Starting phenix.real_space_refine on Thu Jun 19 05:50:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ypu_39494/06_2025/8ypu_39494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ypu_39494/06_2025/8ypu_39494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ypu_39494/06_2025/8ypu_39494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ypu_39494/06_2025/8ypu_39494.map" model { file = "/net/cci-nas-00/data/ceres_data/8ypu_39494/06_2025/8ypu_39494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ypu_39494/06_2025/8ypu_39494.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.332 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 14264 2.51 5 N 3834 2.21 5 O 4322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3377 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 20, 'TRANS': 402} Chain: "B" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3377 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 20, 'TRANS': 402} Chain: "C" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7861 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 38, 'TRANS': 948} Chain: "D" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7861 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 38, 'TRANS': 948} Residues with excluded nonbonded symmetry interactions: 60 residue: pdb=" N GLY A 77 " occ=0.63 ... (2 atoms not shown) pdb=" O GLY A 77 " occ=0.37 residue: pdb=" N SER A 234 " occ=0.39 ... (4 atoms not shown) pdb=" OG SER A 234 " occ=0.31 residue: pdb=" N LYS A 242 " occ=0.35 ... (7 atoms not shown) pdb=" NZ LYS A 242 " occ=0.43 residue: pdb=" N PRO A 256 " occ=0.87 ... (5 atoms not shown) pdb=" CD PRO A 256 " occ=0.53 residue: pdb=" N SER A 261 " occ=0.82 ... (4 atoms not shown) pdb=" OG SER A 261 " occ=0.31 residue: pdb=" N ALA A 279 " occ=0.55 ... (3 atoms not shown) pdb=" CB ALA A 279 " occ=0.41 residue: pdb=" N PHE A 286 " occ=0.47 ... (9 atoms not shown) pdb=" CZ PHE A 286 " occ=0.51 residue: pdb=" N PHE A 301 " occ=0.53 ... (9 atoms not shown) pdb=" CZ PHE A 301 " occ=0.56 residue: pdb=" N ALA A 302 " occ=0.26 ... (3 atoms not shown) pdb=" CB ALA A 302 " occ=0.59 residue: pdb=" N SER A 313 " occ=0.45 ... (4 atoms not shown) pdb=" OG SER A 313 " occ=0.17 residue: pdb=" N GLY A 316 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY A 316 " occ=0.44 residue: pdb=" N GLY A 327 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY A 327 " occ=0.12 ... (remaining 48 not shown) Time building chain proxies: 12.29, per 1000 atoms: 0.55 Number of scatterers: 22476 At special positions: 0 Unit cell: (152.22, 130.98, 128.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 4322 8.00 N 3834 7.00 C 14264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 2.7 seconds 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5260 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 24 sheets defined 27.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.500A pdb=" N ASN A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.917A pdb=" N LEU A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 5.718A pdb=" N ASP A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.585A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 147 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.545A pdb=" N GLU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.995A pdb=" N VAL A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 294 through 300 removed outlier: 4.046A pdb=" N ALA A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.530A pdb=" N LEU A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.724A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'A' and resid 396 through 404 removed outlier: 3.605A pdb=" N THR A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.644A pdb=" N THR A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.504A pdb=" N ASN B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.920A pdb=" N LEU B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 5.718A pdb=" N ASP B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 removed outlier: 3.591A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.829A pdb=" N ILE B 116 " --> pdb=" O GLN B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 120 through 147 Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.542A pdb=" N GLU B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.692A pdb=" N VAL B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 294 through 300 removed outlier: 4.048A pdb=" N ALA B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.517A pdb=" N LEU B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 359 through 372 removed outlier: 3.723A pdb=" N ALA B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 396 through 404 removed outlier: 3.609A pdb=" N THR B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.619A pdb=" N THR B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.665A pdb=" N VAL C 213 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 216 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 243 through 248 removed outlier: 6.905A pdb=" N ALA C 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 removed outlier: 3.533A pdb=" N SER C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 322 through 329 Processing helix chain 'C' and resid 335 through 347 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 530 through 539 Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 980 through 986 removed outlier: 3.786A pdb=" N ILE C 983 " --> pdb=" O ASN C 980 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 986 " --> pdb=" O ILE C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1015 Processing helix chain 'C' and resid 1016 through 1021 removed outlier: 3.838A pdb=" N LYS C1020 " --> pdb=" O SER C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1022 through 1024 No H-bonds generated for 'chain 'C' and resid 1022 through 1024' Processing helix chain 'C' and resid 1044 through 1051 Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.666A pdb=" N VAL D 213 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 216 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 243 through 248 removed outlier: 6.877A pdb=" N ALA D 246 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 312 through 321 removed outlier: 3.504A pdb=" N TYR D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 335 through 347 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 476 through 483 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 627 through 632 Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.586A pdb=" N ARG D 703 " --> pdb=" O GLN D 700 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS D 704 " --> pdb=" O GLY D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 901 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 980 through 986 removed outlier: 3.790A pdb=" N ILE D 983 " --> pdb=" O ASN D 980 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 986 " --> pdb=" O ILE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1015 removed outlier: 3.559A pdb=" N GLN D1014 " --> pdb=" O TYR D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1021 removed outlier: 3.812A pdb=" N LYS D1020 " --> pdb=" O SER D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1024 No H-bonds generated for 'chain 'D' and resid 1022 through 1024' Processing helix chain 'D' and resid 1044 through 1051 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 removed outlier: 5.822A pdb=" N ASN A 176 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 264 through 266 removed outlier: 6.573A pdb=" N PHE A 324 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 412 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.012A pdb=" N ASN B 176 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 266 removed outlier: 6.577A pdb=" N PHE B 324 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 408 through 412 Processing sheet with id=AA9, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.520A pdb=" N ASN C 231 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C 191 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE C 255 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 193 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR C 257 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AB3, first strand: chain 'C' and resid 1067 through 1069 removed outlier: 4.043A pdb=" N ILE C 267 " --> pdb=" O PHE C1101 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS C 264 " --> pdb=" O GLY C 372 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY C 372 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C 361 " --> pdb=" O ASN C 388 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN C 388 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY C 558 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA C 812 " --> pdb=" O ASP C 791 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE C 793 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN C 810 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS C 795 " --> pdb=" O ASN C 808 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN C 808 " --> pdb=" O LYS C 795 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET C 797 " --> pdb=" O SER C 806 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 806 " --> pdb=" O MET C 797 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER C 813 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 835 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA C 829 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER C 955 " --> pdb=" O LEU C1034 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU C1034 " --> pdb=" O SER C 955 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN C 957 " --> pdb=" O PHE C1032 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE C1032 " --> pdb=" O ASN C 957 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY C 959 " --> pdb=" O ASN C1030 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN C1030 " --> pdb=" O GLY C 959 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR C 961 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS C1028 " --> pdb=" O TYR C 961 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 963 " --> pdb=" O VAL C1026 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C1026 " --> pdb=" O ARG C 963 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 541 through 544 removed outlier: 3.562A pdb=" N ASP C 544 " --> pdb=" O SER C 549 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER C 549 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 730 through 739 removed outlier: 6.801A pdb=" N LEU C 730 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 738 " --> pdb=" O GLY C 742 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY C 742 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 869 through 872 removed outlier: 6.805A pdb=" N ILE C 870 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 877 through 878 removed outlier: 3.633A pdb=" N GLY C 877 " --> pdb=" O LEU C 885 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AB9, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.532A pdb=" N ASN D 231 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU D 191 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE D 255 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 193 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR D 257 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 161 through 165 Processing sheet with id=AC2, first strand: chain 'D' and resid 1067 through 1069 removed outlier: 4.047A pdb=" N ILE D 267 " --> pdb=" O PHE D1101 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS D 264 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY D 372 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE D 361 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN D 388 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY D 558 " --> pdb=" O GLY D 610 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY D 593 " --> pdb=" O PHE D 648 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA D 812 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE D 793 " --> pdb=" O ASN D 810 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN D 810 " --> pdb=" O ILE D 793 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS D 795 " --> pdb=" O ASN D 808 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN D 808 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET D 797 " --> pdb=" O SER D 806 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 806 " --> pdb=" O MET D 797 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER D 813 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP D 835 " --> pdb=" O ASN D 827 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA D 829 " --> pdb=" O PHE D 833 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 955 " --> pdb=" O LEU D1034 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D1034 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN D 957 " --> pdb=" O PHE D1032 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE D1032 " --> pdb=" O ASN D 957 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY D 959 " --> pdb=" O ASN D1030 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN D1030 " --> pdb=" O GLY D 959 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR D 961 " --> pdb=" O LYS D1028 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS D1028 " --> pdb=" O TYR D 961 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG D 963 " --> pdb=" O VAL D1026 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D1026 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 541 through 544 removed outlier: 3.564A pdb=" N ASP D 544 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER D 549 " --> pdb=" O ASP D 544 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 730 through 739 removed outlier: 6.807A pdb=" N LEU D 730 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 738 " --> pdb=" O GLY D 742 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY D 742 " --> pdb=" O ILE D 738 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 869 through 872 removed outlier: 6.816A pdb=" N ILE D 870 " --> pdb=" O ILE D 928 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 877 through 878 removed outlier: 3.680A pdb=" N GLY D 877 " --> pdb=" O LEU D 885 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.15 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7279 1.34 - 1.45: 3712 1.45 - 1.57: 11875 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 22970 Sorted by residual: bond pdb=" N VAL B 28 " pdb=" CA VAL B 28 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.25e+01 bond pdb=" N ILE B 25 " pdb=" CA ILE B 25 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.93e+00 bond pdb=" N GLN D 206 " pdb=" CA GLN D 206 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.17e-02 7.31e+03 8.54e+00 bond pdb=" N ASN B 210 " pdb=" CA ASN B 210 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.55e+00 bond pdb=" N VAL D 204 " pdb=" CA VAL D 204 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.46e+00 ... (remaining 22965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 30512 2.03 - 4.07: 547 4.07 - 6.10: 64 6.10 - 8.13: 21 8.13 - 10.17: 4 Bond angle restraints: 31148 Sorted by residual: angle pdb=" N TYR B 22 " pdb=" CA TYR B 22 " pdb=" C TYR B 22 " ideal model delta sigma weight residual 110.91 102.99 7.92 1.17e+00 7.31e-01 4.58e+01 angle pdb=" C THR D 471 " pdb=" CA THR D 471 " pdb=" CB THR D 471 " ideal model delta sigma weight residual 111.18 120.06 -8.88 1.56e+00 4.11e-01 3.24e+01 angle pdb=" N SER B 160 " pdb=" CA SER B 160 " pdb=" C SER B 160 " ideal model delta sigma weight residual 112.68 119.80 -7.12 1.33e+00 5.65e-01 2.87e+01 angle pdb=" N ARG D1005 " pdb=" CA ARG D1005 " pdb=" C ARG D1005 " ideal model delta sigma weight residual 111.52 118.48 -6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" N SER B 21 " pdb=" CA SER B 21 " pdb=" C SER B 21 " ideal model delta sigma weight residual 108.19 102.15 6.04 1.29e+00 6.01e-01 2.19e+01 ... (remaining 31143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 11971 17.50 - 35.00: 1356 35.00 - 52.51: 330 52.51 - 70.01: 68 70.01 - 87.51: 25 Dihedral angle restraints: 13750 sinusoidal: 5520 harmonic: 8230 Sorted by residual: dihedral pdb=" CA PHE D 648 " pdb=" C PHE D 648 " pdb=" N SER D 649 " pdb=" CA SER D 649 " ideal model delta harmonic sigma weight residual 180.00 153.79 26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C THR D 471 " pdb=" N THR D 471 " pdb=" CA THR D 471 " pdb=" CB THR D 471 " ideal model delta harmonic sigma weight residual -122.00 -134.75 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ALA D 246 " pdb=" N ALA D 246 " pdb=" CA ALA D 246 " pdb=" CB ALA D 246 " ideal model delta harmonic sigma weight residual -122.60 -134.50 11.90 0 2.50e+00 1.60e-01 2.27e+01 ... (remaining 13747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3115 0.088 - 0.177: 258 0.177 - 0.265: 9 0.265 - 0.354: 5 0.354 - 0.442: 5 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA SER B 112 " pdb=" N SER B 112 " pdb=" C SER B 112 " pdb=" CB SER B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA ALA D 246 " pdb=" N ALA D 246 " pdb=" C ALA D 246 " pdb=" CB ALA D 246 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA SER B 21 " pdb=" N SER B 21 " pdb=" C SER B 21 " pdb=" CB SER B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 3389 not shown) Planarity restraints: 4054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 335 " 0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO D 336 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 336 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 336 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 343 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 344 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 343 " -0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO A 344 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.047 5.00e-02 4.00e+02 ... (remaining 4051 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 253 2.63 - 3.20: 18761 3.20 - 3.77: 34275 3.77 - 4.33: 52167 4.33 - 4.90: 87455 Nonbonded interactions: 192911 Sorted by model distance: nonbonded pdb=" OH TYR B 207 " pdb=" OE2 GLU D 744 " model vdw 2.065 3.040 nonbonded pdb=" OH TYR A 207 " pdb=" OE2 GLU C 744 " model vdw 2.075 3.040 nonbonded pdb=" OD1 ASN D 138 " pdb=" OD1 ASN D 231 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR A 137 " pdb=" OE1 GLU A 269 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR B 137 " pdb=" OE1 GLU B 269 " model vdw 2.117 3.040 ... (remaining 192906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.80 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.110 Set scattering table: 0.190 Process input model: 48.620 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2812 helix: -0.52 (0.19), residues: 716 sheet: 0.64 (0.17), residues: 794 loop : -0.30 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 835 HIS 0.004 0.001 HIS A 132 PHE 0.032 0.002 PHE D 698 TYR 0.022 0.002 TYR C1010 ARG 0.010 0.001 ARG C 666 Details of bonding type rmsd hydrogen bonds : bond 0.10535 ( 1066) hydrogen bonds : angle 6.09749 ( 3027) covalent geometry : bond 0.00617 (22970) covalent geometry : angle 0.67705 (31148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 2.689 Fit side-chains REVERT: A 415 LYS cc_start: 0.6570 (mtpm) cc_final: 0.6362 (ttpt) REVERT: C 468 ASN cc_start: 0.8987 (m-40) cc_final: 0.8701 (m110) REVERT: C 626 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8152 (mt-10) REVERT: C 1083 ASN cc_start: 0.9210 (t0) cc_final: 0.8786 (t160) REVERT: D 533 MET cc_start: 0.9364 (tpt) cc_final: 0.9151 (tpt) REVERT: D 626 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8131 (mt-10) REVERT: D 650 THR cc_start: 0.9390 (p) cc_final: 0.9161 (m) REVERT: D 1083 ASN cc_start: 0.9190 (t0) cc_final: 0.8894 (t160) outliers start: 6 outliers final: 2 residues processed: 284 average time/residue: 1.5318 time to fit residues: 503.3093 Evaluate side-chains 254 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 117 optimal weight: 0.0170 chunk 72 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 210 ASN B 52 ASN C 373 ASN C 504 ASN ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 ASN D 373 ASN D 504 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.091501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.084206 restraints weight = 26900.074| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 0.46 r_work: 0.2563 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 343 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 371 | |-----------------------------------------------------------------------------| r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22970 Z= 0.169 Angle : 0.557 6.998 31148 Z= 0.296 Chirality : 0.044 0.177 3392 Planarity : 0.005 0.066 4054 Dihedral : 4.695 52.847 3126 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.48 % Allowed : 17.25 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2812 helix: -0.11 (0.19), residues: 700 sheet: 0.58 (0.17), residues: 798 loop : -0.30 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 835 HIS 0.003 0.001 HIS B 132 PHE 0.027 0.002 PHE D 970 TYR 0.018 0.001 TYR C 385 ARG 0.004 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 1066) hydrogen bonds : angle 5.21749 ( 3027) covalent geometry : bond 0.00404 (22970) covalent geometry : angle 0.55714 (31148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 259 time to evaluate : 2.777 Fit side-chains REVERT: A 115 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: C 336 PRO cc_start: 0.5905 (Cg_exo) cc_final: 0.5629 (Cg_endo) REVERT: C 359 ASP cc_start: 0.8767 (p0) cc_final: 0.8407 (p0) REVERT: C 604 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9011 (tp) REVERT: C 817 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8987 (pttt) REVERT: C 1083 ASN cc_start: 0.9138 (t0) cc_final: 0.8767 (t160) REVERT: D 359 ASP cc_start: 0.8673 (p0) cc_final: 0.8185 (p0) REVERT: D 604 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9015 (tp) REVERT: D 817 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8981 (pttt) REVERT: D 1083 ASN cc_start: 0.9104 (t0) cc_final: 0.8833 (t160) outliers start: 85 outliers final: 35 residues processed: 319 average time/residue: 1.4371 time to fit residues: 534.1421 Evaluate side-chains 292 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1096 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Chi-restraints excluded: chain D residue 1096 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 1 optimal weight: 0.0470 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 105 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 779 ASN C 913 ASN D 504 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.087588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.075529 restraints weight = 26734.021| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 0.78 r_work: 0.2564 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2463 r_free = 0.2463 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 371 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2449 r_free = 0.2449 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 389 | |-----------------------------------------------------------------------------| r_final: 0.2449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22970 Z= 0.131 Angle : 0.508 7.150 31148 Z= 0.271 Chirality : 0.043 0.158 3392 Planarity : 0.004 0.060 4054 Dihedral : 4.508 51.199 3126 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.85 % Allowed : 16.76 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2812 helix: 0.18 (0.20), residues: 700 sheet: 0.62 (0.17), residues: 792 loop : -0.24 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 835 HIS 0.003 0.001 HIS C 635 PHE 0.027 0.001 PHE D 698 TYR 0.017 0.001 TYR C 385 ARG 0.002 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 1066) hydrogen bonds : angle 4.96759 ( 3027) covalent geometry : bond 0.00309 (22970) covalent geometry : angle 0.50773 (31148) *********************** 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 353 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 259 time to evaluate : 2.608 Fit side-chains REVERT: A 115 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: A 161 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8578 (pt) REVERT: A 326 VAL cc_start: 0.8785 (t) cc_final: 0.8473 (t) REVERT: B 115 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: B 161 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8635 (pt) REVERT: B 289 LEU cc_start: 0.7714 (tp) cc_final: 0.7495 (tp) REVERT: C 200 GLU cc_start: 0.8750 (tp30) cc_final: 0.8470 (tp30) REVERT: C 468 ASN cc_start: 0.8970 (m-40) cc_final: 0.8634 (m110) REVERT: C 487 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: C 690 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9114 (tp) REVERT: C 817 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9077 (pttt) REVERT: C 1060 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8976 (tp) REVERT: C 1083 ASN cc_start: 0.9177 (t0) cc_final: 0.8831 (t160) REVERT: D 200 GLU cc_start: 0.8767 (tp30) cc_final: 0.8490 (tp30) REVERT: D 487 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8463 (mm-30) REVERT: D 648 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: D 690 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9117 (tp) REVERT: D 817 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9077 (pttt) REVERT: D 1060 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8956 (tp) REVERT: D 1083 ASN cc_start: 0.9140 (t0) cc_final: 0.8853 (t160) outliers start: 94 outliers final: 36 residues processed: 330 average time/residue: 1.3652 time to fit residues: 527.1130 Evaluate side-chains 298 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 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 147 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 322 LEU 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 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 263 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 256 optimal weight: 0.0170 chunk 157 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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 C 913 ASN C1100 ASN D 504 ASN D 779 ASN D 913 ASN D1100 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.086140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.071532 restraints weight = 27154.339| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 0.84 r_work: 0.2447 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2345 r_free = 0.2345 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 389 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2334 r_free = 0.2334 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 407 | |-----------------------------------------------------------------------------| r_final: 0.2334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0826 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= 0.188 Angle : 0.562 8.713 31148 Z= 0.296 Chirality : 0.045 0.200 3392 Planarity : 0.005 0.057 4054 Dihedral : 4.551 20.356 3124 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.18 % Allowed : 17.05 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2812 helix: 0.13 (0.19), residues: 700 sheet: 0.57 (0.17), residues: 798 loop : -0.27 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 835 HIS 0.003 0.001 HIS A 132 PHE 0.032 0.002 PHE D 970 TYR 0.018 0.002 TYR C 385 ARG 0.004 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1066) hydrogen bonds : angle 5.00443 ( 3027) covalent geometry : bond 0.00458 (22970) covalent geometry : angle 0.56205 (31148) *********************** 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 358 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 256 time to evaluate : 2.612 Fit side-chains REVERT: A 115 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 161 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8505 (pt) REVERT: A 326 VAL cc_start: 0.8882 (t) cc_final: 0.8572 (t) REVERT: B 115 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: B 161 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8608 (pt) REVERT: C 157 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8607 (mt0) REVERT: C 468 ASN cc_start: 0.8925 (m-40) cc_final: 0.8610 (m110) REVERT: C 487 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: C 533 MET cc_start: 0.9260 (tpt) cc_final: 0.8990 (tpt) REVERT: C 656 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8984 (mtp) REVERT: C 690 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9146 (tp) REVERT: C 817 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9063 (pttt) REVERT: C 1060 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8987 (tp) REVERT: C 1083 ASN cc_start: 0.9101 (t0) cc_final: 0.8710 (t160) REVERT: D 157 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8514 (mt0) REVERT: D 487 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8471 (mm-30) REVERT: D 648 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: D 690 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9129 (tp) REVERT: D 817 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9080 (pttt) REVERT: D 1060 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8987 (tp) REVERT: D 1083 ASN cc_start: 0.9113 (t0) cc_final: 0.8792 (t160) outliers start: 102 outliers final: 55 residues processed: 330 average time/residue: 1.2313 time to fit residues: 470.7812 Evaluate side-chains 328 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 426 TYR 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 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 656 MET Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 746 MET Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 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 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 231 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 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 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 183 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 146 optimal weight: 0.3980 chunk 253 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 779 ASN C 913 ASN D 504 ASN D 695 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.087268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.2576 r_free = 0.2576 target = 0.072584 restraints weight = 26800.280| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 0.85 r_work: 0.2475 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 407 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 467 | |-----------------------------------------------------------------------------| r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22970 Z= 0.152 Angle : 0.527 6.957 31148 Z= 0.279 Chirality : 0.044 0.198 3392 Planarity : 0.004 0.055 4054 Dihedral : 4.467 19.880 3124 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.02 % Allowed : 17.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2812 helix: 0.25 (0.19), residues: 700 sheet: 0.56 (0.17), residues: 798 loop : -0.28 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 835 HIS 0.003 0.001 HIS C 635 PHE 0.026 0.001 PHE D 698 TYR 0.017 0.001 TYR C 385 ARG 0.003 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 1066) hydrogen bonds : angle 4.92450 ( 3027) covalent geometry : bond 0.00365 (22970) covalent geometry : angle 0.52676 (31148) *********************** 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 352 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 254 time to evaluate : 2.620 Fit side-chains REVERT: A 115 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: A 161 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8483 (pt) REVERT: A 318 ARG cc_start: 0.7312 (tpt-90) cc_final: 0.7075 (mmt180) REVERT: A 326 VAL cc_start: 0.8939 (t) cc_final: 0.8629 (t) REVERT: B 161 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8573 (pt) REVERT: B 289 LEU cc_start: 0.7961 (tp) cc_final: 0.7699 (tp) REVERT: C 157 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: C 410 ASN cc_start: 0.7861 (t0) cc_final: 0.7540 (t0) REVERT: C 468 ASN cc_start: 0.8917 (m-40) cc_final: 0.8562 (m110) REVERT: C 487 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: C 690 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9118 (tp) REVERT: C 706 MET cc_start: 0.9146 (ttm) cc_final: 0.8841 (ttp) REVERT: C 817 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8977 (pttt) REVERT: C 1083 ASN cc_start: 0.9077 (t0) cc_final: 0.8729 (t160) REVERT: D 157 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: D 487 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8499 (mm-30) REVERT: D 648 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: D 690 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9098 (tp) REVERT: D 817 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9012 (pttt) REVERT: D 1083 ASN cc_start: 0.9101 (t0) cc_final: 0.8798 (t160) outliers start: 98 outliers final: 53 residues processed: 326 average time/residue: 1.2096 time to fit residues: 458.4272 Evaluate side-chains 319 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 161 ILE 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 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 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 746 MET Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 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 345 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 571 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 237 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 779 ASN C 913 ASN D 504 ASN D 569 GLN D 695 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.088563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.076782 restraints weight = 26595.458| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 0.61 r_work: 0.2511 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 467 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 535 | |-----------------------------------------------------------------------------| r_final: 0.2413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22970 Z= 0.128 Angle : 0.505 6.582 31148 Z= 0.269 Chirality : 0.043 0.176 3392 Planarity : 0.004 0.054 4054 Dihedral : 4.360 20.682 3124 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.77 % Allowed : 18.03 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2812 helix: 0.34 (0.20), residues: 704 sheet: 0.60 (0.17), residues: 796 loop : -0.24 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 835 HIS 0.003 0.001 HIS D 635 PHE 0.023 0.001 PHE D 970 TYR 0.016 0.001 TYR C 385 ARG 0.002 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 1066) hydrogen bonds : angle 4.83968 ( 3027) covalent geometry : bond 0.00304 (22970) covalent geometry : angle 0.50535 (31148) *********************** 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 351 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 259 time to evaluate : 2.678 Fit side-chains REVERT: A 161 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8538 (pt) REVERT: A 318 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7170 (mmt180) REVERT: A 326 VAL cc_start: 0.8961 (t) cc_final: 0.8660 (t) REVERT: A 408 MET cc_start: 0.8413 (mtm) cc_final: 0.8121 (mtm) REVERT: B 118 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 161 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8592 (pt) REVERT: B 289 LEU cc_start: 0.8053 (tp) cc_final: 0.7795 (tp) REVERT: B 341 ASP cc_start: 0.5343 (m-30) cc_final: 0.4227 (m-30) REVERT: C 157 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: C 200 GLU cc_start: 0.8677 (tp30) cc_final: 0.8317 (tp30) REVERT: C 468 ASN cc_start: 0.8953 (m-40) cc_final: 0.8584 (m110) REVERT: C 487 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: C 690 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9098 (tp) REVERT: C 779 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8378 (m110) REVERT: C 817 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8933 (pttt) REVERT: C 1083 ASN cc_start: 0.9077 (t0) cc_final: 0.8750 (t160) REVERT: D 157 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: D 200 GLU cc_start: 0.8697 (tp30) cc_final: 0.8393 (tp30) REVERT: D 487 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8482 (mm-30) REVERT: D 533 MET cc_start: 0.9264 (tpt) cc_final: 0.9036 (tpt) REVERT: D 648 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: D 690 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9080 (tp) REVERT: D 817 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8978 (pttt) REVERT: D 1083 ASN cc_start: 0.9109 (t0) cc_final: 0.8823 (t160) outliers start: 92 outliers final: 53 residues processed: 324 average time/residue: 1.2459 time to fit residues: 466.5555 Evaluate side-chains 318 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 161 ILE 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 264 LYS 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 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 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 LYS 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 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 247 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 278 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 504 ASN C 779 ASN C 913 ASN D 504 ASN D 695 ASN D 779 ASN D 913 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.089343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.076119 restraints weight = 26637.964| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 0.71 r_work: 0.2483 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 535 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 566 | |-----------------------------------------------------------------------------| r_final: 0.2387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22970 Z= 0.125 Angle : 0.504 6.843 31148 Z= 0.267 Chirality : 0.043 0.148 3392 Planarity : 0.004 0.053 4054 Dihedral : 4.328 19.757 3124 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.57 % Allowed : 18.61 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 2812 helix: 0.39 (0.20), residues: 704 sheet: 0.64 (0.17), residues: 794 loop : -0.23 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 835 HIS 0.003 0.001 HIS D 635 PHE 0.028 0.001 PHE D 698 TYR 0.018 0.001 TYR C 385 ARG 0.005 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 1066) hydrogen bonds : angle 4.80481 ( 3027) covalent geometry : bond 0.00296 (22970) covalent geometry : angle 0.50375 (31148) *********************** 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 340 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 2.635 Fit side-chains REVERT: A 161 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8561 (pt) REVERT: A 248 MET cc_start: 0.7237 (mtm) cc_final: 0.6307 (mtp) REVERT: A 310 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7502 (mmm-85) REVERT: A 318 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7383 (mmt180) REVERT: A 326 VAL cc_start: 0.8948 (t) cc_final: 0.8657 (t) REVERT: A 408 MET cc_start: 0.8465 (mtm) cc_final: 0.8196 (mtm) REVERT: B 115 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: B 118 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 161 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8613 (pt) REVERT: B 289 LEU cc_start: 0.8108 (tp) cc_final: 0.7815 (tp) REVERT: B 341 ASP cc_start: 0.5461 (m-30) cc_final: 0.4400 (m-30) REVERT: C 157 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8537 (mt0) REVERT: C 200 GLU cc_start: 0.8705 (tp30) cc_final: 0.8356 (tp30) REVERT: C 468 ASN cc_start: 0.8960 (m-40) cc_final: 0.8566 (m110) REVERT: C 487 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: C 690 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 817 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8947 (pttt) REVERT: C 1083 ASN cc_start: 0.9084 (t0) cc_final: 0.8760 (t160) REVERT: D 157 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: D 200 GLU cc_start: 0.8718 (tp30) cc_final: 0.8368 (tp30) REVERT: D 487 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8467 (mm-30) REVERT: D 648 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: D 690 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9092 (tp) REVERT: D 817 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8992 (pttt) REVERT: D 1083 ASN cc_start: 0.9136 (t0) cc_final: 0.8861 (t160) outliers start: 87 outliers final: 55 residues processed: 318 average time/residue: 1.2433 time to fit residues: 459.3088 Evaluate side-chains 317 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain 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 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 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 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 LYS 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 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 216 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 179 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 248 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 373 ASN C 504 ASN C 779 ASN C 913 ASN D 504 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 = 0.2846 r_free = 0.2846 target = 0.090534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.076143 restraints weight = 26610.977| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 0.70 r_work: 0.2501 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 566 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 586 | |-----------------------------------------------------------------------------| r_final: 0.2404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1134 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= 0.112 Angle : 0.486 6.234 31148 Z= 0.259 Chirality : 0.042 0.144 3392 Planarity : 0.004 0.053 4054 Dihedral : 4.220 20.711 3124 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.44 % Allowed : 18.77 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2812 helix: 0.51 (0.20), residues: 700 sheet: 0.68 (0.17), residues: 794 loop : -0.18 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.003 0.001 HIS D 635 PHE 0.020 0.001 PHE D 970 TYR 0.016 0.001 TYR C 385 ARG 0.005 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 1066) hydrogen bonds : angle 4.71972 ( 3027) covalent geometry : bond 0.00263 (22970) covalent geometry : angle 0.48640 (31148) *********************** 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 349 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 265 time to evaluate : 3.057 Fit side-chains REVERT: A 118 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 156 LEU cc_start: 0.8857 (mp) cc_final: 0.8509 (mt) REVERT: A 161 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (pt) REVERT: A 218 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8179 (tp40) REVERT: A 248 MET cc_start: 0.7194 (mtm) cc_final: 0.6566 (mtp) REVERT: A 310 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7570 (mmm-85) REVERT: A 318 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7402 (mmt180) REVERT: A 326 VAL cc_start: 0.8963 (t) cc_final: 0.8671 (t) REVERT: B 115 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: B 118 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 161 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8620 (pt) REVERT: B 289 LEU cc_start: 0.8105 (tp) cc_final: 0.7814 (tp) REVERT: C 157 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: C 200 GLU cc_start: 0.8694 (tp30) cc_final: 0.8337 (tp30) REVERT: C 336 PRO cc_start: 0.7143 (Cg_exo) cc_final: 0.6792 (Cg_endo) REVERT: C 468 ASN cc_start: 0.8941 (m-40) cc_final: 0.8503 (m110) REVERT: C 487 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: C 690 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9099 (tp) REVERT: C 817 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8930 (pttt) REVERT: C 1060 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8928 (tp) REVERT: C 1083 ASN cc_start: 0.9100 (t0) cc_final: 0.8809 (t160) REVERT: D 157 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8542 (mt0) REVERT: D 200 GLU cc_start: 0.8711 (tp30) cc_final: 0.8353 (tp30) REVERT: D 487 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8482 (mm-30) REVERT: D 648 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: D 690 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9078 (tp) REVERT: D 817 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8983 (pttt) REVERT: D 1083 ASN cc_start: 0.9109 (t0) cc_final: 0.8857 (t160) outliers start: 84 outliers final: 50 residues processed: 330 average time/residue: 1.2280 time to fit residues: 469.8596 Evaluate side-chains 319 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain 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 276 MET 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 779 ASN Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1070 SER Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain 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 254 VAL Chi-restraints excluded: chain D residue 276 MET 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 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 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 11 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 167 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 695 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 = 0.2837 r_free = 0.2837 target = 0.089927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.075191 restraints weight = 26566.579| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 0.73 r_work: 0.2473 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 586 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 603 | |-----------------------------------------------------------------------------| r_final: 0.2380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22970 Z= 0.145 Angle : 0.517 6.576 31148 Z= 0.273 Chirality : 0.043 0.201 3392 Planarity : 0.004 0.052 4054 Dihedral : 4.299 19.285 3124 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.32 % Allowed : 18.93 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2812 helix: 0.44 (0.20), residues: 700 sheet: 0.63 (0.17), residues: 796 loop : -0.18 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 835 HIS 0.003 0.001 HIS C 635 PHE 0.028 0.001 PHE D 698 TYR 0.018 0.001 TYR C 385 ARG 0.004 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 1066) hydrogen bonds : angle 4.76817 ( 3027) covalent geometry : bond 0.00350 (22970) covalent geometry : angle 0.51665 (31148) *********************** 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 336 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 255 time to evaluate : 3.910 Fit side-chains REVERT: A 118 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 161 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8558 (pt) REVERT: A 218 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8166 (tp40) REVERT: A 248 MET cc_start: 0.7271 (mtm) cc_final: 0.6523 (mtp) REVERT: A 310 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7607 (mmm-85) REVERT: A 318 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7420 (mmt180) REVERT: A 326 VAL cc_start: 0.8988 (t) cc_final: 0.8708 (t) REVERT: B 115 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: B 118 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 161 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8628 (pt) REVERT: B 289 LEU cc_start: 0.8187 (tp) cc_final: 0.7866 (tp) REVERT: C 157 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: C 200 GLU cc_start: 0.8716 (tp30) cc_final: 0.8362 (tp30) REVERT: C 468 ASN cc_start: 0.8960 (m-40) cc_final: 0.8538 (m110) REVERT: C 487 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: C 690 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9115 (tp) REVERT: C 817 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8925 (pttt) REVERT: C 1083 ASN cc_start: 0.9096 (t0) cc_final: 0.8763 (t160) REVERT: D 157 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8545 (mt0) REVERT: D 200 GLU cc_start: 0.8724 (tp30) cc_final: 0.8378 (tp30) REVERT: D 487 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8469 (mm-30) REVERT: D 533 MET cc_start: 0.9215 (tpt) cc_final: 0.8954 (tpt) REVERT: D 648 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: D 690 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9088 (tp) REVERT: D 817 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8978 (pttt) REVERT: D 1083 ASN cc_start: 0.9114 (t0) cc_final: 0.8845 (t160) outliers start: 81 outliers final: 56 residues processed: 314 average time/residue: 1.4684 time to fit residues: 533.0048 Evaluate side-chains 319 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 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 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 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 264 LYS 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 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 259 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 258 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 D 373 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 = 0.2825 r_free = 0.2825 target = 0.089089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.073762 restraints weight = 26721.360| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 0.69 r_work: 0.2470 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2382 r_free = 0.2382 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 603 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2382 r_free = 0.2382 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 620 | |-----------------------------------------------------------------------------| r_final: 0.2382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22970 Z= 0.176 Angle : 0.548 7.837 31148 Z= 0.288 Chirality : 0.045 0.187 3392 Planarity : 0.004 0.059 4054 Dihedral : 4.455 19.911 3124 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.11 % Allowed : 19.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2812 helix: 0.30 (0.19), residues: 704 sheet: 0.60 (0.17), residues: 796 loop : -0.21 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 835 HIS 0.003 0.001 HIS D 635 PHE 0.031 0.002 PHE D 970 TYR 0.019 0.002 TYR C 385 ARG 0.004 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 1066) hydrogen bonds : angle 4.87042 ( 3027) covalent geometry : bond 0.00429 (22970) covalent geometry : angle 0.54793 (31148) ********************** 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 332 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 2.596 Fit side-chains REVERT: A 118 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 161 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8560 (pt) REVERT: A 248 MET cc_start: 0.7357 (mtm) cc_final: 0.6570 (mtp) REVERT: A 310 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (mmm-85) REVERT: A 318 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7451 (mmt180) REVERT: A 326 VAL cc_start: 0.9017 (t) cc_final: 0.8745 (t) REVERT: B 115 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 161 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8628 (pt) REVERT: B 341 ASP cc_start: 0.5508 (m-30) cc_final: 0.4519 (m-30) REVERT: C 157 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: C 468 ASN cc_start: 0.8946 (m-40) cc_final: 0.8564 (m110) REVERT: C 487 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: C 533 MET cc_start: 0.9314 (tpt) cc_final: 0.9109 (tpt) REVERT: C 690 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9109 (tp) REVERT: C 817 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8950 (pttt) REVERT: C 1083 ASN cc_start: 0.9091 (t0) cc_final: 0.8737 (t160) REVERT: D 157 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: D 373 ASN cc_start: 0.8061 (m110) cc_final: 0.7838 (m-40) REVERT: D 487 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8476 (mm-30) REVERT: D 648 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: D 690 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9090 (tp) REVERT: D 817 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8997 (pttt) REVERT: D 1083 ASN cc_start: 0.9114 (t0) cc_final: 0.8820 (t160) outliers start: 76 outliers final: 59 residues processed: 318 average time/residue: 1.3232 time to fit residues: 486.0885 Evaluate side-chains 325 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 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 675 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 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 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 264 LYS 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 676 ASP Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 917 THR Chi-restraints excluded: chain D residue 933 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 958 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1070 SER Chi-restraints excluded: chain D residue 1071 SER Chi-restraints excluded: chain D residue 1094 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 254 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 695 ASN D 504 ASN D 779 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.089446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.074387 restraints weight = 26528.035| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 0.72 r_work: 0.2465 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 620 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2364 r_free = 0.2364 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 620 | |-----------------------------------------------------------------------------| r_final: 0.2364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 22970 Z= 0.208 Angle : 0.720 59.147 31148 Z= 0.411 Chirality : 0.046 0.739 3392 Planarity : 0.004 0.059 4054 Dihedral : 4.517 42.299 3124 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.20 % Allowed : 19.47 % Favored : 77.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2812 helix: 0.30 (0.19), residues: 704 sheet: 0.58 (0.17), residues: 796 loop : -0.21 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 835 HIS 0.004 0.001 HIS B 258 PHE 0.031 0.001 PHE D 970 TYR 0.019 0.001 TYR C 385 ARG 0.006 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 1066) hydrogen bonds : angle 4.89174 ( 3027) covalent geometry : bond 0.00454 (22970) covalent geometry : angle 0.72045 (31148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16426.84 seconds wall clock time: 287 minutes 31.40 seconds (17251.40 seconds total)