Starting phenix.real_space_refine on Sat Aug 23 16:39:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi0_33845/08_2025/7yi0_33845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi0_33845/08_2025/7yi0_33845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yi0_33845/08_2025/7yi0_33845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi0_33845/08_2025/7yi0_33845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yi0_33845/08_2025/7yi0_33845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi0_33845/08_2025/7yi0_33845.map" } resolution = 3.2 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= 0.003 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: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 83 5.16 5 C 8599 2.51 5 N 2248 2.21 5 O 2493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13430 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4233 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 7, 'TRANS': 495} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1473 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2553 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 293} Chain breaks: 5 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1259 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9039 SG CYS D 263 41.201 36.453 82.439 1.00 61.30 S ATOM 9056 SG CYS D 266 44.396 38.503 81.827 1.00 45.48 S ATOM 9209 SG CYS D 286 41.321 39.307 79.739 1.00 44.47 S ATOM 9120 SG CYS D 275 32.091 27.627 84.823 1.00 91.60 S ATOM 9141 SG CYS D 278 35.407 25.729 84.699 1.00100.47 S ATOM 9344 SG CYS D 303 34.533 27.734 81.648 1.00 97.48 S ATOM 9367 SG CYS D 306 33.034 24.499 82.584 1.00 96.48 S ATOM 10288 SG CYS D 440 76.941 54.356 80.421 1.00 27.45 S ATOM 10314 SG CYS D 443 80.030 53.856 78.101 1.00 20.60 S ATOM 10503 SG CYS D 466 78.101 57.037 77.898 1.00 27.76 S ATOM 10100 SG CYS D 417 82.257 64.253 84.254 1.00 23.71 S ATOM 10127 SG CYS D 420 84.485 67.113 85.478 1.00 37.16 S ATOM 10383 SG CYS D 451 80.921 67.832 84.252 1.00 46.26 S ATOM 11280 SG CYS F 275 95.951 11.973 36.652 1.00118.29 S ATOM 11301 SG CYS F 278 92.897 13.490 36.787 1.00108.57 S ATOM 11199 SG CYS F 263 96.088 18.843 25.157 1.00 96.00 S ATOM 11216 SG CYS F 266 95.207 20.546 21.917 1.00104.06 S ATOM 11369 SG CYS F 286 98.591 21.687 24.196 1.00106.90 S Time building chain proxies: 3.28, per 1000 atoms: 0.24 Number of scatterers: 13430 At special positions: 0 Unit cell: (129.8, 111.1, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 83 16.00 O 2493 8.00 N 2248 7.00 C 8599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 599.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 263 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 278 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 306 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 275 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 440 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 451 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 278 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 275 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 286 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 263 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 266 " Number of angles added : 15 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3132 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 9 sheets defined 56.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.714A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 714 through 725 removed outlier: 3.571A pdb=" N THR A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.620A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 837 removed outlier: 3.765A pdb=" N LYS A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 removed outlier: 4.187A pdb=" N LYS A 864 " --> pdb=" O MET A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 891 through 928 removed outlier: 3.841A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS A 926 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 6.095A pdb=" N LYS A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.738A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.593A pdb=" N GLU A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1141 through 1163 Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.532A pdb=" N TYR A1240 " --> pdb=" O PHE A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1256 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.719A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.085A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A1287 " --> pdb=" O GLN A1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.751A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.762A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.551A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 105 removed outlier: 4.050A pdb=" N VAL B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.532A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.504A pdb=" N LYS B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 263 removed outlier: 3.522A pdb=" N SER B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.021A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.263A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.664A pdb=" N ARG B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 removed outlier: 3.520A pdb=" N GLU B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.533A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.876A pdb=" N GLN C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.547A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.756A pdb=" N SER C 336 " --> pdb=" O ARG C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 348 through 369 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.732A pdb=" N VAL C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 168 through 175 removed outlier: 4.283A pdb=" N LEU D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET D 175 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.816A pdb=" N THR D 405 " --> pdb=" O ASN D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.719A pdb=" N SER D 434 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 removed outlier: 3.520A pdb=" N ILE D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS D 565 " --> pdb=" O VAL D 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 321 through 330 Processing helix chain 'F' and resid 331 through 334 removed outlier: 3.814A pdb=" N LYS F 334 " --> pdb=" O ASN F 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 331 through 334' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.676A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 567 removed outlier: 3.953A pdb=" N ASP F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 241 Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.531A pdb=" N SER E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'E' and resid 271 through 297 removed outlier: 3.819A pdb=" N LYS E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 317 removed outlier: 4.397A pdb=" N LEU E 304 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 317 " --> pdb=" O SER E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 325 removed outlier: 3.663A pdb=" N ILE E 325 " --> pdb=" O PRO E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 removed outlier: 3.719A pdb=" N ARG E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 350 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 238 removed outlier: 8.286A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLU D 177 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 63 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER D 179 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 65 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'D' and resid 365 through 366 Processing sheet with id=AA7, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA8, first strand: chain 'D' and resid 505 through 506 removed outlier: 7.381A pdb=" N TYR D 506 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 273 through 274 635 hydrogen bonds defined for protein. 1812 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: 2.14 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4281 1.34 - 1.46: 3135 1.46 - 1.58: 6182 1.58 - 1.70: 0 1.70 - 1.81: 122 Bond restraints: 13720 Sorted by residual: bond pdb=" C LEU E 248 " pdb=" N PRO E 249 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.42e+00 bond pdb=" CA THR D 439 " pdb=" CB THR D 439 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.37e-02 5.33e+03 1.20e+00 bond pdb=" CB GLU E 340 " pdb=" CG GLU E 340 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" N THR D 439 " pdb=" CA THR D 439 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.31e-02 5.83e+03 9.20e-01 bond pdb=" CB GLU A1171 " pdb=" CG GLU A1171 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.77e-01 ... (remaining 13715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 18300 2.34 - 4.67: 165 4.67 - 7.01: 23 7.01 - 9.35: 5 9.35 - 11.69: 1 Bond angle restraints: 18494 Sorted by residual: angle pdb=" N GLN A 937 " pdb=" CA GLN A 937 " pdb=" C GLN A 937 " ideal model delta sigma weight residual 114.62 107.49 7.13 1.14e+00 7.69e-01 3.91e+01 angle pdb=" CA GLN A 937 " pdb=" C GLN A 937 " pdb=" N ALA A 938 " ideal model delta sigma weight residual 119.71 115.10 4.61 1.17e+00 7.31e-01 1.55e+01 angle pdb=" CA LYS A 936 " pdb=" CB LYS A 936 " pdb=" CG LYS A 936 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA GLU A1171 " pdb=" CB GLU A1171 " pdb=" CG GLU A1171 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA THR D 439 " pdb=" CB THR D 439 " pdb=" CG2 THR D 439 " ideal model delta sigma weight residual 110.50 116.19 -5.69 1.70e+00 3.46e-01 1.12e+01 ... (remaining 18489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7316 17.93 - 35.86: 724 35.86 - 53.79: 211 53.79 - 71.72: 30 71.72 - 89.65: 8 Dihedral angle restraints: 8289 sinusoidal: 3454 harmonic: 4835 Sorted by residual: dihedral pdb=" CA LEU E 248 " pdb=" C LEU E 248 " pdb=" N PRO E 249 " pdb=" CA PRO E 249 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LYS A 936 " pdb=" C LYS A 936 " pdb=" N GLN A 937 " pdb=" CA GLN A 937 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1613 0.052 - 0.104: 341 0.104 - 0.156: 40 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CB THR A1000 " pdb=" CA THR A1000 " pdb=" OG1 THR A1000 " pdb=" CG2 THR A1000 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA THR D 439 " pdb=" N THR D 439 " pdb=" C THR D 439 " pdb=" CB THR D 439 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA HIS A 785 " pdb=" N HIS A 785 " pdb=" C HIS A 785 " pdb=" CB HIS A 785 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 1995 not shown) Planarity restraints: 2351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 90 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 91 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 248 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO E 249 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 249 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 249 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 466 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 467 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 467 " -0.024 5.00e-02 4.00e+02 ... (remaining 2348 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 186 2.66 - 3.22: 12477 3.22 - 3.78: 20357 3.78 - 4.34: 28988 4.34 - 4.90: 46732 Nonbonded interactions: 108740 Sorted by model distance: nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.105 3.040 nonbonded pdb=" OG SER B 123 " pdb=" OD2 ASP B 165 " model vdw 2.109 3.040 nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.165 2.230 nonbonded pdb=" O ILE E 342 " pdb=" OG1 THR E 345 " model vdw 2.172 3.040 nonbonded pdb=" N ASP B 140 " pdb=" OD1 ASP B 140 " model vdw 2.187 3.120 ... (remaining 108735 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13742 Z= 0.129 Angle : 0.586 14.443 18509 Z= 0.306 Chirality : 0.042 0.260 1998 Planarity : 0.004 0.051 2351 Dihedral : 15.666 89.653 5157 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.93 % Allowed : 15.07 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1604 helix: 1.01 (0.18), residues: 805 sheet: 0.09 (0.55), residues: 91 loop : -1.66 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 369 TYR 0.018 0.001 TYR F 556 PHE 0.017 0.001 PHE A 935 TRP 0.009 0.001 TRP D 428 HIS 0.017 0.001 HIS A 785 Details of bonding type rmsd covalent geometry : bond 0.00280 (13720) covalent geometry : angle 0.56757 (18494) hydrogen bonds : bond 0.15115 ( 635) hydrogen bonds : angle 6.04936 ( 1812) metal coordination : bond 0.00958 ( 22) metal coordination : angle 5.20811 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 365 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1168 VAL cc_start: 0.8215 (t) cc_final: 0.7809 (t) REVERT: B 40 MET cc_start: 0.7028 (tpt) cc_final: 0.6421 (tpp) outliers start: 14 outliers final: 4 residues processed: 376 average time/residue: 0.1399 time to fit residues: 73.6591 Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 214 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN A 785 HIS A 909 GLN A 913 ASN A 947 GLN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN C 393 GLN D 325 ASN F 347 ASN F 350 GLN E 317 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.219781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.174800 restraints weight = 16890.078| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.68 r_work: 0.3855 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13742 Z= 0.201 Angle : 0.729 15.215 18509 Z= 0.378 Chirality : 0.046 0.217 1998 Planarity : 0.005 0.071 2351 Dihedral : 5.310 48.091 1779 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 3.65 % Allowed : 17.46 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.21), residues: 1604 helix: 0.88 (0.18), residues: 816 sheet: -0.32 (0.51), residues: 94 loop : -1.71 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 826 TYR 0.027 0.002 TYR A1316 PHE 0.032 0.002 PHE E 289 TRP 0.014 0.002 TRP A 719 HIS 0.014 0.002 HIS A 785 Details of bonding type rmsd covalent geometry : bond 0.00460 (13720) covalent geometry : angle 0.70824 (18494) hydrogen bonds : bond 0.05237 ( 635) hydrogen bonds : angle 4.70170 ( 1812) metal coordination : bond 0.01226 ( 22) metal coordination : angle 6.07380 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.7584 (m-80) cc_final: 0.7383 (m-80) REVERT: A 714 LYS cc_start: 0.7342 (mmmt) cc_final: 0.6784 (mttt) REVERT: A 764 PHE cc_start: 0.5208 (OUTLIER) cc_final: 0.4213 (t80) REVERT: A 1008 GLU cc_start: 0.7921 (mp0) cc_final: 0.6741 (mp0) REVERT: B 19 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7868 (mtp180) REVERT: B 129 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 240 ASP cc_start: 0.8312 (m-30) cc_final: 0.8101 (m-30) REVERT: B 283 CYS cc_start: 0.8025 (p) cc_final: 0.7436 (p) REVERT: B 305 MET cc_start: 0.6744 (ptp) cc_final: 0.6441 (ptm) REVERT: D 470 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6756 (p) REVERT: E 256 MET cc_start: 0.3906 (ttp) cc_final: 0.2646 (mtt) REVERT: E 368 MET cc_start: 0.3460 (ttp) cc_final: 0.2508 (tpp) outliers start: 55 outliers final: 20 residues processed: 243 average time/residue: 0.1199 time to fit residues: 43.3083 Evaluate side-chains 171 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 154 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 142 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN B 38 HIS ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN D 325 ASN D 355 ASN E 330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.216310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.171076 restraints weight = 16808.815| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.48 r_work: 0.3812 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13742 Z= 0.144 Angle : 0.602 14.850 18509 Z= 0.310 Chirality : 0.042 0.186 1998 Planarity : 0.004 0.065 2351 Dihedral : 4.700 33.774 1773 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.79 % Allowed : 18.73 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1604 helix: 1.25 (0.18), residues: 811 sheet: -0.43 (0.51), residues: 95 loop : -1.57 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 381 TYR 0.014 0.001 TYR B 347 PHE 0.024 0.001 PHE E 289 TRP 0.012 0.001 TRP A 719 HIS 0.006 0.001 HIS F 283 Details of bonding type rmsd covalent geometry : bond 0.00318 (13720) covalent geometry : angle 0.58506 (18494) hydrogen bonds : bond 0.04533 ( 635) hydrogen bonds : angle 4.38079 ( 1812) metal coordination : bond 0.01290 ( 22) metal coordination : angle 4.95993 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.7808 (m-80) cc_final: 0.7559 (m-80) REVERT: A 936 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8295 (ttmm) REVERT: A 986 TYR cc_start: 0.7293 (m-10) cc_final: 0.6851 (m-80) REVERT: A 1287 ARG cc_start: 0.5915 (ttm170) cc_final: 0.5508 (mtp180) REVERT: A 1305 PHE cc_start: 0.7481 (t80) cc_final: 0.7258 (t80) REVERT: B 62 GLU cc_start: 0.7765 (tp30) cc_final: 0.7421 (tt0) REVERT: B 73 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: B 222 ARG cc_start: 0.7310 (mtm110) cc_final: 0.7037 (mtm-85) REVERT: D 171 LEU cc_start: 0.3780 (OUTLIER) cc_final: 0.3090 (tp) REVERT: D 438 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5526 (mtp) REVERT: D 470 SER cc_start: 0.6871 (OUTLIER) cc_final: 0.6632 (p) REVERT: D 553 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: E 256 MET cc_start: 0.3683 (ttp) cc_final: 0.2276 (mtt) REVERT: E 368 MET cc_start: 0.3073 (ttp) cc_final: 0.1930 (tpt) outliers start: 42 outliers final: 20 residues processed: 229 average time/residue: 0.1237 time to fit residues: 41.5183 Evaluate side-chains 184 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN D 325 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN E 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.216311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171102 restraints weight = 16562.728| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.38 r_work: 0.3819 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13742 Z= 0.119 Angle : 0.557 12.148 18509 Z= 0.287 Chirality : 0.041 0.181 1998 Planarity : 0.004 0.068 2351 Dihedral : 4.393 30.278 1771 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.79 % Allowed : 19.06 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1604 helix: 1.37 (0.18), residues: 815 sheet: -0.47 (0.54), residues: 93 loop : -1.39 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 381 TYR 0.012 0.001 TYR D 356 PHE 0.019 0.001 PHE E 289 TRP 0.007 0.001 TRP D 447 HIS 0.007 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00255 (13720) covalent geometry : angle 0.54400 (18494) hydrogen bonds : bond 0.03960 ( 635) hydrogen bonds : angle 4.26154 ( 1812) metal coordination : bond 0.00910 ( 22) metal coordination : angle 4.17377 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.7835 (m-80) cc_final: 0.7529 (m-80) REVERT: A 986 TYR cc_start: 0.7396 (m-10) cc_final: 0.6881 (m-80) REVERT: A 1300 MET cc_start: 0.7274 (ttp) cc_final: 0.6963 (ttm) REVERT: B 28 ASP cc_start: 0.8138 (m-30) cc_final: 0.7886 (t0) REVERT: B 62 GLU cc_start: 0.7852 (tp30) cc_final: 0.7481 (tt0) REVERT: B 88 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7207 (ttp-110) REVERT: B 117 TYR cc_start: 0.7979 (t80) cc_final: 0.7719 (t80) REVERT: B 222 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6542 (mtm110) REVERT: D 171 LEU cc_start: 0.3787 (OUTLIER) cc_final: 0.3045 (tp) REVERT: D 438 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.5451 (mtp) REVERT: D 470 SER cc_start: 0.6841 (OUTLIER) cc_final: 0.6614 (p) REVERT: D 553 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: F 332 ASN cc_start: 0.5994 (t0) cc_final: 0.4954 (p0) REVERT: E 256 MET cc_start: 0.3721 (ttp) cc_final: 0.2211 (mtt) REVERT: E 367 LEU cc_start: 0.5257 (tp) cc_final: 0.5030 (mm) REVERT: E 368 MET cc_start: 0.2789 (ttp) cc_final: 0.1708 (tpt) outliers start: 42 outliers final: 20 residues processed: 207 average time/residue: 0.1234 time to fit residues: 37.5954 Evaluate side-chains 178 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1150 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 331 ASN C 353 GLN D 174 ASN D 268 GLN D 325 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.209190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164162 restraints weight = 16708.741| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.34 r_work: 0.3747 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13742 Z= 0.176 Angle : 0.629 16.176 18509 Z= 0.326 Chirality : 0.043 0.194 1998 Planarity : 0.005 0.065 2351 Dihedral : 4.700 22.663 1769 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.59 % Allowed : 19.79 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.21), residues: 1604 helix: 1.27 (0.18), residues: 816 sheet: -0.98 (0.51), residues: 103 loop : -1.37 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 381 TYR 0.016 0.002 TYR B 347 PHE 0.028 0.002 PHE A1269 TRP 0.013 0.001 TRP A1151 HIS 0.010 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00400 (13720) covalent geometry : angle 0.61251 (18494) hydrogen bonds : bond 0.04930 ( 635) hydrogen bonds : angle 4.51623 ( 1812) metal coordination : bond 0.01181 ( 22) metal coordination : angle 5.11219 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 871 TYR cc_start: 0.4970 (OUTLIER) cc_final: 0.4626 (t80) REVERT: A 873 LYS cc_start: 0.4599 (ttmt) cc_final: 0.4254 (mmtt) REVERT: A 1300 MET cc_start: 0.7155 (ttp) cc_final: 0.6895 (ttm) REVERT: A 1311 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5743 (t70) REVERT: B 19 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.7205 (mtt-85) REVERT: B 28 ASP cc_start: 0.8083 (m-30) cc_final: 0.7747 (t0) REVERT: B 62 GLU cc_start: 0.7910 (tp30) cc_final: 0.7507 (mt-10) REVERT: B 72 GLN cc_start: 0.8337 (tt0) cc_final: 0.7518 (mp10) REVERT: B 222 ARG cc_start: 0.7302 (mtm110) cc_final: 0.6907 (mtm-85) REVERT: D 171 LEU cc_start: 0.4163 (OUTLIER) cc_final: 0.3460 (tp) REVERT: D 438 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.5750 (mtp) REVERT: D 470 SER cc_start: 0.6940 (OUTLIER) cc_final: 0.6637 (p) REVERT: F 332 ASN cc_start: 0.6634 (t0) cc_final: 0.5389 (p0) REVERT: E 256 MET cc_start: 0.3292 (ttp) cc_final: 0.2121 (mtt) REVERT: E 301 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6185 (pt) REVERT: E 351 SER cc_start: 0.6392 (m) cc_final: 0.5964 (t) REVERT: E 367 LEU cc_start: 0.5605 (tp) cc_final: 0.5323 (mm) REVERT: E 368 MET cc_start: 0.2333 (ttp) cc_final: 0.0840 (tpt) outliers start: 54 outliers final: 33 residues processed: 218 average time/residue: 0.1214 time to fit residues: 38.8865 Evaluate side-chains 199 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain B residue 34 TYR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.204581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160271 restraints weight = 16839.942| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.59 r_work: 0.3690 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13742 Z= 0.202 Angle : 0.655 15.279 18509 Z= 0.342 Chirality : 0.044 0.201 1998 Planarity : 0.005 0.068 2351 Dihedral : 4.850 28.755 1769 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.12 % Allowed : 19.99 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.21), residues: 1604 helix: 1.10 (0.18), residues: 823 sheet: -1.00 (0.51), residues: 103 loop : -1.38 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 333 TYR 0.015 0.002 TYR B 347 PHE 0.021 0.002 PHE A1269 TRP 0.013 0.002 TRP A1151 HIS 0.008 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00457 (13720) covalent geometry : angle 0.63909 (18494) hydrogen bonds : bond 0.04941 ( 635) hydrogen bonds : angle 4.57915 ( 1812) metal coordination : bond 0.01471 ( 22) metal coordination : angle 5.03659 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 860 MET cc_start: 0.4956 (mmt) cc_final: 0.4516 (tpt) REVERT: A 874 GLU cc_start: 0.4679 (OUTLIER) cc_final: 0.3750 (pt0) REVERT: A 986 TYR cc_start: 0.7549 (m-10) cc_final: 0.7322 (m-80) REVERT: A 1135 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 1300 MET cc_start: 0.7070 (ttp) cc_final: 0.6840 (ttm) REVERT: A 1304 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 1305 PHE cc_start: 0.7636 (t80) cc_final: 0.7362 (t80) REVERT: B 62 GLU cc_start: 0.7826 (tp30) cc_final: 0.7586 (mt-10) REVERT: B 72 GLN cc_start: 0.8428 (tt0) cc_final: 0.8212 (mt0) REVERT: B 222 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7167 (mtm-85) REVERT: D 171 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4051 (tp) REVERT: D 373 SER cc_start: 0.8740 (t) cc_final: 0.8480 (p) REVERT: D 438 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.5852 (mtp) REVERT: D 470 SER cc_start: 0.7045 (OUTLIER) cc_final: 0.6779 (p) REVERT: D 559 LYS cc_start: 0.6044 (mttt) cc_final: 0.5717 (tttt) REVERT: F 338 LYS cc_start: 0.6924 (ttmt) cc_final: 0.6308 (mtpp) REVERT: F 552 PHE cc_start: 0.3460 (OUTLIER) cc_final: 0.2397 (m-80) REVERT: E 301 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6220 (pt) REVERT: E 351 SER cc_start: 0.6452 (m) cc_final: 0.6095 (t) REVERT: E 368 MET cc_start: 0.2286 (ttp) cc_final: 0.0465 (tpt) outliers start: 62 outliers final: 38 residues processed: 220 average time/residue: 0.1159 time to fit residues: 38.2092 Evaluate side-chains 204 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1289 GLN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.208524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.164180 restraints weight = 16725.362| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.46 r_work: 0.3737 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13742 Z= 0.127 Angle : 0.573 12.788 18509 Z= 0.298 Chirality : 0.042 0.188 1998 Planarity : 0.004 0.070 2351 Dihedral : 4.504 26.031 1769 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.05 % Allowed : 21.85 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1604 helix: 1.39 (0.18), residues: 816 sheet: -0.22 (0.55), residues: 93 loop : -1.23 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 381 TYR 0.013 0.001 TYR B 347 PHE 0.016 0.001 PHE B 251 TRP 0.019 0.001 TRP A1151 HIS 0.004 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00279 (13720) covalent geometry : angle 0.56180 (18494) hydrogen bonds : bond 0.04159 ( 635) hydrogen bonds : angle 4.37939 ( 1812) metal coordination : bond 0.01010 ( 22) metal coordination : angle 4.06935 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 791 GLU cc_start: 0.6018 (mp0) cc_final: 0.5585 (mt-10) REVERT: A 874 GLU cc_start: 0.4659 (OUTLIER) cc_final: 0.3949 (pt0) REVERT: A 1135 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7721 (mt) REVERT: A 1304 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7816 (tm-30) REVERT: B 62 GLU cc_start: 0.7720 (tp30) cc_final: 0.7479 (mt-10) REVERT: B 72 GLN cc_start: 0.8318 (tt0) cc_final: 0.7520 (mp10) REVERT: D 171 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4048 (tp) REVERT: D 438 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.5567 (mtp) REVERT: D 509 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7951 (tt) REVERT: D 559 LYS cc_start: 0.6028 (mttt) cc_final: 0.5743 (tttt) REVERT: F 332 ASN cc_start: 0.7066 (t0) cc_final: 0.5886 (p0) REVERT: F 338 LYS cc_start: 0.7092 (ttmt) cc_final: 0.6467 (mtpp) REVERT: E 301 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6077 (pt) REVERT: E 308 GLU cc_start: -0.3080 (OUTLIER) cc_final: -0.3570 (pt0) REVERT: E 351 SER cc_start: 0.6471 (m) cc_final: 0.6125 (t) REVERT: E 368 MET cc_start: 0.1164 (ttp) cc_final: -0.0192 (tpt) outliers start: 46 outliers final: 31 residues processed: 209 average time/residue: 0.1131 time to fit residues: 35.5745 Evaluate side-chains 200 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1289 GLN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** F 562 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 = 0.4456 r_free = 0.4456 target = 0.209044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164515 restraints weight = 16451.396| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.23 r_work: 0.3766 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.8053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13742 Z= 0.131 Angle : 0.579 12.806 18509 Z= 0.302 Chirality : 0.042 0.190 1998 Planarity : 0.004 0.072 2351 Dihedral : 4.430 25.922 1769 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.52 % Allowed : 21.45 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.22), residues: 1604 helix: 1.44 (0.18), residues: 817 sheet: -0.14 (0.56), residues: 93 loop : -1.16 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 381 TYR 0.012 0.001 TYR B 347 PHE 0.016 0.001 PHE B 251 TRP 0.019 0.001 TRP E 365 HIS 0.004 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00292 (13720) covalent geometry : angle 0.56697 (18494) hydrogen bonds : bond 0.04165 ( 635) hydrogen bonds : angle 4.34594 ( 1812) metal coordination : bond 0.01031 ( 22) metal coordination : angle 4.10151 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.5440 (OUTLIER) cc_final: 0.3970 (t80) REVERT: A 791 GLU cc_start: 0.6040 (mp0) cc_final: 0.5609 (mt-10) REVERT: A 874 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.4273 (pt0) REVERT: A 982 LYS cc_start: 0.6268 (mtmt) cc_final: 0.5900 (mtmt) REVERT: A 1135 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7733 (mt) REVERT: A 1304 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 1305 PHE cc_start: 0.7448 (t80) cc_final: 0.7211 (t80) REVERT: B 62 GLU cc_start: 0.7638 (tp30) cc_final: 0.7346 (mt-10) REVERT: B 88 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7330 (ttp-110) REVERT: D 171 LEU cc_start: 0.4030 (OUTLIER) cc_final: 0.3452 (tp) REVERT: D 316 MET cc_start: 0.3519 (tmm) cc_final: 0.3315 (tmm) REVERT: D 438 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.5621 (mtp) REVERT: D 509 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7969 (tt) REVERT: D 559 LYS cc_start: 0.6083 (mttt) cc_final: 0.5842 (tttt) REVERT: F 338 LYS cc_start: 0.6946 (ttmt) cc_final: 0.6226 (mtpp) REVERT: F 552 PHE cc_start: 0.3486 (OUTLIER) cc_final: 0.2931 (m-80) REVERT: E 301 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6112 (pt) REVERT: E 351 SER cc_start: 0.6415 (m) cc_final: 0.6048 (t) REVERT: E 365 TRP cc_start: 0.6315 (t60) cc_final: 0.5826 (t60) REVERT: E 368 MET cc_start: 0.1307 (ttp) cc_final: -0.0153 (tpt) outliers start: 53 outliers final: 35 residues processed: 215 average time/residue: 0.1142 time to fit residues: 36.7855 Evaluate side-chains 205 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.209833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166443 restraints weight = 16602.268| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.51 r_work: 0.3750 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13742 Z= 0.125 Angle : 0.585 12.056 18509 Z= 0.303 Chirality : 0.041 0.193 1998 Planarity : 0.004 0.075 2351 Dihedral : 4.353 24.956 1769 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.66 % Allowed : 22.64 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.22), residues: 1604 helix: 1.56 (0.19), residues: 811 sheet: -0.07 (0.56), residues: 94 loop : -1.08 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 381 TYR 0.015 0.001 TYR D 506 PHE 0.016 0.001 PHE E 289 TRP 0.018 0.001 TRP A1151 HIS 0.003 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00274 (13720) covalent geometry : angle 0.57408 (18494) hydrogen bonds : bond 0.03967 ( 635) hydrogen bonds : angle 4.32634 ( 1812) metal coordination : bond 0.00957 ( 22) metal coordination : angle 4.00888 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.5292 (OUTLIER) cc_final: 0.3801 (t80) REVERT: A 791 GLU cc_start: 0.6042 (mp0) cc_final: 0.5604 (mt-10) REVERT: A 874 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.4406 (pt0) REVERT: A 982 LYS cc_start: 0.6291 (mtmt) cc_final: 0.5939 (mtmt) REVERT: A 1135 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7786 (mt) REVERT: A 1304 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 1305 PHE cc_start: 0.7438 (t80) cc_final: 0.7177 (t80) REVERT: B 62 GLU cc_start: 0.7721 (tp30) cc_final: 0.7435 (mt-10) REVERT: D 171 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3444 (tp) REVERT: D 316 MET cc_start: 0.3505 (tmm) cc_final: 0.3297 (tmm) REVERT: D 438 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5488 (mtp) REVERT: D 509 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7960 (tt) REVERT: D 559 LYS cc_start: 0.6384 (mttt) cc_final: 0.5949 (tmtt) REVERT: F 322 ILE cc_start: 0.8495 (tp) cc_final: 0.8253 (pt) REVERT: F 332 ASN cc_start: 0.7451 (t0) cc_final: 0.6327 (p0) REVERT: F 338 LYS cc_start: 0.6888 (ttmt) cc_final: 0.6176 (mtpp) REVERT: F 552 PHE cc_start: 0.3390 (OUTLIER) cc_final: 0.2955 (m-80) REVERT: E 301 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6093 (pt) REVERT: E 351 SER cc_start: 0.6403 (m) cc_final: 0.5996 (t) REVERT: E 365 TRP cc_start: 0.6189 (t60) cc_final: 0.5695 (t60) REVERT: E 368 MET cc_start: 0.0302 (ttp) cc_final: -0.0647 (tpt) outliers start: 40 outliers final: 29 residues processed: 200 average time/residue: 0.1185 time to fit residues: 35.1367 Evaluate side-chains 199 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 331 ASN ** C 353 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 = 0.4451 r_free = 0.4451 target = 0.208296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.163796 restraints weight = 16386.803| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.23 r_work: 0.3756 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.8355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13742 Z= 0.140 Angle : 0.591 13.100 18509 Z= 0.308 Chirality : 0.042 0.203 1998 Planarity : 0.004 0.076 2351 Dihedral : 4.410 25.485 1769 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.92 % Allowed : 21.98 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1604 helix: 1.50 (0.18), residues: 819 sheet: -0.45 (0.53), residues: 104 loop : -1.04 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 381 TYR 0.012 0.001 TYR B 347 PHE 0.024 0.001 PHE F 326 TRP 0.021 0.001 TRP A1151 HIS 0.004 0.001 HIS A1293 Details of bonding type rmsd covalent geometry : bond 0.00315 (13720) covalent geometry : angle 0.57882 (18494) hydrogen bonds : bond 0.04223 ( 635) hydrogen bonds : angle 4.32438 ( 1812) metal coordination : bond 0.00977 ( 22) metal coordination : angle 4.23148 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 764 PHE cc_start: 0.5260 (OUTLIER) cc_final: 0.3751 (t80) REVERT: A 791 GLU cc_start: 0.6143 (mp0) cc_final: 0.5701 (mt-10) REVERT: A 874 GLU cc_start: 0.4896 (OUTLIER) cc_final: 0.4390 (pt0) REVERT: A 1135 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7823 (mt) REVERT: A 1194 MET cc_start: 0.5975 (ptm) cc_final: 0.5716 (ptp) REVERT: A 1304 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 1305 PHE cc_start: 0.7439 (t80) cc_final: 0.7156 (t80) REVERT: B 62 GLU cc_start: 0.7685 (tp30) cc_final: 0.7417 (mt-10) REVERT: B 88 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7368 (ttp-110) REVERT: B 313 TYR cc_start: 0.6993 (m-80) cc_final: 0.6772 (m-80) REVERT: D 316 MET cc_start: 0.3562 (tmm) cc_final: 0.3343 (tmm) REVERT: D 373 SER cc_start: 0.8661 (t) cc_final: 0.8424 (p) REVERT: D 438 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.5526 (mtp) REVERT: D 509 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7971 (tt) REVERT: D 559 LYS cc_start: 0.6160 (mttt) cc_final: 0.5796 (tttt) REVERT: D 560 MET cc_start: 0.5415 (mmm) cc_final: 0.4840 (mmm) REVERT: F 322 ILE cc_start: 0.8494 (tp) cc_final: 0.8289 (pt) REVERT: F 328 LYS cc_start: 0.7189 (pptt) cc_final: 0.6854 (tppt) REVERT: F 338 LYS cc_start: 0.6770 (ttmt) cc_final: 0.6099 (mtpp) REVERT: F 552 PHE cc_start: 0.3288 (OUTLIER) cc_final: 0.2856 (m-80) REVERT: E 301 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6203 (pt) REVERT: E 308 GLU cc_start: -0.3014 (OUTLIER) cc_final: -0.3708 (pt0) REVERT: E 351 SER cc_start: 0.6545 (m) cc_final: 0.6165 (t) REVERT: E 365 TRP cc_start: 0.6252 (t60) cc_final: 0.5701 (t60) REVERT: E 368 MET cc_start: 0.0168 (ttp) cc_final: -0.0607 (tpt) outliers start: 44 outliers final: 34 residues processed: 203 average time/residue: 0.0964 time to fit residues: 28.8513 Evaluate side-chains 208 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 885 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN F 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.209156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165424 restraints weight = 16584.769| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.27 r_work: 0.3768 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.8468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13742 Z= 0.129 Angle : 0.579 12.488 18509 Z= 0.301 Chirality : 0.041 0.198 1998 Planarity : 0.004 0.075 2351 Dihedral : 4.368 25.276 1769 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.86 % Allowed : 22.44 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1604 helix: 1.55 (0.19), residues: 813 sheet: 0.01 (0.56), residues: 94 loop : -1.02 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 381 TYR 0.011 0.001 TYR B 347 PHE 0.028 0.001 PHE F 326 TRP 0.020 0.001 TRP A1151 HIS 0.005 0.001 HIS A1293 Details of bonding type rmsd covalent geometry : bond 0.00287 (13720) covalent geometry : angle 0.56762 (18494) hydrogen bonds : bond 0.04028 ( 635) hydrogen bonds : angle 4.30229 ( 1812) metal coordination : bond 0.00954 ( 22) metal coordination : angle 3.99875 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3634.03 seconds wall clock time: 63 minutes 16.70 seconds (3796.70 seconds total)