) covalent geometry : angle 0.59315 (31956) *********************** 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 : 2.451 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: 0.3799 time to fit residues: 195.3131 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 : 2.516 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.077259 restraints weight = 27603.397| |-----------------------------------------------------------------------------| 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: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 301 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 334 | |-----------------------------------------------------------------------------| r_final: 0.2490 ------------------------------------------------------------------------------- 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 23570 Z= 0.109 Angle : 0.487 6.926 31958 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 : 4.34 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 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 1131) hydrogen bonds : angle 4.95010 ( 3171) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.22976 ( 2) covalent geometry : bond 0.00239 (23569) covalent geometry : angle 0.48737 (31956) *********************** 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 : 2.408 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7218 (t80) cc_final: 0.7014 (t80) REVERT: A 356 LYS cc_start: 0.7589 (mptp) cc_final: 0.7213 (mmtt) REVERT: B 329 LEU cc_start: 0.6299 (mm) cc_final: 0.5755 (mm) REVERT: B 363 TYR cc_start: 0.4751 (t80) cc_final: 0.4392 (t80) REVERT: C 316 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8342 (mt) REVERT: C 320 TYR cc_start: 0.8826 (m-10) cc_final: 0.8429 (m-10) REVERT: C 746 MET cc_start: 0.9141 (mtt) cc_final: 0.8888 (mtt) REVERT: D 282 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8124 (t0) REVERT: D 349 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: D 515 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 583 ASN cc_start: 0.8445 (m-40) cc_final: 0.8233 (m110) REVERT: D 704 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7321 (mmtm) REVERT: D 850 ARG cc_start: 0.8342 (mmp-170) cc_final: 0.7657 (mmt180) outliers start: 62 outliers final: 34 residues processed: 355 average time/residue: 0.3621 time to fit residues: 198.8253 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 : 2.955 ------------------------------------------------------------------------------- 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: 5.9990 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 = 0.2992 r_free = 0.2992 target = 0.096528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.071984 restraints weight = 27638.524| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 1.27 r_work: 0.2515 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 334 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2393 r_free = 0.2393 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 328 | |-----------------------------------------------------------------------------| r_final: 0.2393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 23570 Z= 0.312 Angle : 0.631 7.463 31958 Z= 0.330 Chirality : 0.048 0.185 3485 Planarity : 0.005 0.060 4158 Dihedral : 4.839 57.336 3210 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.23 % Allowed : 16.03 % Favored : 80.74 % 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: 0.09 (0.15), residues: 2884 helix: 0.33 (0.19), residues: 743 sheet: 0.22 (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 0.021 0.002 TYR A 426 ARG 0.009 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 1131) hydrogen bonds : angle 5.22371 ( 3171) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.29844 ( 2) covalent geometry : bond 0.00772 (23569) covalent geometry : angle 0.63118 (31956) *********************** 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 364 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7348 (t80) cc_final: 0.7141 (t80) REVERT: A 272 MET cc_start: 0.8145 (mmt) cc_final: 0.7795 (mmt) REVERT: A 318 ARG cc_start: 0.7796 (tpt90) cc_final: 0.7546 (tpt90) REVERT: A 385 GLU cc_start: 0.7814 (tp30) cc_final: 0.7553 (tp30) REVERT: B 363 TYR cc_start: 0.5390 (t80) cc_final: 0.5138 (t80) REVERT: B 407 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7397 (ttt-90) REVERT: C 298 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: C 320 TYR cc_start: 0.9010 (m-10) cc_final: 0.8547 (m-10) REVERT: C 374 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: C 412 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8525 (mtp) REVERT: C 579 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.8132 (mtt90) REVERT: D 282 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8186 (t0) REVERT: D 349 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: D 515 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.8907 (mt) outliers start: 81 outliers final: 56 residues processed: 331 average time/residue: 0.4529 time to fit residues: 226.9785 Evaluate side-chains 337 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 3.665 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 279 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 202 optimal weight: 0.5980 chunk 246 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.098234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.073297 restraints weight = 27759.623| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 1.30 r_work: 0.2522 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2431 r_free = 0.2431 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 328 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 354 | |-----------------------------------------------------------------------------| r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23570 Z= 0.122 Angle : 0.489 6.558 31958 Z= 0.262 Chirality : 0.043 0.184 3485 Planarity : 0.004 0.057 4158 Dihedral : 4.496 59.036 3210 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.99 % Allowed : 16.79 % Favored : 80.22 % 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: 0.29 (0.16), residues: 2884 helix: 0.62 (0.19), residues: 753 sheet: 0.30 (0.17), residues: 816 loop : 0.03 (0.18), 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 745 PHE 0.015 0.001 PHE C 970 TYR 0.017 0.001 TYR A 100 ARG 0.007 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1131) hydrogen bonds : angle 4.86387 ( 3171) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.10162 ( 2) covalent geometry : bond 0.00281 (23569) covalent geometry : angle 0.48893 (31956) *********************** 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 370 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 2.479 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8005 (mmt) cc_final: 0.7710 (mmt) REVERT: A 305 ASP cc_start: 0.7157 (t0) cc_final: 0.6921 (t0) REVERT: A 329 LEU cc_start: 0.8484 (mm) cc_final: 0.8195 (mm) REVERT: A 356 LYS cc_start: 0.7781 (mptp) cc_final: 0.7474 (mmmt) REVERT: A 385 GLU cc_start: 0.7921 (tp30) cc_final: 0.7695 (tp30) REVERT: B 329 LEU cc_start: 0.6662 (mm) cc_final: 0.6307 (mm) REVERT: B 363 TYR cc_start: 0.5733 (t80) cc_final: 0.5525 (t80) REVERT: B 375 LYS cc_start: 0.5177 (OUTLIER) cc_final: 0.4915 (tttm) REVERT: B 389 GLU cc_start: 0.6542 (tp30) cc_final: 0.5644 (tp30) REVERT: B 407 ARG cc_start: 0.7721 (ttt-90) cc_final: 0.7408 (ttt-90) REVERT: C 298 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: C 320 TYR cc_start: 0.8951 (m-10) cc_final: 0.8509 (m-10) REVERT: C 374 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: C 579 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8162 (mtt90) REVERT: C 746 MET cc_start: 0.9251 (mtt) cc_final: 0.9001 (mtt) REVERT: C 949 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: D 264 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8085 (mmtt) REVERT: D 282 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8154 (t0) REVERT: D 295 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8826 (tp) REVERT: D 349 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: D 850 ARG cc_start: 0.8572 (mmp-170) cc_final: 0.7959 (mmp-170) REVERT: D 928 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8722 (mm) outliers start: 75 outliers final: 48 residues processed: 340 average time/residue: 0.4006 time to fit residues: 208.1448 Evaluate side-chains 343 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 3.9990 chunk 104 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 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: 2.3988 ------------------------------------------------------------------------------- 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 = 0.2966 r_free = 0.2966 target = 0.095146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.069652 restraints weight = 27875.341| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 1.30 r_work: 0.2437 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 354 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2335 r_free = 0.2335 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 396 | |-----------------------------------------------------------------------------| r_final: 0.2335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 23570 Z= 0.284 Angle : 0.601 6.955 31958 Z= 0.315 Chirality : 0.047 0.188 3485 Planarity : 0.005 0.058 4158 Dihedral : 4.734 53.393 3210 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.03 % Allowed : 15.99 % Favored : 79.98 % 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: 744 sheet: 0.18 (0.17), residues: 826 loop : -0.10 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 96 HIS 0.010 0.001 HIS D 745 PHE 0.024 0.002 PHE C 970 TYR 0.021 0.002 TYR C 385 ARG 0.008 0.001 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 1131) hydrogen bonds : angle 5.10912 ( 3171) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.22687 ( 2) covalent geometry : bond 0.00697 (23569) covalent geometry : angle 0.60094 (31956) *********************** 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 382 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 281 time to evaluate : 2.865 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8061 (mmt) cc_final: 0.7749 (mmt) REVERT: A 305 ASP cc_start: 0.7224 (t0) cc_final: 0.6991 (t0) REVERT: A 310 ARG cc_start: 0.6071 (mtp180) cc_final: 0.5705 (mtp180) REVERT: A 385 GLU cc_start: 0.8104 (tp30) cc_final: 0.7810 (tp30) REVERT: B 329 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6521 (mm) REVERT: B 375 LYS cc_start: 0.5318 (OUTLIER) cc_final: 0.5059 (tttm) REVERT: B 389 GLU cc_start: 0.6828 (tp30) cc_final: 0.6149 (tp30) REVERT: C 320 TYR cc_start: 0.9039 (m-10) cc_final: 0.8529 (m-10) REVERT: C 374 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: C 412 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8550 (mtp) REVERT: C 515 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9122 (mt) REVERT: C 1047 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6737 (ttm) REVERT: D 264 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8108 (mmtt) REVERT: D 282 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8199 (t0) REVERT: D 295 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8809 (tp) REVERT: D 349 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: D 515 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8889 (mt) REVERT: D 690 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9350 (tp) REVERT: D 755 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8730 (mttt) REVERT: D 928 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8725 (mm) REVERT: E 5 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8092 (mm) outliers start: 101 outliers final: 72 residues processed: 350 average time/residue: 0.3753 time to fit residues: 201.5823 Evaluate side-chains 360 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 275 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 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 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 410 ASN 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 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 967 SER Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1047 MET 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: 7.9990 chunk 164 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 211 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 524 GLN D 745 HIS ** 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 = 0.3006 r_free = 0.3006 target = 0.097883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.072205 restraints weight = 27547.956| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 1.27 r_work: 0.2480 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2374 r_free = 0.2374 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 396 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 465 | |-----------------------------------------------------------------------------| r_final: 0.2366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23570 Z= 0.158 Angle : 0.512 7.449 31958 Z= 0.272 Chirality : 0.044 0.189 3485 Planarity : 0.004 0.055 4158 Dihedral : 4.508 52.901 3210 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.59 % Allowed : 16.59 % Favored : 79.82 % 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: 0.19 (0.17), residues: 826 loop : -0.04 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 96 HIS 0.003 0.001 HIS D 560 PHE 0.017 0.001 PHE D 503 TYR 0.016 0.001 TYR A 100 ARG 0.006 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1131) hydrogen bonds : angle 4.88070 ( 3171) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.12576 ( 2) covalent geometry : bond 0.00377 (23569) covalent geometry : angle 0.51175 (31956) *********************** 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 387 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 297 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: A 272 MET cc_start: 0.7816 (mmt) cc_final: 0.7525 (mmt) REVERT: A 305 ASP cc_start: 0.7323 (t0) cc_final: 0.7062 (t0) REVERT: A 310 ARG cc_start: 0.6463 (mtp180) cc_final: 0.6000 (mtp180) REVERT: A 329 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (mm) REVERT: A 385 GLU cc_start: 0.8043 (tp30) cc_final: 0.7751 (tp30) REVERT: B 64 MET cc_start: 0.8926 (ptp) cc_final: 0.8666 (ptt) REVERT: B 329 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6557 (mm) REVERT: B 375 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.5046 (tttm) REVERT: B 389 GLU cc_start: 0.6718 (tp30) cc_final: 0.5892 (tp30) REVERT: C 298 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: C 320 TYR cc_start: 0.8942 (m-10) cc_final: 0.8453 (m-10) REVERT: C 374 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: C 515 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9110 (mt) REVERT: C 949 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8427 (tp30) REVERT: D 264 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8071 (mmtt) REVERT: D 282 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8128 (t0) REVERT: D 295 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8786 (tp) REVERT: D 349 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: D 515 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.8830 (mt) REVERT: D 755 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8612 (mttt) REVERT: D 850 ARG cc_start: 0.8499 (mmp-170) cc_final: 0.7904 (mmp-170) REVERT: D 928 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8665 (mm) outliers start: 90 outliers final: 60 residues processed: 355 average time/residue: 0.3759 time to fit residues: 205.5780 Evaluate side-chains 358 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 285 time to evaluate : 2.453 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 349 GLU 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 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 1096 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 143 optimal weight: 0.8980 chunk 142 optimal weight: 0.0970 chunk 273 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 274 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN B 98 ASN C 458 ASN D 745 HIS D 832 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.072539 restraints weight = 27652.094| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 1.29 r_work: 0.2487 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2385 r_free = 0.2385 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 465 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 541 | |-----------------------------------------------------------------------------| r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23570 Z= 0.117 Angle : 0.483 6.418 31958 Z= 0.258 Chirality : 0.043 0.187 3485 Planarity : 0.004 0.054 4158 Dihedral : 4.319 51.461 3210 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.39 % Allowed : 16.91 % Favored : 79.70 % 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: 0.31 (0.16), residues: 2884 helix: 0.69 (0.19), residues: 755 sheet: 0.25 (0.17), residues: 826 loop : 0.05 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 96 HIS 0.005 0.001 HIS D 745 PHE 0.017 0.001 PHE D 503 TYR 0.018 0.001 TYR A 100 ARG 0.013 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 1131) hydrogen bonds : angle 4.74689 ( 3171) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.10064 ( 2) covalent geometry : bond 0.00271 (23569) covalent geometry : angle 0.48326 (31956) *********************** 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 382 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 297 time to evaluate : 2.905 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: A 272 MET cc_start: 0.7753 (mmt) cc_final: 0.7416 (mmt) REVERT: A 305 ASP cc_start: 0.7461 (t0) cc_final: 0.7204 (t0) REVERT: A 310 ARG cc_start: 0.6802 (mtp180) cc_final: 0.6379 (mtp180) REVERT: A 356 LYS cc_start: 0.8004 (mptp) cc_final: 0.7328 (mmtt) REVERT: A 385 GLU cc_start: 0.8192 (tp30) cc_final: 0.7897 (tp30) REVERT: B 64 MET cc_start: 0.8994 (ptp) cc_final: 0.8740 (ptt) REVERT: B 329 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6645 (mm) REVERT: B 389 GLU cc_start: 0.6880 (tp30) cc_final: 0.5929 (tp30) REVERT: C 268 ASN cc_start: 0.8564 (m-40) cc_final: 0.8292 (m-40) REVERT: C 320 TYR cc_start: 0.8926 (m-10) cc_final: 0.8404 (m-10) REVERT: C 374 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: C 386 GLN cc_start: 0.9228 (tp40) cc_final: 0.8953 (tp-100) REVERT: C 486 ASN cc_start: 0.9128 (t0) cc_final: 0.8906 (t0) REVERT: C 515 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9132 (mt) REVERT: C 949 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: D 264 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8092 (mmtt) REVERT: D 282 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8141 (t0) REVERT: D 295 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8878 (tp) REVERT: D 515 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.8839 (mt) REVERT: D 690 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9221 (tp) REVERT: D 755 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8652 (mttt) REVERT: D 850 ARG cc_start: 0.8499 (mmp-170) cc_final: 0.7945 (mmp-170) outliers start: 85 outliers final: 56 residues processed: 351 average time/residue: 0.4398 time to fit residues: 237.0210 Evaluate side-chains 353 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 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 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 C residue 120 THR 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 410 ASN 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 688 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 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 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 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 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 942 THR 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: 6.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN C 524 GLN 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 = 0.2970 r_free = 0.2970 target = 0.095612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.068702 restraints weight = 27762.962| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 1.26 r_work: 0.2422 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2333 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2330 r_free = 0.2330 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 541 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2326 r_free = 0.2326 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 23570 Z= 0.369 Angle : 0.670 8.844 31958 Z= 0.347 Chirality : 0.050 0.195 3485 Planarity : 0.005 0.056 4158 Dihedral : 4.778 52.835 3207 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.67 % Allowed : 17.15 % Favored : 79.19 % 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: -0.13 (0.15), residues: 2884 helix: 0.23 (0.19), residues: 746 sheet: 0.02 (0.17), residues: 840 loop : -0.17 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS D 560 PHE 0.029 0.003 PHE C 970 TYR 0.022 0.002 TYR C 244 ARG 0.013 0.001 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1131) hydrogen bonds : angle 5.20446 ( 3171) SS BOND : bond 0.00427 ( 1) SS BOND : angle 0.28742 ( 2) covalent geometry : bond 0.00909 (23569) covalent geometry : angle 0.66967 (31956) *********************** 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 371 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 279 time to evaluate : 2.687 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: A 272 MET cc_start: 0.7938 (mmt) cc_final: 0.7559 (mmt) REVERT: A 305 ASP cc_start: 0.7413 (t0) cc_final: 0.7156 (t0) REVERT: A 310 ARG cc_start: 0.6870 (mtp180) cc_final: 0.6517 (mtp180) REVERT: A 385 GLU cc_start: 0.8241 (tp30) cc_final: 0.7887 (tp30) REVERT: B 64 MET cc_start: 0.8999 (ptp) cc_final: 0.8754 (ptt) REVERT: B 329 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6712 (mm) REVERT: B 389 GLU cc_start: 0.7022 (tp30) cc_final: 0.6103 (tp30) REVERT: C 320 TYR cc_start: 0.8992 (m-10) cc_final: 0.8370 (m-10) REVERT: C 374 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: C 515 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9100 (mt) REVERT: C 949 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: D 264 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8022 (mmtt) REVERT: D 282 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8214 (t0) REVERT: D 295 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8820 (tp) REVERT: D 515 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.8915 (mt) REVERT: D 690 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9355 (tp) REVERT: D 736 ASP cc_start: 0.8108 (t0) cc_final: 0.7709 (m-30) REVERT: D 928 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8714 (mm) REVERT: E 5 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8018 (mm) outliers start: 92 outliers final: 66 residues processed: 342 average time/residue: 0.4612 time to fit residues: 249.0983 Evaluate side-chains 350 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 273 time to evaluate : 3.502 ------------------------------------------------------------------------------- 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 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 127 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 331 LEU 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 410 ASN 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 668 ASP 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 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 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 1060 ILE 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 161 optimal weight: 0.1980 chunk 213 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 267 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 ASN C 524 GLN E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.098349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.071618 restraints weight = 27734.875| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 1.22 r_work: 0.2470 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2392 r_free = 0.2392 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| r_final: 0.2390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23570 Z= 0.114 Angle : 0.491 6.414 31958 Z= 0.263 Chirality : 0.043 0.191 3485 Planarity : 0.004 0.059 4158 Dihedral : 4.362 51.625 3207 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.87 % Allowed : 17.78 % Favored : 79.35 % 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: 0.19 (0.16), residues: 2884 helix: 0.58 (0.19), residues: 756 sheet: 0.18 (0.17), residues: 826 loop : -0.02 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 96 HIS 0.003 0.001 HIS D 586 PHE 0.021 0.001 PHE D 503 TYR 0.018 0.001 TYR A 100 ARG 0.013 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 1131) hydrogen bonds : angle 4.80778 ( 3171) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.07500 ( 2) covalent geometry : bond 0.00262 (23569) covalent geometry : angle 0.49104 (31956) *********************** 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 360 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 288 time to evaluate : 2.641 Fit side-chains REVERT: A 88 PHE cc_start: 0.7693 (t80) cc_final: 0.7446 (t80) REVERT: A 272 MET cc_start: 0.7751 (mmt) cc_final: 0.7480 (mmt) REVERT: A 305 ASP cc_start: 0.7515 (t0) cc_final: 0.7266 (t0) REVERT: A 310 ARG cc_start: 0.6942 (mtp180) cc_final: 0.6518 (mtp180) REVERT: A 356 LYS cc_start: 0.8062 (mptp) cc_final: 0.7318 (mmtt) REVERT: A 385 GLU cc_start: 0.8183 (tp30) cc_final: 0.7891 (tp30) REVERT: B 329 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6736 (mm) REVERT: B 389 GLU cc_start: 0.6986 (tp30) cc_final: 0.5975 (tp30) REVERT: C 268 ASN cc_start: 0.8509 (m-40) cc_final: 0.8243 (m-40) REVERT: C 298 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: C 320 TYR cc_start: 0.8902 (m-10) cc_final: 0.8319 (m-10) REVERT: C 486 ASN cc_start: 0.9150 (t0) cc_final: 0.8875 (t0) REVERT: C 515 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9111 (mt) REVERT: C 949 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8450 (tp30) REVERT: D 264 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8079 (mmtt) REVERT: D 282 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (t0) REVERT: D 295 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8814 (tp) REVERT: D 515 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.8836 (mt) REVERT: D 690 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9281 (tp) REVERT: D 755 LYS cc_start: 0.8961 (mtmm) cc_final: 0.8670 (mttt) REVERT: D 850 ARG cc_start: 0.8461 (mmp-170) cc_final: 0.7913 (mmp-170) REVERT: D 928 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8721 (mm) outliers start: 72 outliers final: 53 residues processed: 331 average time/residue: 0.3952 time to fit residues: 198.7435 Evaluate side-chains 348 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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 351 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 297 LEU 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 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 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS 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 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 958 LEU 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 362 ASN 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 515 LEU 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 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 157 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.070165 restraints weight = 27757.707| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 1.21 r_work: 0.2445 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2359 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 651 | |-----------------------------------------------------------------------------| r_final: 0.2367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23570 Z= 0.195 Angle : 0.547 7.348 31958 Z= 0.288 Chirality : 0.045 0.196 3485 Planarity : 0.004 0.060 4158 Dihedral : 4.445 51.097 3207 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.75 % Allowed : 17.86 % Favored : 79.39 % 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: 0.14 (0.15), residues: 2884 helix: 0.54 (0.19), residues: 754 sheet: 0.14 (0.17), residues: 834 loop : -0.04 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS D 560 PHE 0.024 0.002 PHE C 503 TYR 0.018 0.002 TYR C 385 ARG 0.015 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1131) hydrogen bonds : angle 4.89626 ( 3171) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.16739 ( 2) covalent geometry : bond 0.00474 (23569) covalent geometry : angle 0.54703 (31956) ********************** 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 355 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 2.673 Fit side-chains REVERT: A 122 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: A 272 MET cc_start: 0.7805 (mmt) cc_final: 0.7512 (mmt) REVERT: A 305 ASP cc_start: 0.7551 (t0) cc_final: 0.7333 (t0) REVERT: A 310 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6562 (mtp180) REVERT: A 356 LYS cc_start: 0.8116 (mptp) cc_final: 0.7397 (mmtt) REVERT: A 385 GLU cc_start: 0.8238 (tp30) cc_final: 0.7862 (tp30) REVERT: B 329 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6805 (mm) REVERT: B 389 GLU cc_start: 0.7045 (tp30) cc_final: 0.6050 (tp30) REVERT: C 268 ASN cc_start: 0.8515 (m-40) cc_final: 0.8250 (m-40) REVERT: C 320 TYR cc_start: 0.8909 (m-10) cc_final: 0.8287 (m-10) REVERT: C 515 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9124 (mt) REVERT: C 949 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: D 264 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8166 (mmtt) REVERT: D 282 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8154 (t0) REVERT: D 295 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8774 (tp) REVERT: D 515 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.8869 (mt) REVERT: D 690 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9274 (tp) REVERT: D 755 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8678 (mttt) REVERT: D 928 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8744 (mm) outliers start: 69 outliers final: 57 residues processed: 330 average time/residue: 0.3904 time to fit residues: 196.0244 Evaluate side-chains 348 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 2.413 ------------------------------------------------------------------------------- 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 351 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 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 C residue 120 THR 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 410 ASN Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 573 LYS 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 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 958 LEU 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 362 ASN Chi-restraints excluded: chain D residue 369 LEU 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 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 805 VAL Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 942 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 74 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.098725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.071423 restraints weight = 27559.608| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 1.22 r_work: 0.2493 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2393 r_free = 0.2393 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 651 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2392 r_free = 0.2392 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 695 | |-----------------------------------------------------------------------------| r_final: 0.2392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23570 Z= 0.133 Angle : 0.498 6.417 31958 Z= 0.265 Chirality : 0.043 0.191 3485 Planarity : 0.004 0.061 4158 Dihedral : 4.291 49.565 3207 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.83 % Allowed : 17.74 % 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: 0.27 (0.16), residues: 2884 helix: 0.65 (0.19), residues: 756 sheet: 0.23 (0.17), residues: 826 loop : 0.02 (0.18), residues: 1302 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 0.023 0.001 PHE C 503 TYR 0.018 0.001 TYR A 100 ARG 0.014 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 1131) hydrogen bonds : angle 4.74783 ( 3171) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.11226 ( 2) covalent geometry : bond 0.00316 (23569) covalent geometry : angle 0.49785 (31956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13001.51 seconds wall clock time: 228 minutes 3.32 seconds (13683.32 seconds total)