Starting phenix.real_space_refine on Thu Nov 20 23:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f0k_4165/11_2025/6f0k_4165_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f0k_4165/11_2025/6f0k_4165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6f0k_4165/11_2025/6f0k_4165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f0k_4165/11_2025/6f0k_4165.map" model { file = "/net/cci-nas-00/data/ceres_data/6f0k_4165/11_2025/6f0k_4165_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f0k_4165/11_2025/6f0k_4165_trim.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Fe 21 7.16 5 S 102 5.16 5 C 13192 2.51 5 N 3475 2.21 5 O 3501 1.98 5 H 19577 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "B ARG 268": not complete - not flipped Residue "B ARG 285": not complete - not flipped Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39868 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3253 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "B" Number of atoms: 14877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 14877 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 69, 'TRANS': 891} Chain: "C" Number of atoms: 7234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 7234 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain: "D" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2656 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 13, 'TRANS': 157} Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2818 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 16, 'TRANS': 165} Chain: "F" Number of atoms: 6308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 6308 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain: "H" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2433 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15587 SG CYS B 877 85.250 70.092 49.180 1.00 58.24 S ATOM 15972 SG CYS B 903 88.185 72.952 48.056 1.00 54.69 S ATOM 15877 SG CYS B 897 87.771 68.752 44.076 1.00 52.19 S ATOM 15972 SG CYS B 903 88.185 72.952 48.056 1.00 54.69 S ATOM 15428 SG CYS B 865 97.302 74.866 51.557 1.00 49.56 S ATOM 15535 SG CYS B 873 91.925 75.044 52.472 1.00 54.76 S ATOM 16021 SG CYS B 907 95.472 79.689 50.127 1.00 54.76 S ATOM 15472 SG CYS B 868 95.716 78.747 56.213 1.00 55.18 S ATOM 17190 SG CYS B 976 108.848 70.852 50.397 1.00 52.77 S ATOM 16742 SG CYS B 949 106.840 66.268 51.898 1.00 48.84 S ATOM 14681 SG CYS B 817 105.519 68.574 46.570 1.00 52.91 S ATOM 16697 SG CYS B 946 103.020 70.967 52.034 1.00 49.60 S ATOM 14592 SG CYS B 810 117.426 73.883 46.826 1.00 59.01 S ATOM 17244 SG CYS B 980 116.557 73.998 52.083 1.00 54.49 S ATOM 14626 SG CYS B 813 113.156 73.802 50.004 1.00 54.79 S ATOM 14561 SG CYS B 807 114.424 79.058 50.646 1.00 61.36 S Time building chain proxies: 7.02, per 1000 atoms: 0.18 Number of scatterers: 39868 At special positions: 0 Unit cell: (165.6, 136.62, 105.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 21 26.01 S 102 16.00 O 3501 8.00 N 3475 7.00 C 13192 6.00 H 19577 1.00 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1101 " pdb="FE1 F3S B1101 " - pdb=" SG CYS B 877 " pdb="FE4 F3S B1101 " - pdb=" SG CYS B 903 " pdb="FE3 F3S B1101 " - pdb=" SG CYS B 897 " pdb=" SF4 B1102 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 865 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 868 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 907 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 873 " pdb=" SF4 B1103 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 976 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 949 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 946 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 817 " pdb=" SF4 B1104 " pdb="FE3 SF4 B1104 " - pdb=" SG CYS B 813 " pdb="FE1 SF4 B1104 " - pdb=" SG CYS B 810 " pdb="FE2 SF4 B1104 " - pdb=" SG CYS B 980 " pdb="FE4 SF4 B1104 " - pdb=" SG CYS B 807 " Number of angles added : 45 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4682 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 45.3% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 8 through 10 No H-bonds generated for 'chain 'A' and resid 8 through 10' Processing helix chain 'A' and resid 11 through 29 removed outlier: 3.506A pdb=" N GLY A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.562A pdb=" N HIS A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 4.105A pdb=" N CYS A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.556A pdb=" N HIS A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.774A pdb=" N CYS A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.931A pdb=" N GLU A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.769A pdb=" N GLU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 4.099A pdb=" N GLN B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 178 removed outlier: 3.698A pdb=" N GLN B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.619A pdb=" N ARG B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 4.445A pdb=" N GLN B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.930A pdb=" N GLU B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.568A pdb=" N ALA B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 350 removed outlier: 3.845A pdb=" N ILE B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 377 removed outlier: 3.707A pdb=" N ASN B 374 " --> pdb=" O CYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.591A pdb=" N ALA B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.160A pdb=" N GLN B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.710A pdb=" N ARG B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.721A pdb=" N GLN B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 593 Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.796A pdb=" N GLN B 789 " --> pdb=" O GLN B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 821 removed outlier: 3.667A pdb=" N ALA B 816 " --> pdb=" O ALA B 812 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 817 " --> pdb=" O CYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 871 through 877 removed outlier: 3.551A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 876 " --> pdb=" O PRO B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 906 removed outlier: 3.820A pdb=" N ASN B 906 " --> pdb=" O TYR B 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 902 through 906' Processing helix chain 'B' and resid 926 through 930 Processing helix chain 'B' and resid 950 through 963 removed outlier: 3.886A pdb=" N ALA B 956 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 963 " --> pdb=" O GLN B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.569A pdb=" N CYS B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1002 removed outlier: 3.548A pdb=" N LYS B 999 " --> pdb=" O ASN B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.619A pdb=" N GLU C 31 " --> pdb=" O HIS C 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 68 removed outlier: 3.794A pdb=" N SER C 50 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.510A pdb=" N VAL C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.786A pdb=" N THR C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 139 removed outlier: 3.680A pdb=" N GLU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 164 through 187 removed outlier: 3.780A pdb=" N VAL C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 201 removed outlier: 4.138A pdb=" N ALA C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 255 removed outlier: 4.644A pdb=" N ASN C 227 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Proline residue: C 241 - end of helix removed outlier: 3.595A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 289 removed outlier: 4.270A pdb=" N ALA C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 331 removed outlier: 3.785A pdb=" N LEU C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 312 " --> pdb=" O MET C 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP C 331 " --> pdb=" O PHE C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.815A pdb=" N PHE C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 368 removed outlier: 3.587A pdb=" N TRP C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR C 356 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 365 - end of helix Processing helix chain 'C' and resid 377 through 401 removed outlier: 3.857A pdb=" N PHE C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 400 " --> pdb=" O PHE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 442 removed outlier: 3.527A pdb=" N PHE C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.789A pdb=" N LYS C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 453' Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.911A pdb=" N HIS D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 42 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 96 removed outlier: 4.670A pdb=" N THR D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 96 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 121 Proline residue: D 118 - end of helix Processing helix chain 'D' and resid 121 through 137 removed outlier: 3.757A pdb=" N ALA D 131 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.610A pdb=" N THR D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'E' and resid 99 through 110 removed outlier: 3.676A pdb=" N VAL E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.688A pdb=" N ILE E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 190 removed outlier: 4.033A pdb=" N VAL E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'F' and resid 37 through 51 removed outlier: 4.062A pdb=" N LEU F 41 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 removed outlier: 3.586A pdb=" N TRP F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 90 removed outlier: 4.151A pdb=" N PHE F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 107 removed outlier: 3.592A pdb=" N GLU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TRP F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 115 removed outlier: 3.857A pdb=" N VAL F 111 " --> pdb=" O TRP F 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.668A pdb=" N LEU F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 122 " --> pdb=" O PRO F 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 164 removed outlier: 3.710A pdb=" N VAL F 160 " --> pdb=" O PRO F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.752A pdb=" N ALA F 173 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR F 178 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU F 179 " --> pdb=" O LYS F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 4.483A pdb=" N VAL F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 181 through 185' Processing helix chain 'F' and resid 192 through 219 removed outlier: 4.300A pdb=" N MET F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) Proline residue: F 204 - end of helix removed outlier: 3.792A pdb=" N GLY F 207 " --> pdb=" O MET F 203 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N MET F 219 " --> pdb=" O TYR F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 253 removed outlier: 3.685A pdb=" N PHE F 235 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY F 244 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 296 removed outlier: 4.263A pdb=" N PHE F 268 " --> pdb=" O ARG F 264 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 270 " --> pdb=" O PRO F 266 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE F 281 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE F 285 " --> pdb=" O PHE F 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 309 removed outlier: 3.522A pdb=" N TYR F 305 " --> pdb=" O GLU F 301 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG F 306 " --> pdb=" O THR F 302 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU F 309 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 325 through 332 Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.591A pdb=" N VAL F 344 " --> pdb=" O THR F 340 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 349 " --> pdb=" O GLY F 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE F 354 " --> pdb=" O TRP F 350 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE F 357 " --> pdb=" O ILE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 400 removed outlier: 4.128A pdb=" N CYS F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP F 382 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 397 " --> pdb=" O PHE F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 415 Processing helix chain 'H' and resid 32 through 61 removed outlier: 3.584A pdb=" N GLU H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 97 removed outlier: 4.179A pdb=" N ALA H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR H 74 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU H 78 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU H 86 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 95 " --> pdb=" O TRP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 135 removed outlier: 3.999A pdb=" N LEU H 119 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA H 129 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 167 removed outlier: 3.868A pdb=" N GLN H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 179 removed outlier: 3.852A pdb=" N TYR H 176 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 105 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.614A pdb=" N GLY B 446 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU B 415 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 445 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU B 417 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AA6, first strand: chain 'B' and resid 471 through 473 removed outlier: 3.748A pdb=" N GLY B 472 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.653A pdb=" N ARG B 575 " --> pdb=" O VAL B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 844 through 845 Processing sheet with id=AA9, first strand: chain 'B' and resid 882 through 883 removed outlier: 4.020A pdb=" N VAL B 883 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 913 through 914 Processing sheet with id=AB2, first strand: chain 'D' and resid 52 through 54 removed outlier: 4.143A pdb=" N ASP D 52 " --> pdb=" O PHE D 166 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.21 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.42: 28741 1.42 - 2.02: 11750 2.02 - 2.61: 49 2.61 - 3.21: 0 3.21 - 3.81: 3 Bond restraints: 40543 Sorted by residual: bond pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " ideal model delta sigma weight residual 2.258 3.812 -1.554 2.00e-02 2.50e+03 6.04e+03 bond pdb=" S4 F3S B1101 " pdb="FE1 F3S B1101 " ideal model delta sigma weight residual 2.233 3.763 -1.530 2.00e-02 2.50e+03 5.86e+03 bond pdb=" S2 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 2.300 3.809 -1.509 2.00e-02 2.50e+03 5.69e+03 bond pdb=" CAB HEC A 301 " pdb=" CBB HEC A 301 " ideal model delta sigma weight residual 1.544 1.308 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" CAB HEC A 302 " pdb=" CBB HEC A 302 " ideal model delta sigma weight residual 1.544 1.315 0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 40538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.31: 73083 9.31 - 18.63: 25 18.63 - 27.94: 13 27.94 - 37.26: 9 37.26 - 46.57: 2 Bond angle restraints: 73132 Sorted by residual: angle pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " pdb=" S3 F3S B1101 " ideal model delta sigma weight residual 114.75 68.18 46.57 3.00e+00 1.11e-01 2.41e+02 angle pdb=" S3 F3S B1101 " pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " ideal model delta sigma weight residual 112.59 70.67 41.92 3.00e+00 1.11e-01 1.95e+02 angle pdb=" CA CYS A 206 " pdb=" CB CYS A 206 " pdb=" SG CYS A 206 " ideal model delta sigma weight residual 114.40 85.29 29.11 2.30e+00 1.89e-01 1.60e+02 angle pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 74.86 38.28 36.58 3.00e+00 1.11e-01 1.49e+02 angle pdb="FE1 F3S B1101 " pdb=" S2 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 72.09 36.95 35.14 3.00e+00 1.11e-01 1.37e+02 ... (remaining 73127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 18742 35.93 - 71.86: 343 71.86 - 107.80: 22 107.80 - 143.73: 0 143.73 - 179.66: 2 Dihedral angle restraints: 19109 sinusoidal: 10063 harmonic: 9046 Sorted by residual: dihedral pdb=" CD ARG B 268 " pdb=" NE ARG B 268 " pdb=" CZ ARG B 268 " pdb=" NH1 ARG B 268 " ideal model delta sinusoidal sigma weight residual 0.00 179.66 -179.66 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG B 285 " pdb=" NE ARG B 285 " pdb=" CZ ARG B 285 " pdb=" NH1 ARG B 285 " ideal model delta sinusoidal sigma weight residual 0.00 179.66 -179.66 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C2C HEC A 301 " pdb=" C3C HEC A 301 " pdb=" CAC HEC A 301 " pdb=" CBC HEC A 301 " ideal model delta sinusoidal sigma weight residual 60.00 -25.00 85.00 2 1.00e+01 1.00e-02 4.76e+01 ... (remaining 19106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.130: 3057 1.130 - 2.260: 4 2.260 - 3.391: 0 3.391 - 4.521: 0 4.521 - 5.651: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" S2 F3S B1101 " pdb="FE1 F3S B1101 " pdb="FE3 F3S B1101 " pdb="FE4 F3S B1101 " both_signs ideal model delta sigma weight residual False 10.77 5.12 5.65 2.00e-01 2.50e+01 7.98e+02 chirality pdb=" CG LEU F 327 " pdb=" CB LEU F 327 " pdb=" CD1 LEU F 327 " pdb=" CD2 LEU F 327 " both_signs ideal model delta sigma weight residual False -2.59 -0.79 -1.80 2.00e-01 2.50e+01 8.07e+01 chirality pdb=" CG LEU F 303 " pdb=" CB LEU F 303 " pdb=" CD1 LEU F 303 " pdb=" CD2 LEU F 303 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.92e+01 ... (remaining 3059 not shown) Planarity restraints: 5986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEC A 301 " 0.014 2.00e-02 2.50e+03 4.80e-02 5.18e+01 pdb=" C1B HEC A 301 " 0.014 2.00e-02 2.50e+03 pdb=" C2B HEC A 301 " -0.018 2.00e-02 2.50e+03 pdb=" C3B HEC A 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4B HEC A 301 " -0.013 2.00e-02 2.50e+03 pdb=" CAB HEC A 301 " 0.094 2.00e-02 2.50e+03 pdb=" CHB HEC A 301 " 0.054 2.00e-02 2.50e+03 pdb=" CHC HEC A 301 " -0.049 2.00e-02 2.50e+03 pdb=" CMB HEC A 301 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " -0.001 2.00e-02 2.50e+03 3.46e-02 2.69e+01 pdb=" C2C HEC A 303 " 0.017 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " 0.004 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " -0.062 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " -0.044 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " 0.033 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.059 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 305 " -0.008 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" C2C HEC A 305 " 0.027 2.00e-02 2.50e+03 pdb=" C3C HEC A 305 " 0.004 2.00e-02 2.50e+03 pdb=" C4C HEC A 305 " 0.004 2.00e-02 2.50e+03 pdb=" CAC HEC A 305 " -0.054 2.00e-02 2.50e+03 pdb=" CHC HEC A 305 " -0.028 2.00e-02 2.50e+03 pdb=" CHD HEC A 305 " 0.031 2.00e-02 2.50e+03 pdb=" CMC HEC A 305 " 0.039 2.00e-02 2.50e+03 pdb=" NC HEC A 305 " -0.015 2.00e-02 2.50e+03 ... (remaining 5983 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 676 2.10 - 2.73: 71081 2.73 - 3.35: 117307 3.35 - 3.98: 147227 3.98 - 4.60: 234510 Nonbonded interactions: 570801 Sorted by model distance: nonbonded pdb=" O THR B 808 " pdb="HG22 THR B 808 " model vdw 1.480 2.620 nonbonded pdb="HG22 VAL B 295 " pdb="HG22 THR B 808 " model vdw 1.580 2.440 nonbonded pdb="HH12 ARG B 901 " pdb=" O HIS C 139 " model vdw 1.638 2.450 nonbonded pdb=" O ASN F 154 " pdb=" H PHE F 157 " model vdw 1.645 2.450 nonbonded pdb=" HG1 THR B 579 " pdb=" O ALA B 591 " model vdw 1.666 2.450 ... (remaining 570796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.250 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 46.840 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.023 1.554 21001 Z= 1.177 Angle : 1.814 70.899 28787 Z= 0.607 Chirality : 0.138 5.651 3062 Planarity : 0.008 0.077 3661 Dihedral : 11.891 179.659 7377 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.14), residues: 2490 helix: -3.63 (0.11), residues: 991 sheet: -5.50 (0.32), residues: 72 loop : -3.34 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 743 TYR 0.039 0.003 TYR A 48 PHE 0.032 0.003 PHE C 267 TRP 0.038 0.003 TRP C 74 HIS 0.019 0.003 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.02229 (20966) covalent geometry : angle 1.28821 (28742) hydrogen bonds : bond 0.21940 ( 624) hydrogen bonds : angle 9.84232 ( 1824) metal coordination : bond 0.03217 ( 15) metal coordination : angle 32.33677 ( 45) Misc. bond : bond 0.16401 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 638 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4570 (ttm170) cc_final: 0.4244 (mmt-90) REVERT: A 88 GLN cc_start: 0.7570 (pt0) cc_final: 0.6337 (tm-30) REVERT: A 119 ASP cc_start: 0.8094 (t0) cc_final: 0.7797 (m-30) REVERT: A 168 LEU cc_start: 0.8527 (tp) cc_final: 0.8205 (tt) REVERT: B 154 SER cc_start: 0.8132 (p) cc_final: 0.7860 (p) REVERT: B 598 ILE cc_start: 0.8956 (mm) cc_final: 0.8595 (mt) REVERT: B 820 GLU cc_start: 0.7522 (tp30) cc_final: 0.7284 (tp30) REVERT: B 1019 THR cc_start: 0.7189 (t) cc_final: 0.6465 (m) REVERT: C 318 MET cc_start: 0.7121 (tpt) cc_final: 0.6838 (mmt) REVERT: C 340 TYR cc_start: 0.7791 (t80) cc_final: 0.7521 (t80) REVERT: C 354 TYR cc_start: 0.7653 (t80) cc_final: 0.7252 (t80) REVERT: D 45 LYS cc_start: 0.8691 (mttt) cc_final: 0.8487 (mtmt) REVERT: D 59 ILE cc_start: 0.7615 (pt) cc_final: 0.7326 (pt) REVERT: D 60 HIS cc_start: 0.7419 (m-70) cc_final: 0.6841 (t70) REVERT: D 175 ASP cc_start: 0.7503 (m-30) cc_final: 0.6598 (p0) REVERT: E 51 LEU cc_start: 0.8492 (tp) cc_final: 0.7654 (tp) REVERT: E 159 SER cc_start: 0.8394 (m) cc_final: 0.7760 (t) REVERT: F 175 LYS cc_start: 0.6856 (ttmm) cc_final: 0.6521 (mmtt) REVERT: F 182 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7271 (mmt180) REVERT: F 196 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.6765 (ttt-90) REVERT: F 270 ASP cc_start: 0.8122 (m-30) cc_final: 0.7246 (t70) REVERT: F 300 GLU cc_start: 0.8155 (pp20) cc_final: 0.7936 (pp20) REVERT: F 329 PHE cc_start: 0.8153 (t80) cc_final: 0.7906 (t80) REVERT: H 73 GLN cc_start: 0.6870 (tt0) cc_final: 0.6378 (tt0) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.4672 time to fit residues: 421.3545 Evaluate side-chains 382 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 144 GLN A 191 ASN B 408 GLN B 592 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN B 805 ASN ** B 884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 ASN C 155 GLN F 195 GLN F 371 HIS H 121 GLN H 122 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.134094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121584 restraints weight = 128305.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.125845 restraints weight = 53915.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127964 restraints weight = 24925.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.128427 restraints weight = 15330.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128919 restraints weight = 14086.648| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.540 21001 Z= 0.185 Angle : 1.650 94.525 28787 Z= 0.464 Chirality : 0.077 1.754 3062 Planarity : 0.007 0.073 3661 Dihedral : 9.816 177.759 2816 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 1.30 % Allowed : 9.38 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.14), residues: 2490 helix: -2.77 (0.12), residues: 1078 sheet: -5.43 (0.32), residues: 83 loop : -3.38 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.024 0.002 TYR B 902 PHE 0.034 0.002 PHE F 240 TRP 0.018 0.002 TRP B 562 HIS 0.013 0.002 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00402 (20966) covalent geometry : angle 0.99165 (28742) hydrogen bonds : bond 0.06858 ( 624) hydrogen bonds : angle 7.03943 ( 1824) metal coordination : bond 0.02631 ( 15) metal coordination : angle 33.37326 ( 45) Misc. bond : bond 0.23075 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 440 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4235 (ttm170) cc_final: 0.3964 (mmt-90) REVERT: B 118 GLU cc_start: 0.8072 (pm20) cc_final: 0.7832 (pm20) REVERT: B 598 ILE cc_start: 0.8910 (mm) cc_final: 0.8662 (mt) REVERT: B 608 ILE cc_start: 0.8258 (mp) cc_final: 0.7893 (mt) REVERT: B 820 GLU cc_start: 0.7922 (tp30) cc_final: 0.7678 (tp30) REVERT: B 822 ASN cc_start: 0.8158 (m-40) cc_final: 0.7849 (m-40) REVERT: C 92 TRP cc_start: 0.7657 (m100) cc_final: 0.7289 (m100) REVERT: C 118 ASN cc_start: 0.7618 (t0) cc_final: 0.7344 (t0) REVERT: C 340 TYR cc_start: 0.7601 (t80) cc_final: 0.7305 (t80) REVERT: C 388 ASN cc_start: 0.8564 (t0) cc_final: 0.8329 (t0) REVERT: D 45 LYS cc_start: 0.8716 (mttt) cc_final: 0.8484 (mtmt) REVERT: D 59 ILE cc_start: 0.7188 (pt) cc_final: 0.6542 (pt) REVERT: D 60 HIS cc_start: 0.7512 (m-70) cc_final: 0.6925 (t70) REVERT: D 95 TRP cc_start: 0.7210 (t60) cc_final: 0.6730 (t60) REVERT: E 117 CYS cc_start: 0.6462 (m) cc_final: 0.6205 (m) REVERT: E 129 MET cc_start: 0.6628 (mtt) cc_final: 0.6251 (mtt) REVERT: E 156 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7120 (t0) REVERT: F 167 PHE cc_start: 0.6041 (m-80) cc_final: 0.5825 (m-80) REVERT: F 175 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6591 (mmtt) REVERT: F 196 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.5988 (ttt-90) REVERT: H 55 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7280 (tp30) outliers start: 27 outliers final: 18 residues processed: 453 average time/residue: 0.3876 time to fit residues: 261.0984 Evaluate side-chains 380 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 361 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 805 ASN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 75 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN B 592 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 ASN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.117863 restraints weight = 129662.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121387 restraints weight = 55178.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123560 restraints weight = 26367.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.123816 restraints weight = 16722.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124340 restraints weight = 16111.886| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.601 21001 Z= 0.191 Angle : 1.487 80.517 28787 Z= 0.422 Chirality : 0.080 1.766 3062 Planarity : 0.006 0.076 3661 Dihedral : 9.367 179.463 2816 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 1.59 % Allowed : 11.59 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.15), residues: 2490 helix: -2.27 (0.13), residues: 1087 sheet: -5.39 (0.32), residues: 83 loop : -3.29 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 159 TYR 0.033 0.002 TYR B 909 PHE 0.033 0.002 PHE F 240 TRP 0.017 0.001 TRP H 91 HIS 0.008 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00435 (20966) covalent geometry : angle 0.90572 (28742) hydrogen bonds : bond 0.05969 ( 624) hydrogen bonds : angle 6.38569 ( 1824) metal coordination : bond 0.02029 ( 15) metal coordination : angle 29.85614 ( 45) Misc. bond : bond 0.21442 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 389 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4323 (ttm170) cc_final: 0.4119 (mmt-90) REVERT: B 598 ILE cc_start: 0.8974 (mm) cc_final: 0.8713 (mt) REVERT: B 820 GLU cc_start: 0.8147 (tp30) cc_final: 0.7666 (tp30) REVERT: B 823 ILE cc_start: 0.7950 (pt) cc_final: 0.7620 (pt) REVERT: B 925 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (pt) REVERT: B 929 MET cc_start: 0.7731 (mmp) cc_final: 0.7354 (mmp) REVERT: C 92 TRP cc_start: 0.7917 (m100) cc_final: 0.7518 (m100) REVERT: C 125 THR cc_start: 0.7893 (m) cc_final: 0.7559 (m) REVERT: C 340 TYR cc_start: 0.7778 (t80) cc_final: 0.7446 (t80) REVERT: C 388 ASN cc_start: 0.8626 (t0) cc_final: 0.8356 (t0) REVERT: C 431 LEU cc_start: 0.7653 (tt) cc_final: 0.7350 (tt) REVERT: D 45 LYS cc_start: 0.8755 (mttt) cc_final: 0.8518 (mtmt) REVERT: D 95 TRP cc_start: 0.7396 (t60) cc_final: 0.6857 (t60) REVERT: E 31 LYS cc_start: 0.7803 (mmpt) cc_final: 0.7130 (tttt) REVERT: E 117 CYS cc_start: 0.6694 (m) cc_final: 0.6413 (m) REVERT: E 129 MET cc_start: 0.6801 (mtt) cc_final: 0.6431 (mtt) REVERT: F 82 PHE cc_start: 0.8160 (t80) cc_final: 0.7819 (t80) REVERT: F 167 PHE cc_start: 0.6043 (m-80) cc_final: 0.5778 (m-80) REVERT: F 175 LYS cc_start: 0.7054 (ttmm) cc_final: 0.6788 (mmtt) REVERT: F 196 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.6063 (ttt-90) REVERT: F 400 HIS cc_start: 0.6630 (p90) cc_final: 0.5381 (m-70) REVERT: H 55 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7282 (tp30) outliers start: 33 outliers final: 25 residues processed: 409 average time/residue: 0.3707 time to fit residues: 229.6695 Evaluate side-chains 378 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 187 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115914 restraints weight = 130645.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119267 restraints weight = 54904.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.120398 restraints weight = 30022.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.121419 restraints weight = 21453.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121878 restraints weight = 17157.897| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.589 21001 Z= 0.190 Angle : 1.420 80.706 28787 Z= 0.408 Chirality : 0.080 1.754 3062 Planarity : 0.006 0.073 3661 Dihedral : 9.061 179.835 2816 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 2.26 % Allowed : 12.99 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.15), residues: 2490 helix: -1.88 (0.14), residues: 1092 sheet: -4.89 (0.37), residues: 84 loop : -3.13 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 164 TYR 0.028 0.002 TYR B 902 PHE 0.037 0.002 PHE F 351 TRP 0.016 0.001 TRP B 562 HIS 0.008 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00441 (20966) covalent geometry : angle 0.88875 (28742) hydrogen bonds : bond 0.05314 ( 624) hydrogen bonds : angle 5.96208 ( 1824) metal coordination : bond 0.02255 ( 15) metal coordination : angle 28.04035 ( 45) Misc. bond : bond 0.21706 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 631 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6511 (t0) REVERT: B 823 ILE cc_start: 0.7933 (pt) cc_final: 0.7596 (pt) REVERT: B 925 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7890 (pt) REVERT: B 1009 MET cc_start: 0.8377 (tpp) cc_final: 0.8092 (tpp) REVERT: C 92 TRP cc_start: 0.8015 (m100) cc_final: 0.7624 (m100) REVERT: C 340 TYR cc_start: 0.7849 (t80) cc_final: 0.7515 (t80) REVERT: C 431 LEU cc_start: 0.7575 (tt) cc_final: 0.7359 (tt) REVERT: D 45 LYS cc_start: 0.8819 (mttt) cc_final: 0.8494 (mtmt) REVERT: D 60 HIS cc_start: 0.7499 (m-70) cc_final: 0.7291 (t70) REVERT: D 94 TRP cc_start: 0.5049 (t-100) cc_final: 0.4763 (t-100) REVERT: E 31 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7197 (tttm) REVERT: E 117 CYS cc_start: 0.6751 (m) cc_final: 0.6500 (m) REVERT: E 129 MET cc_start: 0.6984 (mtt) cc_final: 0.6639 (mtt) REVERT: F 66 TYR cc_start: 0.8093 (t80) cc_final: 0.7747 (t80) REVERT: F 167 PHE cc_start: 0.6093 (m-80) cc_final: 0.5822 (m-80) REVERT: F 175 LYS cc_start: 0.7023 (ttmm) cc_final: 0.6793 (mmtt) REVERT: F 196 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.5979 (ttt-90) REVERT: F 309 LEU cc_start: 0.7512 (mt) cc_final: 0.7276 (mm) REVERT: F 400 HIS cc_start: 0.6338 (p90) cc_final: 0.5627 (m-70) REVERT: H 55 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7268 (tp30) outliers start: 47 outliers final: 38 residues processed: 393 average time/residue: 0.3613 time to fit residues: 219.7346 Evaluate side-chains 382 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 342 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 155 optimal weight: 0.4980 chunk 158 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117015 restraints weight = 129044.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120698 restraints weight = 54269.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122732 restraints weight = 25611.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123537 restraints weight = 16113.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123880 restraints weight = 14453.227| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.460 21001 Z= 0.150 Angle : 1.332 80.542 28787 Z= 0.387 Chirality : 0.079 1.741 3062 Planarity : 0.006 0.072 3661 Dihedral : 8.855 179.789 2816 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 2.21 % Allowed : 13.52 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.16), residues: 2490 helix: -1.59 (0.14), residues: 1097 sheet: -4.87 (0.35), residues: 94 loop : -3.00 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 58 TYR 0.022 0.001 TYR B 902 PHE 0.028 0.001 PHE D 111 TRP 0.016 0.001 TRP F 70 HIS 0.008 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00348 (20966) covalent geometry : angle 0.85646 (28742) hydrogen bonds : bond 0.04840 ( 624) hydrogen bonds : angle 5.61095 ( 1824) metal coordination : bond 0.01405 ( 15) metal coordination : angle 25.82248 ( 45) Misc. bond : bond 0.16628 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 358 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7778 (m-30) cc_final: 0.7287 (t0) REVERT: B 275 ARG cc_start: 0.7405 (mtp85) cc_final: 0.7179 (mtp85) REVERT: B 276 MET cc_start: 0.6462 (mtp) cc_final: 0.6253 (mtt) REVERT: B 792 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: B 820 GLU cc_start: 0.7752 (tp30) cc_final: 0.7350 (tm-30) REVERT: B 1009 MET cc_start: 0.8364 (tpp) cc_final: 0.8030 (tpp) REVERT: C 133 LEU cc_start: 0.7444 (pp) cc_final: 0.7234 (pp) REVERT: C 340 TYR cc_start: 0.7794 (t80) cc_final: 0.7485 (t80) REVERT: C 394 GLU cc_start: 0.7194 (tt0) cc_final: 0.6744 (tm-30) REVERT: C 421 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6398 (m-30) REVERT: C 431 LEU cc_start: 0.7416 (tt) cc_final: 0.7154 (tt) REVERT: D 44 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7319 (ppp80) REVERT: D 45 LYS cc_start: 0.8665 (mttt) cc_final: 0.8339 (mtmt) REVERT: D 60 HIS cc_start: 0.7545 (m-70) cc_final: 0.7287 (t70) REVERT: D 94 TRP cc_start: 0.5095 (t-100) cc_final: 0.4812 (t-100) REVERT: E 31 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7276 (tttm) REVERT: E 117 CYS cc_start: 0.6844 (m) cc_final: 0.6615 (m) REVERT: E 129 MET cc_start: 0.6808 (mtt) cc_final: 0.6537 (mtt) REVERT: F 66 TYR cc_start: 0.8135 (t80) cc_final: 0.7876 (t80) REVERT: F 175 LYS cc_start: 0.7039 (ttmm) cc_final: 0.6785 (mmtt) REVERT: F 196 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.5691 (ttt-90) REVERT: F 219 MET cc_start: 0.6501 (tpt) cc_final: 0.6091 (tpt) REVERT: F 351 PHE cc_start: 0.8014 (t80) cc_final: 0.7691 (t80) REVERT: F 400 HIS cc_start: 0.6308 (p90) cc_final: 0.5866 (m-70) REVERT: H 55 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7197 (tp30) outliers start: 46 outliers final: 36 residues processed: 383 average time/residue: 0.3549 time to fit residues: 211.2185 Evaluate side-chains 379 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 340 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 172 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 ASN B1000 GLN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110112 restraints weight = 132828.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113889 restraints weight = 57908.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.115445 restraints weight = 27740.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115546 restraints weight = 18814.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116034 restraints weight = 18544.521| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.706 21001 Z= 0.264 Angle : 1.496 84.492 28787 Z= 0.427 Chirality : 0.082 1.784 3062 Planarity : 0.006 0.072 3661 Dihedral : 8.862 179.934 2816 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 2.79 % Allowed : 13.80 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.15), residues: 2490 helix: -1.51 (0.14), residues: 1094 sheet: -4.93 (0.38), residues: 89 loop : -3.05 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 58 TYR 0.040 0.002 TYR B 902 PHE 0.028 0.002 PHE D 111 TRP 0.017 0.002 TRP B 562 HIS 0.013 0.002 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00613 (20966) covalent geometry : angle 0.92079 (28742) hydrogen bonds : bond 0.05065 ( 624) hydrogen bonds : angle 5.70110 ( 1824) metal coordination : bond 0.02778 ( 15) metal coordination : angle 29.83194 ( 45) Misc. bond : bond 0.26872 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 344 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7932 (m-30) cc_final: 0.7490 (t0) REVERT: B 808 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6103 (t) REVERT: B 902 TYR cc_start: 0.8926 (t80) cc_final: 0.8618 (t80) REVERT: B 1009 MET cc_start: 0.8431 (tpp) cc_final: 0.8042 (tpp) REVERT: C 340 TYR cc_start: 0.8170 (t80) cc_final: 0.7819 (t80) REVERT: C 421 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: C 431 LEU cc_start: 0.7445 (tt) cc_final: 0.7203 (tt) REVERT: D 44 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7479 (ppp80) REVERT: D 45 LYS cc_start: 0.8805 (mttt) cc_final: 0.8573 (mtmt) REVERT: D 94 TRP cc_start: 0.5434 (t-100) cc_final: 0.5062 (t-100) REVERT: E 31 LYS cc_start: 0.7955 (mmpt) cc_final: 0.7392 (tttm) REVERT: E 117 CYS cc_start: 0.7393 (m) cc_final: 0.7186 (m) REVERT: E 129 MET cc_start: 0.7168 (mtt) cc_final: 0.6733 (mtt) REVERT: F 89 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8211 (mp) REVERT: F 175 LYS cc_start: 0.7330 (ttmm) cc_final: 0.6881 (mmtt) REVERT: F 196 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.5858 (ttt-90) REVERT: F 400 HIS cc_start: 0.6450 (p90) cc_final: 0.6037 (m-70) REVERT: H 55 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7326 (tp30) REVERT: H 101 ASP cc_start: 0.6535 (t0) cc_final: 0.6283 (p0) outliers start: 58 outliers final: 46 residues processed: 377 average time/residue: 0.3455 time to fit residues: 202.1210 Evaluate side-chains 366 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 243 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113888 restraints weight = 129539.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117760 restraints weight = 54647.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119200 restraints weight = 25312.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119920 restraints weight = 17087.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120365 restraints weight = 16418.738| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.549 21001 Z= 0.157 Angle : 1.355 81.816 28787 Z= 0.388 Chirality : 0.079 1.773 3062 Planarity : 0.006 0.072 3661 Dihedral : 8.652 179.512 2816 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 2.89 % Allowed : 14.53 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.16), residues: 2490 helix: -1.27 (0.15), residues: 1088 sheet: -4.78 (0.36), residues: 94 loop : -2.92 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 58 TYR 0.037 0.002 TYR B 902 PHE 0.026 0.002 PHE D 111 TRP 0.018 0.001 TRP F 70 HIS 0.008 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00367 (20966) covalent geometry : angle 0.86097 (28742) hydrogen bonds : bond 0.04569 ( 624) hydrogen bonds : angle 5.41413 ( 1824) metal coordination : bond 0.01541 ( 15) metal coordination : angle 26.47955 ( 45) Misc. bond : bond 0.19293 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.9012 (ptmt) cc_final: 0.8688 (ptmm) REVERT: A 119 ASP cc_start: 0.7888 (m-30) cc_final: 0.7379 (t0) REVERT: B 290 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: B 808 THR cc_start: 0.6568 (OUTLIER) cc_final: 0.6145 (t) REVERT: B 929 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7973 (mmp) REVERT: B 1009 MET cc_start: 0.8386 (tpp) cc_final: 0.7773 (tpt) REVERT: C 92 TRP cc_start: 0.8128 (m100) cc_final: 0.7670 (m100) REVERT: C 340 TYR cc_start: 0.8004 (t80) cc_final: 0.7741 (t80) REVERT: C 421 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6509 (m-30) REVERT: D 44 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7493 (ppp80) REVERT: D 45 LYS cc_start: 0.8725 (mttt) cc_final: 0.8391 (mtmt) REVERT: E 31 LYS cc_start: 0.7916 (mmpt) cc_final: 0.7384 (tttm) REVERT: E 151 ASP cc_start: 0.8809 (m-30) cc_final: 0.8483 (t0) REVERT: F 89 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8185 (mp) REVERT: F 175 LYS cc_start: 0.7281 (ttmm) cc_final: 0.6914 (mmtt) REVERT: F 196 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.5456 (tmt-80) REVERT: F 349 ILE cc_start: 0.9027 (mm) cc_final: 0.8655 (mt) REVERT: H 55 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7161 (tp30) outliers start: 60 outliers final: 46 residues processed: 386 average time/residue: 0.3517 time to fit residues: 209.3423 Evaluate side-chains 374 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 322 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.126000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113803 restraints weight = 129520.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117448 restraints weight = 55247.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119401 restraints weight = 26056.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120014 restraints weight = 16863.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120421 restraints weight = 15707.909| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.477 21001 Z= 0.154 Angle : 1.328 83.893 28787 Z= 0.382 Chirality : 0.079 1.767 3062 Planarity : 0.006 0.064 3661 Dihedral : 8.471 179.839 2816 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 2.45 % Allowed : 15.54 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.16), residues: 2490 helix: -1.13 (0.15), residues: 1103 sheet: -4.62 (0.38), residues: 94 loop : -2.88 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 58 TYR 0.045 0.002 TYR B 902 PHE 0.027 0.001 PHE D 111 TRP 0.014 0.001 TRP C 392 HIS 0.009 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00360 (20966) covalent geometry : angle 0.85086 (28742) hydrogen bonds : bond 0.04410 ( 624) hydrogen bonds : angle 5.26403 ( 1824) metal coordination : bond 0.01496 ( 15) metal coordination : angle 25.81194 ( 45) Misc. bond : bond 0.17134 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8659 (ptmm) REVERT: A 119 ASP cc_start: 0.7915 (m-30) cc_final: 0.7412 (t0) REVERT: A 169 TYR cc_start: 0.8720 (m-10) cc_final: 0.8505 (m-10) REVERT: B 512 TYR cc_start: 0.7794 (t80) cc_final: 0.7351 (t80) REVERT: B 808 THR cc_start: 0.6721 (OUTLIER) cc_final: 0.6193 (t) REVERT: B 1009 MET cc_start: 0.8410 (tpp) cc_final: 0.7796 (tpt) REVERT: C 88 ASN cc_start: 0.8922 (m-40) cc_final: 0.8270 (m-40) REVERT: C 92 TRP cc_start: 0.8160 (m100) cc_final: 0.7728 (m100) REVERT: C 340 TYR cc_start: 0.8087 (t80) cc_final: 0.7792 (t80) REVERT: C 421 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6541 (m-30) REVERT: D 44 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7508 (ppp80) REVERT: D 45 LYS cc_start: 0.8756 (mttt) cc_final: 0.8434 (mtmt) REVERT: D 94 TRP cc_start: 0.5470 (t-100) cc_final: 0.5153 (t-100) REVERT: D 104 ASN cc_start: 0.7750 (t0) cc_final: 0.7447 (t0) REVERT: E 31 LYS cc_start: 0.7929 (mmpt) cc_final: 0.7400 (tttm) REVERT: E 151 ASP cc_start: 0.8756 (m-30) cc_final: 0.8467 (t0) REVERT: F 89 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8171 (mp) REVERT: F 175 LYS cc_start: 0.7334 (ttmm) cc_final: 0.6973 (mmtt) REVERT: F 196 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.5413 (tmt-80) REVERT: F 349 ILE cc_start: 0.9038 (mm) cc_final: 0.8731 (mt) REVERT: F 400 HIS cc_start: 0.4133 (m-70) cc_final: 0.3849 (m-70) REVERT: H 55 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7318 (tp30) outliers start: 51 outliers final: 44 residues processed: 366 average time/residue: 0.3486 time to fit residues: 199.0797 Evaluate side-chains 367 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 10 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 217 optimal weight: 0.0030 chunk 239 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 890 ASN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.126236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113826 restraints weight = 129745.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117514 restraints weight = 55296.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119517 restraints weight = 26867.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120072 restraints weight = 17001.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.120495 restraints weight = 15706.330| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.428 21001 Z= 0.147 Angle : 1.296 84.380 28787 Z= 0.378 Chirality : 0.078 1.749 3062 Planarity : 0.006 0.067 3661 Dihedral : 8.322 179.039 2816 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 2.16 % Allowed : 16.07 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.16), residues: 2490 helix: -0.94 (0.15), residues: 1102 sheet: -4.53 (0.38), residues: 94 loop : -2.85 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 58 TYR 0.043 0.001 TYR B 902 PHE 0.026 0.001 PHE D 111 TRP 0.013 0.001 TRP C 225 HIS 0.009 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00347 (20966) covalent geometry : angle 0.84558 (28742) hydrogen bonds : bond 0.04249 ( 624) hydrogen bonds : angle 5.15092 ( 1824) metal coordination : bond 0.01395 ( 15) metal coordination : angle 24.84003 ( 45) Misc. bond : bond 0.15419 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8549 (tp) REVERT: A 113 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8650 (ptmm) REVERT: A 119 ASP cc_start: 0.7931 (m-30) cc_final: 0.7512 (t0) REVERT: B 512 TYR cc_start: 0.7795 (t80) cc_final: 0.7402 (t80) REVERT: B 808 THR cc_start: 0.6587 (OUTLIER) cc_final: 0.6250 (t) REVERT: B 1009 MET cc_start: 0.8428 (tpp) cc_final: 0.7872 (tpt) REVERT: C 56 MET cc_start: 0.7793 (ppp) cc_final: 0.7211 (tmm) REVERT: C 88 ASN cc_start: 0.8909 (m-40) cc_final: 0.8233 (m-40) REVERT: C 92 TRP cc_start: 0.8183 (m100) cc_final: 0.7744 (m100) REVERT: C 340 TYR cc_start: 0.8041 (t80) cc_final: 0.7751 (t80) REVERT: C 421 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6508 (m-30) REVERT: D 44 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7503 (ppp80) REVERT: D 45 LYS cc_start: 0.8781 (mttt) cc_final: 0.8468 (mtmt) REVERT: D 94 TRP cc_start: 0.5461 (t-100) cc_final: 0.5213 (t-100) REVERT: D 104 ASN cc_start: 0.7761 (t0) cc_final: 0.7462 (t0) REVERT: E 31 LYS cc_start: 0.7907 (mmpt) cc_final: 0.7349 (tttm) REVERT: E 52 ASN cc_start: 0.8376 (t0) cc_final: 0.7361 (t0) REVERT: E 151 ASP cc_start: 0.8710 (m-30) cc_final: 0.8426 (t0) REVERT: F 175 LYS cc_start: 0.7367 (ttmm) cc_final: 0.7017 (mmtt) REVERT: F 196 ARG cc_start: 0.7876 (mmt-90) cc_final: 0.5339 (tmt-80) REVERT: F 349 ILE cc_start: 0.9073 (mm) cc_final: 0.8758 (mt) REVERT: H 55 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7261 (tp30) outliers start: 45 outliers final: 39 residues processed: 358 average time/residue: 0.3414 time to fit residues: 191.6729 Evaluate side-chains 365 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 322 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 156 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113659 restraints weight = 129899.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117638 restraints weight = 55431.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119303 restraints weight = 26331.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120126 restraints weight = 17530.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120401 restraints weight = 15871.061| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.413 21001 Z= 0.150 Angle : 1.295 84.895 28787 Z= 0.379 Chirality : 0.079 1.754 3062 Planarity : 0.006 0.076 3661 Dihedral : 8.235 179.239 2816 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 2.26 % Allowed : 16.59 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.16), residues: 2490 helix: -0.84 (0.15), residues: 1103 sheet: -4.15 (0.41), residues: 98 loop : -2.83 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 62 TYR 0.045 0.001 TYR B 902 PHE 0.027 0.001 PHE D 111 TRP 0.014 0.001 TRP C 225 HIS 0.009 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00354 (20966) covalent geometry : angle 0.85109 (28742) hydrogen bonds : bond 0.04168 ( 624) hydrogen bonds : angle 5.09045 ( 1824) metal coordination : bond 0.01402 ( 15) metal coordination : angle 24.68940 ( 45) Misc. bond : bond 0.15027 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7464 (t80) cc_final: 0.6949 (t80) REVERT: A 57 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 113 LYS cc_start: 0.8983 (ptmt) cc_final: 0.8663 (ptmm) REVERT: A 119 ASP cc_start: 0.7927 (m-30) cc_final: 0.7524 (t0) REVERT: B 328 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7167 (mmt180) REVERT: B 512 TYR cc_start: 0.7833 (t80) cc_final: 0.7419 (t80) REVERT: B 808 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6414 (t) REVERT: B 929 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7956 (mmp) REVERT: B 1009 MET cc_start: 0.8437 (tpp) cc_final: 0.7893 (tpt) REVERT: C 56 MET cc_start: 0.7801 (ppp) cc_final: 0.7226 (tmm) REVERT: C 88 ASN cc_start: 0.8923 (m-40) cc_final: 0.8251 (m-40) REVERT: C 92 TRP cc_start: 0.8183 (m100) cc_final: 0.7745 (m100) REVERT: C 340 TYR cc_start: 0.8065 (t80) cc_final: 0.7776 (t80) REVERT: C 421 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: D 44 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7467 (ppp80) REVERT: D 45 LYS cc_start: 0.8759 (mttt) cc_final: 0.8353 (mtmt) REVERT: D 94 TRP cc_start: 0.5534 (t-100) cc_final: 0.5295 (t-100) REVERT: D 104 ASN cc_start: 0.7746 (t0) cc_final: 0.7487 (t0) REVERT: E 31 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7360 (tttm) REVERT: E 151 ASP cc_start: 0.8671 (m-30) cc_final: 0.8438 (t0) REVERT: F 175 LYS cc_start: 0.7417 (ttmm) cc_final: 0.7070 (mmtt) REVERT: F 196 ARG cc_start: 0.7818 (mmt-90) cc_final: 0.5329 (tmt-80) REVERT: F 349 ILE cc_start: 0.9060 (mm) cc_final: 0.8756 (mt) REVERT: F 400 HIS cc_start: 0.4414 (m-70) cc_final: 0.4085 (m-70) REVERT: H 55 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7218 (tp30) outliers start: 47 outliers final: 41 residues processed: 357 average time/residue: 0.3425 time to fit residues: 192.4468 Evaluate side-chains 363 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 770 TRP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 909 TYR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 68 optimal weight: 0.0040 chunk 121 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113382 restraints weight = 130398.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117252 restraints weight = 56224.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.119137 restraints weight = 26524.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119533 restraints weight = 17647.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119910 restraints weight = 16365.731| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.402 21001 Z= 0.149 Angle : 1.284 84.725 28787 Z= 0.377 Chirality : 0.078 1.753 3062 Planarity : 0.006 0.064 3661 Dihedral : 8.151 179.433 2816 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 2.36 % Allowed : 16.79 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.16), residues: 2490 helix: -0.79 (0.15), residues: 1110 sheet: -4.12 (0.41), residues: 98 loop : -2.78 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 161 TYR 0.046 0.002 TYR B 902 PHE 0.026 0.002 PHE D 111 TRP 0.014 0.001 TRP C 225 HIS 0.009 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00354 (20966) covalent geometry : angle 0.84740 (28742) hydrogen bonds : bond 0.04086 ( 624) hydrogen bonds : angle 5.00476 ( 1824) metal coordination : bond 0.01464 ( 15) metal coordination : angle 24.40826 ( 45) Misc. bond : bond 0.14633 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.65 seconds wall clock time: 111 minutes 17.39 seconds (6677.39 seconds total)