Starting phenix.real_space_refine on Fri Sep 19 01:55:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypu_39494/09_2025/8ypu_39494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypu_39494/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ypu_39494/09_2025/8ypu_39494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypu_39494/09_2025/8ypu_39494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ypu_39494/09_2025/8ypu_39494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypu_39494/09_2025/8ypu_39494.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.27, per 1000 atoms: 0.23 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.74 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: 4.33 Time building geometry restraints manager: 2.41 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: 0.01 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.690 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- 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= 0.266 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (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 ARG 0.010 0.001 ARG C 666 TYR 0.022 0.002 TYR C1010 PHE 0.032 0.002 PHE D 698 TRP 0.023 0.002 TRP D 835 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00617 (22970) covalent geometry : angle 0.67705 (31148) hydrogen bonds : bond 0.10535 ( 1066) hydrogen bonds : angle 6.09749 ( 3027) *********************** 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 : 0.969 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: 0.5880 time to fit residues: 191.5449 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 : 0.907 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** D 373 ASN D 504 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 = 0.2902 r_free = 0.2902 target = 0.092928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.084721 restraints weight = 26857.586| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 0.48 r_work: 0.2649 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 343 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 366 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22970 Z= 0.121 Angle : 0.516 7.685 31148 Z= 0.277 Chirality : 0.043 0.165 3392 Planarity : 0.004 0.065 4054 Dihedral : 4.538 52.093 3126 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.99 % Allowed : 17.91 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 2812 helix: 0.02 (0.19), residues: 700 sheet: 0.62 (0.17), residues: 796 loop : -0.24 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 386 TYR 0.017 0.001 TYR C 385 PHE 0.019 0.001 PHE D 970 TRP 0.016 0.001 TRP C 835 HIS 0.002 0.001 HIS D 635 Details of bonding type rmsd covalent geometry : bond 0.00275 (22970) covalent geometry : angle 0.51614 (31148) hydrogen bonds : bond 0.03286 ( 1066) hydrogen bonds : angle 5.14390 ( 3027) *********************** 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 333 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 260 time to evaluate : 0.800 Fit side-chains REVERT: A 115 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 200 GLU cc_start: 0.8650 (tp30) cc_final: 0.8398 (tp30) REVERT: C 336 PRO cc_start: 0.5956 (Cg_exo) cc_final: 0.5705 (Cg_endo) REVERT: C 468 ASN cc_start: 0.8944 (m-40) cc_final: 0.8628 (m110) REVERT: C 604 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9003 (tp) REVERT: C 1083 ASN cc_start: 0.9171 (t0) cc_final: 0.8814 (t160) REVERT: D 200 GLU cc_start: 0.8689 (tp30) cc_final: 0.8432 (tp30) REVERT: D 604 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9007 (tp) REVERT: D 650 THR cc_start: 0.9379 (p) cc_final: 0.9109 (m) REVERT: D 1083 ASN cc_start: 0.9143 (t0) cc_final: 0.8870 (t160) outliers start: 73 outliers final: 30 residues processed: 312 average time/residue: 0.5476 time to fit residues: 197.6163 Evaluate side-chains 283 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 688 SER 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 D residue 181 THR Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 510 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 688 SER Chi-restraints excluded: chain D residue 828 VAL 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 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 117 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 D 504 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.090929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.082850 restraints weight = 26860.099| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 0.47 r_work: 0.2545 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 1.81 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 366 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 396 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22970 Z= 0.187 Angle : 0.561 7.979 31148 Z= 0.296 Chirality : 0.045 0.182 3392 Planarity : 0.005 0.061 4054 Dihedral : 4.649 52.796 3126 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.14 % Allowed : 16.76 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 2812 helix: 0.05 (0.19), residues: 700 sheet: 0.60 (0.17), residues: 798 loop : -0.27 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 398 TYR 0.018 0.002 TYR C 385 PHE 0.031 0.002 PHE D 970 TRP 0.021 0.002 TRP C 835 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00455 (22970) covalent geometry : angle 0.56052 (31148) hydrogen bonds : bond 0.03309 ( 1066) hydrogen bonds : angle 5.07113 ( 3027) *********************** 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 354 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 253 time to evaluate : 0.642 Fit side-chains REVERT: A 115 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 161 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8522 (pt) REVERT: A 326 VAL cc_start: 0.8808 (t) cc_final: 0.8500 (t) REVERT: B 115 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: B 161 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8588 (pt) REVERT: C 336 PRO cc_start: 0.6236 (Cg_exo) cc_final: 0.5905 (Cg_endo) REVERT: C 487 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: C 690 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 779 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8298 (m110) REVERT: C 1083 ASN cc_start: 0.9115 (t0) cc_final: 0.8764 (t160) REVERT: D 487 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8526 (mm-30) REVERT: D 648 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: D 690 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9080 (tp) REVERT: D 1060 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8986 (tp) REVERT: D 1083 ASN cc_start: 0.9098 (t0) cc_final: 0.8817 (t160) outliers start: 101 outliers final: 49 residues processed: 327 average time/residue: 0.5516 time to fit residues: 208.2965 Evaluate side-chains 313 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 264 LYS 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 495 SER 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 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 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 231 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 276 MET 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 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 828 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 1060 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 185 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 215 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 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 = 0.2791 r_free = 0.2791 target = 0.086704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.2571 r_free = 0.2571 target = 0.072330 restraints weight = 26902.300| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 0.79 r_work: 0.2565 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 396 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| r_final: 0.2465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0824 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= 0.155 Angle : 0.531 7.755 31148 Z= 0.282 Chirality : 0.044 0.173 3392 Planarity : 0.004 0.057 4054 Dihedral : 4.488 20.306 3124 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.89 % Allowed : 17.46 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 2812 helix: 0.17 (0.19), residues: 700 sheet: 0.58 (0.17), residues: 798 loop : -0.26 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.017 0.001 TYR C 385 PHE 0.027 0.001 PHE D 970 TRP 0.019 0.001 TRP C 835 HIS 0.003 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00373 (22970) covalent geometry : angle 0.53143 (31148) hydrogen bonds : bond 0.03103 ( 1066) hydrogen bonds : angle 4.97293 ( 3027) *********************** 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 352 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 257 time to evaluate : 0.665 Fit side-chains REVERT: A 115 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 161 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8522 (pt) REVERT: A 326 VAL cc_start: 0.8884 (t) cc_final: 0.8577 (t) REVERT: B 115 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: B 161 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8564 (pt) REVERT: B 310 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7908 (mtp180) REVERT: C 157 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: C 468 ASN cc_start: 0.8924 (m-40) cc_final: 0.8587 (m110) REVERT: C 487 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: C 690 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9106 (tp) REVERT: C 1060 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8952 (tp) REVERT: C 1083 ASN cc_start: 0.9121 (t0) cc_final: 0.8758 (t160) REVERT: D 157 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: D 200 GLU cc_start: 0.8736 (tp30) cc_final: 0.8402 (tp30) REVERT: D 487 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8503 (mm-30) REVERT: D 648 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: D 690 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9099 (tp) REVERT: D 1083 ASN cc_start: 0.9099 (t0) cc_final: 0.8814 (t160) outliers start: 95 outliers final: 49 residues processed: 324 average time/residue: 0.5404 time to fit residues: 202.4056 Evaluate side-chains 317 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 25 ILE 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 404 THR Chi-restraints excluded: chain B residue 409 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 264 LYS 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 828 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 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 264 LYS Chi-restraints excluded: chain D residue 308 ASP 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 828 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 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 165 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 779 ASN C1098 ASN C1100 ASN D 504 ASN D 569 GLN D 695 ASN D 779 ASN D 913 ASN D1100 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.086569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.071290 restraints weight = 26719.090| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 0.76 r_work: 0.2429 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 466 | |-----------------------------------------------------------------------------| r_final: 0.2413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22970 Z= 0.186 Angle : 0.557 8.301 31148 Z= 0.294 Chirality : 0.045 0.174 3392 Planarity : 0.005 0.056 4054 Dihedral : 4.567 19.766 3124 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.43 % Allowed : 16.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 2812 helix: 0.14 (0.19), residues: 700 sheet: 0.55 (0.17), residues: 798 loop : -0.31 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.018 0.002 TYR C 385 PHE 0.032 0.002 PHE D 970 TRP 0.017 0.002 TRP D 835 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00453 (22970) covalent geometry : angle 0.55695 (31148) hydrogen bonds : bond 0.03201 ( 1066) hydrogen bonds : angle 4.99795 ( 3027) *********************** 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 370 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 262 time to evaluate : 0.630 Fit side-chains REVERT: A 115 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 161 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8470 (pt) REVERT: A 326 VAL cc_start: 0.8945 (t) cc_final: 0.8645 (t) REVERT: B 115 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 161 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8586 (pt) REVERT: B 289 LEU cc_start: 0.8084 (tp) cc_final: 0.7819 (tp) REVERT: B 310 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8085 (mmm-85) REVERT: C 157 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: C 487 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: C 690 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9122 (tp) REVERT: C 746 MET cc_start: 0.9052 (mtt) cc_final: 0.8706 (ptp) REVERT: C 779 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8472 (m110) REVERT: C 1060 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8981 (tp) REVERT: C 1083 ASN cc_start: 0.9059 (t0) cc_final: 0.8660 (t160) REVERT: D 157 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8565 (mt0) REVERT: D 487 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8474 (mm-30) REVERT: D 648 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: D 690 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9107 (tp) REVERT: D 1083 ASN cc_start: 0.9103 (t0) cc_final: 0.8787 (t160) outliers start: 108 outliers final: 59 residues processed: 340 average time/residue: 0.5381 time to fit residues: 211.9867 Evaluate side-chains 328 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 625 ASP 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 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 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 264 LYS Chi-restraints excluded: chain D residue 322 LEU 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 625 ASP 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 828 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 174 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 245 optimal weight: 0.0970 chunk 128 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 chunk 158 optimal weight: 0.0980 chunk 149 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 695 ASN C 779 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.089212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.2636 r_free = 0.2636 target = 0.076328 restraints weight = 26635.885| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 0.61 r_work: 0.2526 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2431 r_free = 0.2431 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 466 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2425 r_free = 0.2425 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 526 | |-----------------------------------------------------------------------------| r_final: 0.2425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22970 Z= 0.105 Angle : 0.491 5.970 31148 Z= 0.263 Chirality : 0.042 0.166 3392 Planarity : 0.004 0.054 4054 Dihedral : 4.337 20.676 3124 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.24 % Allowed : 18.20 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 2812 helix: 0.41 (0.20), residues: 700 sheet: 0.61 (0.17), residues: 792 loop : -0.23 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 386 TYR 0.016 0.001 TYR C 385 PHE 0.019 0.001 PHE D 970 TRP 0.015 0.001 TRP B 281 HIS 0.004 0.001 HIS D 635 Details of bonding type rmsd covalent geometry : bond 0.00240 (22970) covalent geometry : angle 0.49106 (31148) hydrogen bonds : bond 0.02849 ( 1066) hydrogen bonds : angle 4.81820 ( 3027) *********************** 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 337 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 1.007 Fit side-chains REVERT: A 161 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8498 (pt) REVERT: A 248 MET cc_start: 0.7051 (mtm) cc_final: 0.6455 (mtp) REVERT: A 326 VAL cc_start: 0.8940 (t) cc_final: 0.8643 (t) REVERT: A 408 MET cc_start: 0.8434 (mtm) cc_final: 0.8154 (mtm) REVERT: B 118 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 161 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8591 (pt) REVERT: B 289 LEU cc_start: 0.8050 (tp) cc_final: 0.7784 (tp) REVERT: B 310 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8031 (mmm-85) REVERT: B 415 LYS cc_start: 0.7209 (mtpm) cc_final: 0.6788 (ttmm) REVERT: C 157 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (mt0) REVERT: C 200 GLU cc_start: 0.8669 (tp30) cc_final: 0.8311 (tp30) REVERT: C 468 ASN cc_start: 0.8951 (m-40) cc_final: 0.8580 (m110) REVERT: C 487 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: C 690 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9087 (tp) REVERT: C 746 MET cc_start: 0.8982 (mtt) cc_final: 0.8634 (ptp) REVERT: C 1083 ASN cc_start: 0.9067 (t0) cc_final: 0.8727 (t160) REVERT: D 157 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: D 200 GLU cc_start: 0.8680 (tp30) cc_final: 0.8314 (tp30) REVERT: D 487 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8512 (mm-30) REVERT: D 648 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: D 690 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9047 (tp) REVERT: D 1083 ASN cc_start: 0.9112 (t0) cc_final: 0.8847 (t160) outliers start: 79 outliers final: 39 residues processed: 316 average time/residue: 0.5454 time to fit residues: 199.4817 Evaluate side-chains 300 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE 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 157 GLN 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 495 SER Chi-restraints excluded: chain C residue 510 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 828 VAL Chi-restraints excluded: chain C residue 894 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 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 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 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 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 779 ASN Chi-restraints excluded: chain D residue 828 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 57 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 142 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 C1098 ASN D 504 ASN D 695 ASN D 779 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.088222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.075137 restraints weight = 26772.658| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 0.71 r_work: 0.2468 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2373 r_free = 0.2373 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 526 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2370 r_free = 0.2370 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 551 | |-----------------------------------------------------------------------------| r_final: 0.2370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22970 Z= 0.174 Angle : 0.545 7.963 31148 Z= 0.287 Chirality : 0.045 0.208 3392 Planarity : 0.004 0.054 4054 Dihedral : 4.452 19.725 3124 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.57 % Allowed : 18.16 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.15), residues: 2812 helix: 0.23 (0.19), residues: 712 sheet: 0.60 (0.17), residues: 796 loop : -0.24 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.019 0.001 TYR C 385 PHE 0.029 0.002 PHE D 698 TRP 0.019 0.002 TRP D 835 HIS 0.003 0.001 HIS D 635 Details of bonding type rmsd covalent geometry : bond 0.00425 (22970) covalent geometry : angle 0.54485 (31148) hydrogen bonds : bond 0.03061 ( 1066) hydrogen bonds : angle 4.88361 ( 3027) *********************** 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 346 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 259 time to evaluate : 0.773 Fit side-chains REVERT: A 118 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 161 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8541 (pt) REVERT: A 326 VAL cc_start: 0.8951 (t) cc_final: 0.8658 (t) REVERT: A 408 MET cc_start: 0.8468 (mtm) cc_final: 0.8192 (mtm) REVERT: B 118 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8043 (mt-10) REVERT: B 161 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8585 (pt) REVERT: B 310 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8071 (mmm-85) REVERT: B 341 ASP cc_start: 0.5552 (m-30) cc_final: 0.4522 (m-30) REVERT: C 157 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: C 468 ASN cc_start: 0.8881 (m-40) cc_final: 0.8517 (m110) REVERT: C 487 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: C 690 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9106 (tp) REVERT: C 746 MET cc_start: 0.9045 (mtt) cc_final: 0.8668 (ptp) REVERT: C 779 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8427 (m110) REVERT: C 1083 ASN cc_start: 0.9090 (t0) cc_final: 0.8715 (t160) REVERT: D 157 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8564 (mt0) REVERT: D 487 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8520 (mm-30) REVERT: D 648 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: D 690 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9092 (tp) REVERT: D 1083 ASN cc_start: 0.9098 (t0) cc_final: 0.8791 (t160) outliers start: 87 outliers final: 52 residues processed: 326 average time/residue: 0.5431 time to fit residues: 205.4154 Evaluate side-chains 315 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 216 ILE 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 495 SER Chi-restraints excluded: chain C residue 510 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 779 ASN 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 216 ILE Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 254 VAL 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 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 828 VAL 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 99 optimal weight: 1.9990 chunk 171 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.2812 r_free = 0.2812 target = 0.088141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.074019 restraints weight = 26608.178| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 0.69 r_work: 0.2467 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2369 |-occupancy refinement: start-------------------------------------------------| | 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: 551 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2367 r_free = 0.2367 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 578 | |-----------------------------------------------------------------------------| r_final: 0.2367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22970 Z= 0.194 Angle : 0.566 8.291 31148 Z= 0.297 Chirality : 0.045 0.192 3392 Planarity : 0.005 0.059 4054 Dihedral : 4.542 20.263 3124 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.48 % Allowed : 18.61 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.15), residues: 2812 helix: 0.11 (0.19), residues: 716 sheet: 0.59 (0.17), residues: 796 loop : -0.26 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 398 TYR 0.019 0.002 TYR C 385 PHE 0.032 0.002 PHE D 970 TRP 0.021 0.002 TRP C 835 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00475 (22970) covalent geometry : angle 0.56567 (31148) hydrogen bonds : bond 0.03167 ( 1066) hydrogen bonds : angle 4.94097 ( 3027) *********************** 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 343 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 258 time to evaluate : 0.835 Fit side-chains REVERT: A 118 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8016 (mt-10) REVERT: A 161 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8542 (pt) REVERT: A 326 VAL cc_start: 0.8963 (t) cc_final: 0.8684 (t) REVERT: B 115 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 118 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 161 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8606 (pt) REVERT: B 289 LEU cc_start: 0.8240 (tp) cc_final: 0.7963 (tp) REVERT: B 310 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7982 (mmm-85) REVERT: B 415 LYS cc_start: 0.7574 (mtpp) cc_final: 0.6981 (mtmt) REVERT: C 157 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: C 468 ASN cc_start: 0.8878 (m-40) cc_final: 0.8532 (m110) REVERT: C 487 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8604 (mt-10) REVERT: C 690 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9122 (tp) REVERT: C 746 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8671 (ptp) REVERT: C 1083 ASN cc_start: 0.9094 (t0) cc_final: 0.8703 (t160) REVERT: D 157 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: D 487 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8500 (mm-30) REVERT: D 648 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: D 690 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9106 (tp) REVERT: D 1083 ASN cc_start: 0.9098 (t0) cc_final: 0.8788 (t160) outliers start: 85 outliers final: 59 residues processed: 323 average time/residue: 0.5534 time to fit residues: 207.1839 Evaluate side-chains 327 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 257 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 495 SER 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 746 MET Chi-restraints excluded: chain C residue 825 THR 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 216 ILE Chi-restraints excluded: chain D residue 231 ASN 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 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 828 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 162 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 504 ASN D 779 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.089005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.074210 restraints weight = 26656.059| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 0.73 r_work: 0.2463 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2369 |-occupancy refinement: start-------------------------------------------------| | 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: 578 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2367 r_free = 0.2367 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 592 | |-----------------------------------------------------------------------------| r_final: 0.2367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.004 0.054 22970 Z= 0.163 Angle : 0.540 7.629 31148 Z= 0.285 Chirality : 0.044 0.181 3392 Planarity : 0.004 0.053 4054 Dihedral : 4.492 19.709 3124 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.36 % Allowed : 19.02 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.15), residues: 2812 helix: 0.20 (0.19), residues: 712 sheet: 0.59 (0.17), residues: 796 loop : -0.25 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.018 0.001 TYR C 385 PHE 0.033 0.001 PHE D 698 TRP 0.019 0.001 TRP C 835 HIS 0.003 0.001 HIS D 635 Details of bonding type rmsd covalent geometry : bond 0.00395 (22970) covalent geometry : angle 0.54042 (31148) hydrogen bonds : bond 0.03048 ( 1066) hydrogen bonds : angle 4.90521 ( 3027) *********************** 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 343 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 261 time to evaluate : 0.767 Fit side-chains REVERT: A 115 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 118 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 161 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8541 (pt) REVERT: A 248 MET cc_start: 0.7155 (mtm) cc_final: 0.6496 (mtp) REVERT: A 289 LEU cc_start: 0.8185 (tp) cc_final: 0.7937 (tp) REVERT: A 326 VAL cc_start: 0.8988 (t) cc_final: 0.8714 (t) REVERT: B 115 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: B 118 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 161 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8595 (pt) REVERT: B 289 LEU cc_start: 0.8282 (tp) cc_final: 0.7997 (tp) REVERT: B 310 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7997 (mmm-85) REVERT: B 415 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7044 (mtmt) REVERT: C 157 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8542 (mt0) REVERT: C 468 ASN cc_start: 0.8878 (m-40) cc_final: 0.8527 (m110) REVERT: C 487 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8583 (mt-10) REVERT: C 690 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9108 (tp) REVERT: C 746 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8652 (ptp) REVERT: C 1083 ASN cc_start: 0.9093 (t0) cc_final: 0.8709 (t160) REVERT: D 157 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: D 648 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: D 690 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9101 (tp) REVERT: D 1083 ASN cc_start: 0.9104 (t0) cc_final: 0.8783 (t160) outliers start: 82 outliers final: 57 residues processed: 324 average time/residue: 0.5618 time to fit residues: 210.3774 Evaluate side-chains 323 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 254 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 495 SER 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 746 MET 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 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 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 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 828 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 132 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 504 ASN D 779 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.089482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.074317 restraints weight = 26640.747| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 0.70 r_work: 0.2475 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- 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: 592 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 609 | |-----------------------------------------------------------------------------| r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22970 Z= 0.155 Angle : 0.534 7.296 31148 Z= 0.282 Chirality : 0.044 0.175 3392 Planarity : 0.004 0.053 4054 Dihedral : 4.460 20.344 3124 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.16 % Allowed : 19.34 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 2812 helix: 0.24 (0.19), residues: 712 sheet: 0.59 (0.17), residues: 796 loop : -0.24 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 407 TYR 0.018 0.001 TYR C 385 PHE 0.035 0.001 PHE D 698 TRP 0.019 0.001 TRP C 835 HIS 0.003 0.001 HIS D 635 Details of bonding type rmsd covalent geometry : bond 0.00375 (22970) covalent geometry : angle 0.53388 (31148) hydrogen bonds : bond 0.03004 ( 1066) hydrogen bonds : angle 4.87983 ( 3027) ********************** 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 335 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 0.727 Fit side-chains REVERT: A 115 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 118 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7989 (mt-10) REVERT: A 161 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8572 (pt) REVERT: A 248 MET cc_start: 0.7115 (mtm) cc_final: 0.6492 (mtp) REVERT: A 289 LEU cc_start: 0.8196 (tp) cc_final: 0.7951 (tp) REVERT: A 326 VAL cc_start: 0.9001 (t) cc_final: 0.8724 (t) REVERT: B 115 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 118 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 161 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8573 (pt) REVERT: B 289 LEU cc_start: 0.8275 (tp) cc_final: 0.8003 (tp) REVERT: B 310 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8020 (mmm-85) REVERT: B 415 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7070 (mtmt) REVERT: C 157 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: C 468 ASN cc_start: 0.8950 (m-40) cc_final: 0.8586 (m110) REVERT: C 487 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: C 690 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9110 (tp) REVERT: C 1083 ASN cc_start: 0.9116 (t0) cc_final: 0.8751 (t160) REVERT: D 157 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: D 533 MET cc_start: 0.9291 (tpt) cc_final: 0.9048 (tpt) REVERT: D 648 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: D 690 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9095 (tp) REVERT: D 1083 ASN cc_start: 0.9099 (t0) cc_final: 0.8784 (t160) outliers start: 77 outliers final: 55 residues processed: 319 average time/residue: 0.5451 time to fit residues: 201.1306 Evaluate side-chains 321 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 B residue 409 VAL Chi-restraints excluded: chain C residue 117 VAL 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 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 495 SER 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 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 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 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 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 828 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 246 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 C1098 ASN D 504 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 = 0.2850 r_free = 0.2850 target = 0.090642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.075852 restraints weight = 26546.708| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 0.68 r_work: 0.2487 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 634 | |-----------------------------------------------------------------------------| r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1073 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= 0.135 Angle : 0.517 6.950 31148 Z= 0.274 Chirality : 0.043 0.159 3392 Planarity : 0.004 0.053 4054 Dihedral : 4.394 19.291 3124 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.99 % Allowed : 19.67 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.15), residues: 2812 helix: 0.32 (0.19), residues: 712 sheet: 0.60 (0.17), residues: 796 loop : -0.22 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.018 0.001 TYR C 385 PHE 0.034 0.001 PHE D 698 TRP 0.017 0.001 TRP D 835 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00323 (22970) covalent geometry : angle 0.51663 (31148) hydrogen bonds : bond 0.02913 ( 1066) hydrogen bonds : angle 4.83510 ( 3027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6810.88 seconds wall clock time: 116 minutes 47.93 seconds (7007.93 seconds total)