Starting phenix.real_space_refine on Fri Jan 24 17:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypu_39494/01_2025/8ypu_39494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypu_39494/01_2025/8ypu_39494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ypu_39494/01_2025/8ypu_39494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypu_39494/01_2025/8ypu_39494.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypu_39494/01_2025/8ypu_39494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypu_39494/01_2025/8ypu_39494.cif" } resolution = 2.97 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= 0.332 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 56 5.16 5 C 14264 2.51 5 N 3834 2.21 5 O 4322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22476 Number of models: 1 Model: "" Number of chains: 4 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: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7861 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 38, 'TRANS': 948} Chain: "D" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7861 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 38, 'TRANS': 948} Residues with excluded nonbonded symmetry interactions: 60 residue: pdb=" N GLY A 77 " occ=0.63 ... (2 atoms not shown) pdb=" O GLY A 77 " occ=0.37 residue: pdb=" N SER A 234 " occ=0.39 ... (4 atoms not shown) pdb=" OG SER A 234 " occ=0.31 residue: pdb=" N LYS A 242 " occ=0.35 ... (7 atoms not shown) pdb=" NZ LYS A 242 " occ=0.43 residue: pdb=" N PRO A 256 " occ=0.87 ... (5 atoms not shown) pdb=" CD PRO A 256 " occ=0.53 residue: pdb=" N SER A 261 " occ=0.82 ... (4 atoms not shown) pdb=" OG SER A 261 " occ=0.31 residue: pdb=" N ALA A 279 " occ=0.55 ... (3 atoms not shown) pdb=" CB ALA A 279 " occ=0.41 residue: pdb=" N PHE A 286 " occ=0.47 ... (9 atoms not shown) pdb=" CZ PHE A 286 " occ=0.51 residue: pdb=" N PHE A 301 " occ=0.53 ... (9 atoms not shown) pdb=" CZ PHE A 301 " occ=0.56 residue: pdb=" N ALA A 302 " occ=0.26 ... (3 atoms not shown) pdb=" CB ALA A 302 " occ=0.59 residue: pdb=" N SER A 313 " occ=0.45 ... (4 atoms not shown) pdb=" OG SER A 313 " occ=0.17 residue: pdb=" N GLY A 316 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY A 316 " occ=0.44 residue: pdb=" N GLY A 327 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY A 327 " occ=0.12 ... (remaining 48 not shown) Time building chain proxies: 12.58, per 1000 atoms: 0.56 Number of scatterers: 22476 At special positions: 0 Unit cell: (152.22, 130.98, 128.62, 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 56 16.00 O 4322 8.00 N 3834 7.00 C 14264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 2.7 seconds 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5260 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 24 sheets defined 27.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.500A pdb=" N ASN A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.917A pdb=" N LEU A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 5.718A pdb=" N ASP A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.585A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 147 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.545A pdb=" N GLU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.995A pdb=" N VAL A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 294 through 300 removed outlier: 4.046A pdb=" N ALA A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.530A pdb=" N LEU A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.724A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.447A 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 396 through 404 removed outlier: 3.605A pdb=" N THR A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.644A 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 35 through 49 removed outlier: 3.504A pdb=" N ASN B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.920A pdb=" N LEU B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 5.718A pdb=" N ASP B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 removed outlier: 3.591A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.829A 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 194 removed outlier: 3.542A pdb=" N GLU B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.692A pdb=" N VAL B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 294 through 300 removed outlier: 4.048A pdb=" N ALA B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.517A pdb=" N LEU B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 359 through 372 removed outlier: 3.723A pdb=" N ALA B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 396 through 404 removed outlier: 3.609A pdb=" N THR B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.619A 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 209 through 216 removed outlier: 3.665A pdb=" N VAL C 213 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.884A 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 237 through 242 Processing helix chain 'C' and resid 243 through 248 removed outlier: 6.905A pdb=" N ALA C 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 removed outlier: 3.533A pdb=" N SER C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 322 through 329 Processing helix chain 'C' and resid 335 through 347 Processing helix chain 'C' and resid 351 through 357 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 539 Processing helix chain 'C' and resid 627 through 632 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: 3.786A pdb=" N ILE C 983 " --> pdb=" O ASN C 980 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 986 " --> pdb=" O ILE C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1015 Processing helix chain 'C' and resid 1016 through 1021 removed outlier: 3.838A 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 1051 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 209 through 216 removed outlier: 3.666A pdb=" N VAL D 213 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 216 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 243 through 248 removed outlier: 6.877A pdb=" N ALA D 246 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 312 through 321 removed outlier: 3.504A pdb=" N TYR D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 335 through 347 Processing helix chain 'D' and resid 351 through 357 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 539 Processing helix chain 'D' and resid 627 through 632 Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.586A pdb=" N ARG D 703 " --> pdb=" O GLN D 700 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS D 704 " --> pdb=" O GLY D 701 " (cutoff:3.500A) 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: 3.790A pdb=" N ILE D 983 " --> pdb=" O ASN D 980 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 986 " --> pdb=" O ILE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1015 removed outlier: 3.559A pdb=" N GLN D1014 " --> pdb=" O TYR D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1021 removed outlier: 3.812A 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 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: 5.822A 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: 6.573A 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: 6.012A 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: 6.577A 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: 3.520A pdb=" N ASN C 231 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C 191 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE C 255 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 193 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.464A 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 1067 through 1069 removed outlier: 4.043A pdb=" N ILE C 267 " --> pdb=" O PHE C1101 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS C 264 " --> pdb=" O GLY C 372 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY C 372 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C 361 " --> pdb=" O ASN C 388 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN C 388 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY C 558 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA C 812 " --> pdb=" O ASP C 791 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE C 793 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN C 810 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS C 795 " --> pdb=" O ASN C 808 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN C 808 " --> pdb=" O LYS C 795 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET C 797 " --> pdb=" O SER C 806 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 806 " --> pdb=" O MET C 797 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER C 813 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 835 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA C 829 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER C 955 " --> pdb=" O LEU C1034 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU C1034 " --> pdb=" O SER C 955 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN C 957 " --> pdb=" O PHE C1032 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE C1032 " --> pdb=" O ASN C 957 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY C 959 " --> pdb=" O ASN C1030 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN C1030 " --> pdb=" O GLY C 959 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR C 961 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS C1028 " --> pdb=" O TYR C 961 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 963 " --> pdb=" O VAL C1026 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C1026 " --> pdb=" O ARG C 963 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 541 through 544 removed outlier: 3.562A pdb=" N ASP C 544 " --> pdb=" O SER C 549 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER C 549 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 730 through 739 removed outlier: 6.801A pdb=" N LEU C 730 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 738 " --> pdb=" O GLY C 742 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY C 742 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 869 through 872 removed outlier: 6.805A pdb=" N ILE C 870 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 877 through 878 removed outlier: 3.633A pdb=" N GLY C 877 " --> pdb=" O LEU C 885 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AB9, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.532A pdb=" N ASN D 231 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU D 191 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE D 255 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 193 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR D 257 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 161 through 165 Processing sheet with id=AC2, first strand: chain 'D' and resid 1067 through 1069 removed outlier: 4.047A pdb=" N ILE D 267 " --> pdb=" O PHE D1101 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS D 264 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY D 372 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE D 361 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN D 388 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY D 558 " --> pdb=" O GLY D 610 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY D 593 " --> pdb=" O PHE D 648 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA D 812 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE D 793 " --> pdb=" O ASN D 810 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN D 810 " --> pdb=" O ILE D 793 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS D 795 " --> pdb=" O ASN D 808 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN D 808 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET D 797 " --> pdb=" O SER D 806 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 806 " --> pdb=" O MET D 797 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER D 813 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP D 835 " --> pdb=" O ASN D 827 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA D 829 " --> pdb=" O PHE D 833 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 955 " --> pdb=" O LEU D1034 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D1034 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN D 957 " --> pdb=" O PHE D1032 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE D1032 " --> pdb=" O ASN D 957 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY D 959 " --> pdb=" O ASN D1030 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN D1030 " --> pdb=" O GLY D 959 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR D 961 " --> pdb=" O LYS D1028 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS D1028 " --> pdb=" O TYR D 961 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG D 963 " --> pdb=" O VAL D1026 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D1026 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 541 through 544 removed outlier: 3.564A pdb=" N ASP D 544 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER D 549 " --> pdb=" O ASP D 544 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 730 through 739 removed outlier: 6.807A pdb=" N LEU D 730 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 738 " --> pdb=" O GLY D 742 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY D 742 " --> pdb=" O ILE D 738 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 869 through 872 removed outlier: 6.816A pdb=" N ILE D 870 " --> pdb=" O ILE D 928 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 877 through 878 removed outlier: 3.680A pdb=" N GLY D 877 " --> pdb=" O LEU D 885 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.23 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7279 1.34 - 1.45: 3712 1.45 - 1.57: 11875 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 22970 Sorted by residual: bond pdb=" N VAL B 28 " pdb=" CA VAL B 28 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.25e+01 bond pdb=" N ILE B 25 " pdb=" CA ILE B 25 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.93e+00 bond pdb=" N GLN D 206 " pdb=" CA GLN D 206 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.17e-02 7.31e+03 8.54e+00 bond pdb=" N ASN B 210 " pdb=" CA ASN B 210 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.55e+00 bond pdb=" N VAL D 204 " pdb=" CA VAL D 204 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.46e+00 ... (remaining 22965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 30512 2.03 - 4.07: 547 4.07 - 6.10: 64 6.10 - 8.13: 21 8.13 - 10.17: 4 Bond angle restraints: 31148 Sorted by residual: angle pdb=" N TYR B 22 " pdb=" CA TYR B 22 " pdb=" C TYR B 22 " ideal model delta sigma weight residual 110.91 102.99 7.92 1.17e+00 7.31e-01 4.58e+01 angle pdb=" C THR D 471 " pdb=" CA THR D 471 " pdb=" CB THR D 471 " ideal model delta sigma weight residual 111.18 120.06 -8.88 1.56e+00 4.11e-01 3.24e+01 angle pdb=" N SER B 160 " pdb=" CA SER B 160 " pdb=" C SER B 160 " ideal model delta sigma weight residual 112.68 119.80 -7.12 1.33e+00 5.65e-01 2.87e+01 angle pdb=" N ARG D1005 " pdb=" CA ARG D1005 " pdb=" C ARG D1005 " ideal model delta sigma weight residual 111.52 118.48 -6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" N SER B 21 " pdb=" CA SER B 21 " pdb=" C SER B 21 " ideal model delta sigma weight residual 108.19 102.15 6.04 1.29e+00 6.01e-01 2.19e+01 ... (remaining 31143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 11971 17.50 - 35.00: 1356 35.00 - 52.51: 330 52.51 - 70.01: 68 70.01 - 87.51: 25 Dihedral angle restraints: 13750 sinusoidal: 5520 harmonic: 8230 Sorted by residual: dihedral pdb=" CA PHE D 648 " pdb=" C PHE D 648 " pdb=" N SER D 649 " pdb=" CA SER D 649 " ideal model delta harmonic sigma weight residual 180.00 153.79 26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C THR D 471 " pdb=" N THR D 471 " pdb=" CA THR D 471 " pdb=" CB THR D 471 " ideal model delta harmonic sigma weight residual -122.00 -134.75 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ALA D 246 " pdb=" N ALA D 246 " pdb=" CA ALA D 246 " pdb=" CB ALA D 246 " ideal model delta harmonic sigma weight residual -122.60 -134.50 11.90 0 2.50e+00 1.60e-01 2.27e+01 ... (remaining 13747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3115 0.088 - 0.177: 258 0.177 - 0.265: 9 0.265 - 0.354: 5 0.354 - 0.442: 5 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA SER B 112 " pdb=" N SER B 112 " pdb=" C SER B 112 " pdb=" CB SER B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA ALA D 246 " pdb=" N ALA D 246 " pdb=" C ALA D 246 " pdb=" CB ALA D 246 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA SER B 21 " pdb=" N SER B 21 " pdb=" C SER B 21 " pdb=" CB SER B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 3389 not shown) Planarity restraints: 4054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 335 " 0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO D 336 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 336 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 336 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 343 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 344 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 343 " -0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO A 344 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.047 5.00e-02 4.00e+02 ... (remaining 4051 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 253 2.63 - 3.20: 18761 3.20 - 3.77: 34275 3.77 - 4.33: 52167 4.33 - 4.90: 87455 Nonbonded interactions: 192911 Sorted by model distance: nonbonded pdb=" OH TYR B 207 " pdb=" OE2 GLU D 744 " model vdw 2.065 3.040 nonbonded pdb=" OH TYR A 207 " pdb=" OE2 GLU C 744 " model vdw 2.075 3.040 nonbonded pdb=" OD1 ASN D 138 " pdb=" OD1 ASN D 231 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR A 137 " pdb=" OE1 GLU A 269 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR B 137 " pdb=" OE1 GLU B 269 " model vdw 2.117 3.040 ... (remaining 192906 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: 0.03 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=0.80 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.090 Set scattering table: 0.190 Process input model: 47.660 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 22970 Z= 0.400 Angle : 0.677 10.165 31148 Z= 0.378 Chirality : 0.052 0.442 3392 Planarity : 0.006 0.090 4054 Dihedral : 16.030 87.511 8490 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.25 % Allowed : 17.38 % Favored : 82.38 % Cbeta Deviations : 0.11 % 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: -0.23 (0.15), residues: 2812 helix: -0.52 (0.19), residues: 716 sheet: 0.64 (0.17), residues: 794 loop : -0.30 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 835 HIS 0.004 0.001 HIS A 132 PHE 0.032 0.002 PHE D 698 TYR 0.022 0.002 TYR C1010 ARG 0.010 0.001 ARG C 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 2.722 Fit side-chains REVERT: A 415 LYS cc_start: 0.6570 (mtpm) cc_final: 0.6362 (ttpt) REVERT: C 468 ASN cc_start: 0.8987 (m-40) cc_final: 0.8701 (m110) REVERT: C 626 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8152 (mt-10) REVERT: C 1083 ASN cc_start: 0.9210 (t0) cc_final: 0.8786 (t160) REVERT: D 533 MET cc_start: 0.9364 (tpt) cc_final: 0.9151 (tpt) REVERT: D 626 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8131 (mt-10) REVERT: D 650 THR cc_start: 0.9390 (p) cc_final: 0.9161 (m) REVERT: D 1083 ASN cc_start: 0.9190 (t0) cc_final: 0.8894 (t160) outliers start: 6 outliers final: 2 residues processed: 284 average time/residue: 1.4053 time to fit residues: 460.7170 Evaluate side-chains 254 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 117 optimal weight: 0.0170 chunk 72 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 210 ASN B 52 ASN C 373 ASN C 504 ASN ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 ASN D 373 ASN D 504 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.091501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.084207 restraints weight = 26900.086| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 0.46 r_work: 0.2565 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 343 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 370 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22970 Z= 0.264 Angle : 0.557 6.998 31148 Z= 0.296 Chirality : 0.044 0.177 3392 Planarity : 0.005 0.066 4054 Dihedral : 4.695 52.848 3126 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.48 % Allowed : 17.25 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2812 helix: -0.11 (0.19), residues: 700 sheet: 0.58 (0.17), residues: 798 loop : -0.30 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 835 HIS 0.003 0.001 HIS B 132 PHE 0.027 0.002 PHE D 970 TYR 0.018 0.001 TYR C 385 ARG 0.004 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 259 time to evaluate : 2.427 Fit side-chains REVERT: A 115 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: C 336 PRO cc_start: 0.5907 (Cg_exo) cc_final: 0.5627 (Cg_endo) REVERT: C 359 ASP cc_start: 0.8765 (p0) cc_final: 0.8405 (p0) REVERT: C 604 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9010 (tp) REVERT: C 817 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8993 (pttt) REVERT: C 1083 ASN cc_start: 0.9137 (t0) cc_final: 0.8765 (t160) REVERT: D 359 ASP cc_start: 0.8673 (p0) cc_final: 0.8184 (p0) REVERT: D 604 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9014 (tp) REVERT: D 817 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8987 (pttt) REVERT: D 1083 ASN cc_start: 0.9104 (t0) cc_final: 0.8832 (t160) outliers start: 85 outliers final: 35 residues processed: 319 average time/residue: 1.2705 time to fit residues: 468.9251 Evaluate side-chains 292 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 1 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 779 ASN C 913 ASN D 504 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.091638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.082978 restraints weight = 26624.614| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 0.50 r_work: 0.2547 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 370 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 403 | |-----------------------------------------------------------------------------| r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22970 Z= 0.235 Angle : 0.525 7.264 31148 Z= 0.280 Chirality : 0.043 0.165 3392 Planarity : 0.004 0.060 4054 Dihedral : 4.582 52.087 3126 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.06 % Allowed : 16.76 % Favored : 79.18 % 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: 0.02 (0.15), residues: 2812 helix: 0.11 (0.19), residues: 700 sheet: 0.56 (0.17), residues: 798 loop : -0.27 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 835 HIS 0.003 0.001 HIS C 635 PHE 0.027 0.001 PHE D 698 TYR 0.018 0.001 TYR C 385 ARG 0.003 0.000 ARG C 398 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 258 time to evaluate : 2.623 Fit side-chains REVERT: A 115 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 161 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8545 (pt) REVERT: A 326 VAL cc_start: 0.8781 (t) cc_final: 0.8464 (t) REVERT: B 115 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: B 161 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8615 (pt) REVERT: C 336 PRO cc_start: 0.6156 (Cg_exo) cc_final: 0.5818 (Cg_endo) REVERT: C 468 ASN cc_start: 0.8937 (m-40) cc_final: 0.8597 (m110) REVERT: C 487 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: C 690 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9077 (tp) REVERT: C 779 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8312 (m110) REVERT: C 817 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8967 (pttt) REVERT: C 1060 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8970 (tp) REVERT: C 1083 ASN cc_start: 0.9121 (t0) cc_final: 0.8780 (t160) REVERT: D 200 GLU cc_start: 0.8677 (tp30) cc_final: 0.8365 (tp30) REVERT: D 308 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: D 487 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8522 (mm-30) REVERT: D 648 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: D 690 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9066 (tp) REVERT: D 817 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8971 (pttt) REVERT: D 1060 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8949 (tp) REVERT: D 1083 ASN cc_start: 0.9097 (t0) cc_final: 0.8817 (t160) outliers start: 99 outliers final: 45 residues processed: 335 average time/residue: 1.3063 time to fit residues: 505.5694 Evaluate side-chains 314 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 263 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 256 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 345 HIS B 345 HIS C 504 ASN C 524 GLN C 779 ASN C 913 ASN C1100 ASN D 504 ASN D 779 ASN D 913 ASN D1100 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.084752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.070244 restraints weight = 27343.868| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 0.80 r_work: 0.2409 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2326 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2305 r_free = 0.2305 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 403 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2293 r_free = 0.2293 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 399 | |-----------------------------------------------------------------------------| r_final: 0.2293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 22970 Z= 0.432 Angle : 0.640 10.760 31148 Z= 0.332 Chirality : 0.048 0.213 3392 Planarity : 0.005 0.067 4054 Dihedral : 4.807 20.065 3124 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.55 % Allowed : 16.52 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2812 helix: -0.21 (0.19), residues: 716 sheet: 0.53 (0.17), residues: 796 loop : -0.39 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 835 HIS 0.005 0.001 HIS A 132 PHE 0.042 0.002 PHE D 970 TYR 0.019 0.002 TYR C 385 ARG 0.006 0.001 ARG D 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 261 time to evaluate : 2.516 Fit side-chains REVERT: A 115 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 161 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8610 (pt) REVERT: B 115 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 161 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8662 (pt) REVERT: B 310 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7879 (mtp180) REVERT: C 157 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: C 656 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.9007 (mtp) REVERT: C 690 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9156 (tp) REVERT: C 817 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9082 (pttt) REVERT: C 1060 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9003 (tp) REVERT: C 1083 ASN cc_start: 0.9106 (t0) cc_final: 0.8698 (t160) REVERT: D 157 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: D 359 ASP cc_start: 0.9034 (p0) cc_final: 0.8629 (p0) REVERT: D 487 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8501 (mm-30) REVERT: D 533 MET cc_start: 0.9277 (tpt) cc_final: 0.9044 (tpt) REVERT: D 648 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: D 690 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9153 (tp) REVERT: D 817 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9100 (pttt) REVERT: D 1060 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8987 (tp) REVERT: D 1083 ASN cc_start: 0.9130 (t0) cc_final: 0.8774 (t160) outliers start: 111 outliers final: 59 residues processed: 346 average time/residue: 1.2288 time to fit residues: 495.3942 Evaluate side-chains 336 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 656 MET Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 746 MET Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 183 optimal weight: 0.6980 chunk 230 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 146 optimal weight: 0.0970 chunk 253 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 268 ASN C 504 ASN C 524 GLN C 695 ASN C 913 ASN C1098 ASN D 504 ASN D 569 GLN D 779 ASN D 913 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.087500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.2577 r_free = 0.2577 target = 0.072609 restraints weight = 26686.073| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 0.89 r_work: 0.2471 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 399 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 473 | |-----------------------------------------------------------------------------| r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22970 Z= 0.215 Angle : 0.523 7.135 31148 Z= 0.278 Chirality : 0.043 0.184 3392 Planarity : 0.004 0.056 4054 Dihedral : 4.528 19.850 3124 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.57 % Allowed : 18.07 % Favored : 78.36 % 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: -0.03 (0.15), residues: 2812 helix: 0.13 (0.19), residues: 704 sheet: 0.51 (0.17), residues: 798 loop : -0.32 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 835 HIS 0.004 0.001 HIS D 635 PHE 0.029 0.001 PHE D 698 TYR 0.016 0.001 TYR C 385 ARG 0.002 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 261 time to evaluate : 2.894 Fit side-chains REVERT: A 115 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 161 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8550 (pt) REVERT: B 115 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 161 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (pt) REVERT: B 289 LEU cc_start: 0.8023 (tp) cc_final: 0.7771 (tp) REVERT: B 310 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8027 (mmm-85) REVERT: C 157 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: C 200 GLU cc_start: 0.8712 (tp30) cc_final: 0.8356 (tp30) REVERT: C 468 ASN cc_start: 0.8925 (m-40) cc_final: 0.8599 (m110) REVERT: C 487 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: C 690 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9111 (tp) REVERT: C 817 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9027 (pttt) REVERT: C 1083 ASN cc_start: 0.9107 (t0) cc_final: 0.8749 (t160) REVERT: D 157 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: D 200 GLU cc_start: 0.8738 (tp30) cc_final: 0.8433 (tp30) REVERT: D 487 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8487 (mm-30) REVERT: D 648 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: D 690 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9095 (tp) REVERT: D 817 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.9046 (pttt) REVERT: D 1083 ASN cc_start: 0.9102 (t0) cc_final: 0.8792 (t160) outliers start: 87 outliers final: 47 residues processed: 324 average time/residue: 1.2857 time to fit residues: 481.5812 Evaluate side-chains 316 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 779 ASN Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 913 ASN C1098 ASN D 504 ASN D 695 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.088113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.075098 restraints weight = 26701.385| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 0.73 r_work: 0.2476 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2380 r_free = 0.2380 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 473 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2375 r_free = 0.2375 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 528 | |-----------------------------------------------------------------------------| r_final: 0.2375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22970 Z= 0.204 Angle : 0.514 6.845 31148 Z= 0.273 Chirality : 0.043 0.254 3392 Planarity : 0.004 0.055 4054 Dihedral : 4.449 20.402 3124 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.98 % Allowed : 17.79 % Favored : 78.24 % 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: 0.05 (0.15), residues: 2812 helix: 0.25 (0.19), residues: 704 sheet: 0.55 (0.17), residues: 796 loop : -0.31 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 835 HIS 0.003 0.001 HIS D 635 PHE 0.024 0.001 PHE D 970 TYR 0.018 0.001 TYR C 385 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 257 time to evaluate : 2.479 Fit side-chains REVERT: A 118 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 161 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8553 (pt) REVERT: A 289 LEU cc_start: 0.7943 (tp) cc_final: 0.7717 (tp) REVERT: A 326 VAL cc_start: 0.8954 (t) cc_final: 0.8658 (t) REVERT: B 161 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8611 (pt) REVERT: B 289 LEU cc_start: 0.8123 (tp) cc_final: 0.7848 (tp) REVERT: B 310 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8008 (mmm-85) REVERT: C 157 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8520 (mt0) REVERT: C 200 GLU cc_start: 0.8703 (tp30) cc_final: 0.8338 (tp30) REVERT: C 468 ASN cc_start: 0.8967 (m-40) cc_final: 0.8598 (m110) REVERT: C 487 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8564 (mt-10) REVERT: C 690 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9106 (tp) REVERT: C 817 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8970 (pttt) REVERT: C 1083 ASN cc_start: 0.9105 (t0) cc_final: 0.8765 (t160) REVERT: D 157 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: D 200 GLU cc_start: 0.8742 (tp30) cc_final: 0.8384 (tp30) REVERT: D 487 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8478 (mm-30) REVERT: D 648 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: D 690 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9103 (tp) REVERT: D 817 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9008 (pttt) REVERT: D 1083 ASN cc_start: 0.9123 (t0) cc_final: 0.8830 (t160) outliers start: 97 outliers final: 57 residues processed: 324 average time/residue: 1.2895 time to fit residues: 484.3437 Evaluate side-chains 321 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 0.0670 chunk 199 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 271 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 913 ASN C1098 ASN D 504 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.088620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.075443 restraints weight = 26606.420| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 0.72 r_work: 0.2471 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 528 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22970 Z= 0.224 Angle : 0.521 7.079 31148 Z= 0.276 Chirality : 0.044 0.210 3392 Planarity : 0.004 0.054 4054 Dihedral : 4.439 19.879 3124 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.93 % Allowed : 18.28 % Favored : 77.79 % 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: 0.07 (0.15), residues: 2812 helix: 0.21 (0.19), residues: 716 sheet: 0.58 (0.17), residues: 796 loop : -0.27 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 835 HIS 0.003 0.001 HIS D 635 PHE 0.030 0.001 PHE D 698 TYR 0.018 0.001 TYR C 385 ARG 0.006 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 257 time to evaluate : 2.595 Fit side-chains REVERT: A 118 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 161 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8546 (pt) REVERT: A 289 LEU cc_start: 0.8010 (tp) cc_final: 0.7772 (tp) REVERT: A 310 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7470 (mmm-85) REVERT: A 326 VAL cc_start: 0.8941 (t) cc_final: 0.8640 (t) REVERT: B 118 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 161 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (pt) REVERT: B 289 LEU cc_start: 0.8164 (tp) cc_final: 0.7883 (tp) REVERT: B 310 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7917 (mmm-85) REVERT: B 341 ASP cc_start: 0.5518 (m-30) cc_final: 0.4443 (m-30) REVERT: C 157 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: C 200 GLU cc_start: 0.8718 (tp30) cc_final: 0.8354 (tp30) REVERT: C 468 ASN cc_start: 0.8958 (m-40) cc_final: 0.8568 (m110) REVERT: C 487 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: C 690 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9117 (tp) REVERT: C 817 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8991 (pttt) REVERT: C 1083 ASN cc_start: 0.9081 (t0) cc_final: 0.8738 (t160) REVERT: D 157 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: D 200 GLU cc_start: 0.8748 (tp30) cc_final: 0.8397 (tp30) REVERT: D 487 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8474 (mm-30) REVERT: D 533 MET cc_start: 0.9328 (tpt) cc_final: 0.9087 (tpt) REVERT: D 648 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: D 690 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9100 (tp) REVERT: D 817 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.9006 (pttt) REVERT: D 1083 ASN cc_start: 0.9124 (t0) cc_final: 0.8830 (t160) outliers start: 96 outliers final: 61 residues processed: 327 average time/residue: 1.2638 time to fit residues: 480.2538 Evaluate side-chains 329 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 779 ASN Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 216 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 913 ASN C1098 ASN D 504 ASN D 524 GLN D 779 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.086912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.073792 restraints weight = 26823.305| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 0.70 r_work: 0.2434 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2357 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2334 r_free = 0.2334 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2331 r_free = 0.2331 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 570 | |-----------------------------------------------------------------------------| r_final: 0.2331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 22970 Z= 0.442 Angle : 0.644 11.130 31148 Z= 0.333 Chirality : 0.049 0.257 3392 Planarity : 0.005 0.065 4054 Dihedral : 4.805 19.778 3124 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.93 % Allowed : 18.20 % Favored : 77.87 % 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: -0.18 (0.15), residues: 2812 helix: -0.14 (0.19), residues: 716 sheet: 0.49 (0.17), residues: 800 loop : -0.37 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 835 HIS 0.004 0.001 HIS A 132 PHE 0.043 0.002 PHE D 970 TYR 0.020 0.002 TYR C 385 ARG 0.006 0.001 ARG C 398 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 260 time to evaluate : 2.772 Fit side-chains REVERT: A 115 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 118 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 161 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8604 (pt) REVERT: B 115 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 161 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8663 (pt) REVERT: B 310 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7975 (mmm-85) REVERT: C 157 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: C 200 GLU cc_start: 0.8753 (tp30) cc_final: 0.8469 (tp30) REVERT: C 359 ASP cc_start: 0.8860 (p0) cc_final: 0.8514 (p0) REVERT: C 533 MET cc_start: 0.9296 (tpt) cc_final: 0.9071 (tpt) REVERT: C 690 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9161 (tp) REVERT: C 817 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9008 (pttt) REVERT: C 1083 ASN cc_start: 0.9063 (t0) cc_final: 0.8667 (t160) REVERT: D 157 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: D 200 GLU cc_start: 0.8769 (tp30) cc_final: 0.8499 (tp30) REVERT: D 359 ASP cc_start: 0.8991 (p0) cc_final: 0.8560 (p0) REVERT: D 410 ASN cc_start: 0.8296 (t0) cc_final: 0.8014 (t0) REVERT: D 487 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8464 (mm-30) REVERT: D 582 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: D 648 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: D 690 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9147 (tp) REVERT: D 817 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9050 (pttt) REVERT: D 1083 ASN cc_start: 0.9114 (t0) cc_final: 0.8765 (t160) outliers start: 96 outliers final: 65 residues processed: 335 average time/residue: 1.2280 time to fit residues: 476.6769 Evaluate side-chains 332 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 LEU 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 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 582 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 913 ASN C1098 ASN D 268 ASN D 504 ASN D 524 GLN D 779 ASN D 913 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.089503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.074778 restraints weight = 26612.934| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 0.72 r_work: 0.2478 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2386 r_free = 0.2386 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 570 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2385 r_free = 0.2385 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 593 | |-----------------------------------------------------------------------------| r_final: 0.2385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22970 Z= 0.199 Angle : 0.515 6.543 31148 Z= 0.273 Chirality : 0.043 0.200 3392 Planarity : 0.004 0.054 4054 Dihedral : 4.474 20.006 3124 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.20 % Allowed : 19.34 % Favored : 77.46 % 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: 0.04 (0.15), residues: 2812 helix: 0.18 (0.19), residues: 714 sheet: 0.57 (0.18), residues: 796 loop : -0.28 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 281 HIS 0.004 0.001 HIS D 635 PHE 0.037 0.001 PHE D 698 TYR 0.016 0.001 TYR C 385 ARG 0.004 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 2.481 Fit side-chains REVERT: A 118 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 161 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8556 (pt) REVERT: A 289 LEU cc_start: 0.8131 (tp) cc_final: 0.7881 (tp) REVERT: A 408 MET cc_start: 0.8355 (mtm) cc_final: 0.8147 (mtm) REVERT: B 115 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 118 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 161 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8606 (pt) REVERT: B 289 LEU cc_start: 0.8234 (tp) cc_final: 0.7957 (tp) REVERT: B 310 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7980 (mmm-85) REVERT: C 157 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: C 200 GLU cc_start: 0.8706 (tp30) cc_final: 0.8336 (tp30) REVERT: C 410 ASN cc_start: 0.7940 (t0) cc_final: 0.7517 (t0) REVERT: C 468 ASN cc_start: 0.8947 (m-40) cc_final: 0.8582 (m110) REVERT: C 487 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: C 690 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 817 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8971 (pttt) REVERT: C 1083 ASN cc_start: 0.9108 (t0) cc_final: 0.8770 (t160) REVERT: D 157 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: D 200 GLU cc_start: 0.8732 (tp30) cc_final: 0.8356 (tp30) REVERT: D 487 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8489 (mm-30) REVERT: D 648 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: D 690 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9093 (tp) REVERT: D 817 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9028 (pttt) REVERT: D 1083 ASN cc_start: 0.9120 (t0) cc_final: 0.8833 (t160) outliers start: 78 outliers final: 55 residues processed: 321 average time/residue: 1.2743 time to fit residues: 475.3534 Evaluate side-chains 320 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 259 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 258 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 ASN C 779 ASN C 913 ASN C1098 ASN D 268 ASN D 504 ASN D 695 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.075907 restraints weight = 26711.840| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 0.73 r_work: 0.2478 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 593 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2378 r_free = 0.2378 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 617 | |-----------------------------------------------------------------------------| r_final: 0.2378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22970 Z= 0.200 Angle : 0.512 6.774 31148 Z= 0.271 Chirality : 0.043 0.170 3392 Planarity : 0.004 0.054 4054 Dihedral : 4.377 20.490 3124 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.07 % Allowed : 19.51 % Favored : 77.42 % 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: 0.12 (0.15), residues: 2812 helix: 0.28 (0.19), residues: 716 sheet: 0.60 (0.18), residues: 794 loop : -0.25 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 281 HIS 0.004 0.001 HIS D 635 PHE 0.023 0.001 PHE D 970 TYR 0.017 0.001 TYR C 385 ARG 0.004 0.000 ARG A 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 256 time to evaluate : 2.683 Fit side-chains REVERT: A 115 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 161 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8540 (pt) REVERT: A 289 LEU cc_start: 0.8141 (tp) cc_final: 0.7905 (tp) REVERT: A 326 VAL cc_start: 0.9006 (t) cc_final: 0.8720 (t) REVERT: B 115 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 118 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 161 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8595 (pt) REVERT: B 289 LEU cc_start: 0.8233 (tp) cc_final: 0.7972 (tp) REVERT: B 310 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7981 (mmm-85) REVERT: B 341 ASP cc_start: 0.5628 (m-30) cc_final: 0.4619 (m-30) REVERT: C 157 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: C 200 GLU cc_start: 0.8701 (tp30) cc_final: 0.8286 (tp30) REVERT: C 468 ASN cc_start: 0.8953 (m-40) cc_final: 0.8558 (m110) REVERT: C 487 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: C 690 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9105 (tp) REVERT: C 779 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8533 (m110) REVERT: C 817 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8958 (pttt) REVERT: C 1083 ASN cc_start: 0.9084 (t0) cc_final: 0.8753 (t160) REVERT: D 157 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: D 200 GLU cc_start: 0.8737 (tp30) cc_final: 0.8348 (tp30) REVERT: D 487 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8429 (mm-30) REVERT: D 648 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: D 690 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9089 (tp) REVERT: D 817 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9013 (pttt) REVERT: D 1083 ASN cc_start: 0.9132 (t0) cc_final: 0.8874 (t160) outliers start: 75 outliers final: 55 residues processed: 317 average time/residue: 1.3353 time to fit residues: 491.4858 Evaluate side-chains 324 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 254 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 160 optimal weight: 0.0570 chunk 209 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 ASN C 913 ASN C1098 ASN D 504 ASN D 779 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.090362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.074183 restraints weight = 26487.762| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 0.73 r_work: 0.2476 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2392 r_free = 0.2392 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 617 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2391 r_free = 0.2391 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 635 | |-----------------------------------------------------------------------------| r_final: 0.2391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 22970 Z= 0.249 Angle : 0.687 59.199 31148 Z= 0.395 Chirality : 0.044 0.533 3392 Planarity : 0.004 0.053 4054 Dihedral : 4.445 43.897 3124 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 19.55 % Favored : 77.50 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2812 helix: 0.29 (0.19), residues: 716 sheet: 0.58 (0.18), residues: 794 loop : -0.24 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.004 0.001 HIS D 635 PHE 0.023 0.001 PHE D 970 TYR 0.018 0.001 TYR C 385 ARG 0.006 0.000 ARG B 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14625.12 seconds wall clock time: 260 minutes 35.44 seconds (15635.44 seconds total)