Starting phenix.real_space_refine on Thu May 15 16:26:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi0_33845/05_2025/7yi0_33845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi0_33845/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi0_33845/05_2025/7yi0_33845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi0_33845/05_2025/7yi0_33845.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi0_33845/05_2025/7yi0_33845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi0_33845/05_2025/7yi0_33845.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.13, per 1000 atoms: 0.68 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.33 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: 3.57 Time building geometry restraints manager: 4.23 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- 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 : 8.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (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 TRP 0.009 0.001 TRP D 428 HIS 0.017 0.001 HIS A 785 PHE 0.017 0.001 PHE A 935 TYR 0.018 0.001 TYR F 556 ARG 0.008 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.15115 ( 635) hydrogen bonds : angle 6.04936 ( 1812) metal coordination : bond 0.00958 ( 22) metal coordination : angle 5.20811 ( 15) covalent geometry : bond 0.00280 (13720) covalent geometry : angle 0.56757 (18494) *********************** 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 : 1.527 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: 0.6422 (tpp) outliers start: 14 outliers final: 4 residues processed: 376 average time/residue: 0.2983 time to fit residues: 157.6116 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 : 1.551 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN A 909 GLN A 913 ASN A 947 GLN ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN C 393 GLN D 325 ASN ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN E 317 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.229391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.184534 restraints weight = 16991.268| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.61 r_work: 0.3972 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13742 Z= 0.141 Angle : 0.627 15.851 18509 Z= 0.323 Chirality : 0.042 0.204 1998 Planarity : 0.005 0.059 2351 Dihedral : 4.924 52.148 1779 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.86 % Allowed : 16.60 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1604 helix: 1.20 (0.18), residues: 819 sheet: 0.08 (0.53), residues: 90 loop : -1.60 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 782 HIS 0.014 0.001 HIS A 785 PHE 0.026 0.002 PHE E 289 TYR 0.018 0.002 TYR B 347 ARG 0.006 0.001 ARG A 826 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 635) hydrogen bonds : angle 4.46465 ( 1812) metal coordination : bond 0.01363 ( 22) metal coordination : angle 6.05325 ( 15) covalent geometry : bond 0.00306 (13720) covalent geometry : angle 0.60321 (18494) *********************** 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 262 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.4066 (t80) REVERT: A 812 GLU cc_start: 0.6955 (tp30) cc_final: 0.6685 (mm-30) REVERT: A 952 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.6973 (tp) REVERT: A 1008 GLU cc_start: 0.7884 (mp0) cc_final: 0.7512 (mp0) REVERT: B 73 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: B 114 ASP cc_start: 0.8269 (m-30) cc_final: 0.8046 (m-30) REVERT: F 316 MET cc_start: 0.2634 (mpm) cc_final: 0.1463 (ppp) REVERT: E 256 MET cc_start: 0.4256 (ttp) cc_final: 0.2877 (mtt) outliers start: 43 outliers final: 14 residues processed: 246 average time/residue: 0.2465 time to fit residues: 89.2555 Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 952 ILE 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 226 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 315 LYS 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 543 ASP 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 160 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 138 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 HIS B 38 HIS ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN D 329 GLN D 355 ASN D 545 ASN F 347 ASN E 330 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.222908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.178142 restraints weight = 17257.125| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.29 r_work: 0.3900 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4675 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= 0.131 Angle : 0.580 12.960 18509 Z= 0.299 Chirality : 0.042 0.185 1998 Planarity : 0.004 0.062 2351 Dihedral : 4.318 29.568 1771 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.12 % Allowed : 18.13 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1604 helix: 1.43 (0.18), residues: 814 sheet: -0.05 (0.53), residues: 89 loop : -1.46 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 261 HIS 0.009 0.001 HIS A 785 PHE 0.025 0.001 PHE E 289 TYR 0.017 0.002 TYR B 58 ARG 0.006 0.001 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 635) hydrogen bonds : angle 4.24631 ( 1812) metal coordination : bond 0.00891 ( 22) metal coordination : angle 4.47559 ( 15) covalent geometry : bond 0.00284 (13720) covalent geometry : angle 0.56596 (18494) *********************** 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 230 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 764 PHE cc_start: 0.5059 (OUTLIER) cc_final: 0.3989 (t80) REVERT: A 812 GLU cc_start: 0.7137 (tp30) cc_final: 0.6880 (mm-30) REVERT: A 1008 GLU cc_start: 0.7832 (mp0) cc_final: 0.6851 (mp0) REVERT: A 1300 MET cc_start: 0.7406 (ttp) cc_final: 0.7135 (ttp) REVERT: B 19 ARG cc_start: 0.8003 (mtp180) cc_final: 0.7746 (mtp180) REVERT: B 117 TYR cc_start: 0.7757 (t80) cc_final: 0.7504 (t80) REVERT: B 222 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6882 (mtm110) REVERT: D 438 MET cc_start: 0.6549 (mtp) cc_final: 0.6221 (mtp) REVERT: D 470 SER cc_start: 0.6920 (OUTLIER) cc_final: 0.6633 (p) REVERT: D 553 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6715 (m-30) REVERT: E 256 MET cc_start: 0.3701 (ttp) cc_final: 0.2206 (mtt) REVERT: E 360 GLU cc_start: 0.7439 (tt0) cc_final: 0.7194 (tm-30) REVERT: E 368 MET cc_start: 0.3085 (ttp) cc_final: 0.1858 (tpt) outliers start: 32 outliers final: 13 residues processed: 222 average time/residue: 0.2438 time to fit residues: 80.8149 Evaluate side-chains 176 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP 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 553 ASP Chi-restraints excluded: chain F residue 316 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 140 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 0.0030 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN D 268 GLN D 325 ASN D 495 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.219880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.174685 restraints weight = 16777.040| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.31 r_work: 0.3871 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13742 Z= 0.124 Angle : 0.550 11.676 18509 Z= 0.288 Chirality : 0.041 0.189 1998 Planarity : 0.004 0.064 2351 Dihedral : 4.225 21.725 1769 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.72 % Allowed : 19.06 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1604 helix: 1.36 (0.18), residues: 824 sheet: -0.12 (0.53), residues: 90 loop : -1.41 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.030 0.001 HIS A1221 PHE 0.017 0.001 PHE E 289 TYR 0.014 0.001 TYR B 347 ARG 0.006 0.000 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 635) hydrogen bonds : angle 4.19677 ( 1812) metal coordination : bond 0.00944 ( 22) metal coordination : angle 4.13912 ( 15) covalent geometry : bond 0.00269 (13720) covalent geometry : angle 0.53701 (18494) *********************** 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 221 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.5077 (OUTLIER) cc_final: 0.3976 (t80) REVERT: A 911 GLU cc_start: 0.7425 (tt0) cc_final: 0.7193 (tt0) REVERT: A 1300 MET cc_start: 0.7475 (ttp) cc_final: 0.7149 (ttp) REVERT: B 19 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7673 (mtp180) REVERT: B 99 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.7254 (ttm-80) REVERT: B 222 ARG cc_start: 0.6978 (mtm110) cc_final: 0.6706 (mtm110) REVERT: B 288 MET cc_start: 0.8108 (ttp) cc_final: 0.7743 (ttm) REVERT: D 171 LEU cc_start: 0.3364 (OUTLIER) cc_final: 0.2834 (tp) REVERT: D 470 SER cc_start: 0.6677 (OUTLIER) cc_final: 0.6392 (p) REVERT: D 553 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: F 560 MET cc_start: 0.5254 (ppp) cc_final: 0.3303 (ttm) REVERT: E 256 MET cc_start: 0.3837 (ttp) cc_final: 0.2627 (mtt) REVERT: E 368 MET cc_start: 0.3316 (ttp) cc_final: 0.2240 (tpt) outliers start: 41 outliers final: 20 residues processed: 212 average time/residue: 0.2507 time to fit residues: 78.0773 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 1164 MET 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 275 SER 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 D residue 171 LEU Chi-restraints excluded: chain D residue 335 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 553 ASP Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 159 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 ASN A1150 HIS ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN D 325 ASN F 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.209571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164811 restraints weight = 16672.333| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.51 r_work: 0.3730 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13742 Z= 0.194 Angle : 0.652 16.622 18509 Z= 0.340 Chirality : 0.045 0.229 1998 Planarity : 0.005 0.065 2351 Dihedral : 4.787 23.488 1769 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.19 % Allowed : 20.05 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1604 helix: 1.15 (0.18), residues: 823 sheet: -1.01 (0.51), residues: 102 loop : -1.37 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 912 HIS 0.010 0.001 HIS A 785 PHE 0.025 0.002 PHE A 717 TYR 0.017 0.002 TYR B 347 ARG 0.007 0.001 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 635) hydrogen bonds : angle 4.52369 ( 1812) metal coordination : bond 0.01179 ( 22) metal coordination : angle 5.30131 ( 15) covalent geometry : bond 0.00447 (13720) covalent geometry : angle 0.63448 (18494) *********************** 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 235 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 PHE cc_start: 0.5320 (m-80) cc_final: 0.4949 (m-80) REVERT: A 873 LYS cc_start: 0.4737 (ttmt) cc_final: 0.4487 (mmtt) REVERT: A 986 TYR cc_start: 0.7177 (m-80) cc_final: 0.6770 (m-80) REVERT: A 1021 PHE cc_start: 0.8386 (t80) cc_final: 0.8132 (t80) REVERT: A 1300 MET cc_start: 0.7169 (ttp) cc_final: 0.6966 (ttm) REVERT: B 72 GLN cc_start: 0.8292 (tt0) cc_final: 0.7771 (mp10) REVERT: B 99 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7457 (ttm-80) REVERT: B 340 TYR cc_start: 0.7181 (t80) cc_final: 0.6974 (t80) REVERT: D 171 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3441 (tp) REVERT: D 470 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6737 (p) REVERT: D 505 TYR cc_start: 0.8703 (m-80) cc_final: 0.8390 (m-80) REVERT: D 509 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7731 (tt) REVERT: D 538 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7915 (mtmt) REVERT: D 553 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: F 552 PHE cc_start: 0.3325 (OUTLIER) cc_final: 0.2317 (m-80) REVERT: E 256 MET cc_start: 0.3367 (ttp) cc_final: 0.2079 (mtt) REVERT: E 301 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6241 (pt) REVERT: E 351 SER cc_start: 0.6318 (m) cc_final: 0.5922 (t) REVERT: E 367 LEU cc_start: 0.5497 (tp) cc_final: 0.5175 (mm) REVERT: E 368 MET cc_start: 0.2729 (ttp) cc_final: 0.1072 (tpt) outliers start: 48 outliers final: 24 residues processed: 226 average time/residue: 0.2635 time to fit residues: 85.7195 Evaluate side-chains 186 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR 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 335 ASP 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 335 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 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 D residue 553 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 327 ILE 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 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 32 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN A1221 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN D 174 ASN D 325 ASN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.212216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166970 restraints weight = 16906.480| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.39 r_work: 0.3777 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13742 Z= 0.130 Angle : 0.563 13.032 18509 Z= 0.295 Chirality : 0.042 0.189 1998 Planarity : 0.004 0.066 2351 Dihedral : 4.460 22.196 1769 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.86 % Allowed : 20.85 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1604 helix: 1.39 (0.18), residues: 816 sheet: -0.45 (0.54), residues: 93 loop : -1.23 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 261 HIS 0.010 0.001 HIS A 785 PHE 0.038 0.001 PHE F 326 TYR 0.012 0.001 TYR D 506 ARG 0.006 0.000 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 635) hydrogen bonds : angle 4.35195 ( 1812) metal coordination : bond 0.01067 ( 22) metal coordination : angle 4.10514 ( 15) covalent geometry : bond 0.00284 (13720) covalent geometry : angle 0.55135 (18494) *********************** 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 213 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 751 PHE cc_start: 0.5188 (m-80) cc_final: 0.4886 (m-80) REVERT: A 873 LYS cc_start: 0.4377 (ttmt) cc_final: 0.4159 (mptt) REVERT: A 986 TYR cc_start: 0.7065 (m-80) cc_final: 0.6789 (m-80) REVERT: A 1008 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 1135 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7585 (mp) REVERT: A 1300 MET cc_start: 0.7106 (ttp) cc_final: 0.6901 (ttm) REVERT: A 1304 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 62 GLU cc_start: 0.7843 (tp30) cc_final: 0.7461 (mt-10) REVERT: B 72 GLN cc_start: 0.8250 (tt0) cc_final: 0.7682 (mp10) REVERT: B 99 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.7386 (ttm-80) REVERT: D 171 LEU cc_start: 0.4327 (OUTLIER) cc_final: 0.3679 (tp) REVERT: D 470 SER cc_start: 0.6679 (OUTLIER) cc_final: 0.6469 (p) REVERT: D 505 TYR cc_start: 0.8601 (m-80) cc_final: 0.8252 (m-80) REVERT: D 538 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7890 (mtmt) REVERT: D 553 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: E 256 MET cc_start: 0.3290 (ttp) cc_final: 0.2029 (mtt) REVERT: E 367 LEU cc_start: 0.5396 (tp) cc_final: 0.5154 (mm) REVERT: E 368 MET cc_start: 0.2464 (ttp) cc_final: 0.0909 (tpt) outliers start: 43 outliers final: 31 residues processed: 206 average time/residue: 0.2608 time to fit residues: 78.2489 Evaluate side-chains 196 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 704 GLU 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 1008 GLU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1164 MET 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 1289 GLN Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 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 277 THR Chi-restraints excluded: chain D residue 335 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 437 ILE Chi-restraints excluded: chain D residue 452 VAL 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 F residue 324 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG 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 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** B 231 ASN ** 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.211919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166901 restraints weight = 16851.387| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.40 r_work: 0.3779 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.7311 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= 0.125 Angle : 0.549 12.594 18509 Z= 0.286 Chirality : 0.041 0.195 1998 Planarity : 0.004 0.071 2351 Dihedral : 4.301 21.768 1769 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.05 % Allowed : 20.98 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1604 helix: 1.48 (0.18), residues: 817 sheet: 0.18 (0.56), residues: 92 loop : -1.16 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 261 HIS 0.009 0.001 HIS A 785 PHE 0.024 0.001 PHE F 326 TYR 0.012 0.001 TYR B 347 ARG 0.005 0.000 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 635) hydrogen bonds : angle 4.24109 ( 1812) metal coordination : bond 0.01005 ( 22) metal coordination : angle 3.93712 ( 15) covalent geometry : bond 0.00276 (13720) covalent geometry : angle 0.53776 (18494) *********************** 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 215 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 PHE cc_start: 0.5384 (m-80) cc_final: 0.5069 (m-80) REVERT: A 765 MET cc_start: 0.6655 (tpt) cc_final: 0.6449 (tpt) REVERT: A 860 MET cc_start: 0.5176 (mmt) cc_final: 0.4950 (tpt) REVERT: A 912 TRP cc_start: 0.8490 (m100) cc_final: 0.8280 (m100) REVERT: A 986 TYR cc_start: 0.7133 (m-80) cc_final: 0.6863 (m-80) REVERT: A 1135 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 1304 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 1305 PHE cc_start: 0.7142 (t80) cc_final: 0.6896 (t80) REVERT: B 62 GLU cc_start: 0.7859 (tp30) cc_final: 0.7514 (mt-10) REVERT: B 72 GLN cc_start: 0.8280 (tt0) cc_final: 0.7640 (mp10) REVERT: B 99 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7299 (ttm-80) REVERT: B 313 TYR cc_start: 0.6938 (m-80) cc_final: 0.6609 (m-80) REVERT: D 171 LEU cc_start: 0.4416 (OUTLIER) cc_final: 0.3981 (tp) REVERT: D 316 MET cc_start: 0.3374 (tmm) cc_final: 0.3099 (tmm) REVERT: D 505 TYR cc_start: 0.8621 (m-80) cc_final: 0.8125 (m-80) REVERT: D 538 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7861 (mtmt) REVERT: D 553 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: D 559 LYS cc_start: 0.5442 (mttt) cc_final: 0.5117 (tttt) REVERT: D 560 MET cc_start: 0.3656 (tpp) cc_final: 0.3165 (tpp) REVERT: F 552 PHE cc_start: 0.3116 (OUTLIER) cc_final: 0.2572 (m-80) REVERT: E 256 MET cc_start: 0.3561 (ttp) cc_final: 0.2338 (mtt) REVERT: E 296 MET cc_start: 0.5707 (tmm) cc_final: 0.5502 (tmm) REVERT: E 301 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6082 (pt) REVERT: E 368 MET cc_start: 0.2543 (ttp) cc_final: 0.0631 (tpt) outliers start: 46 outliers final: 30 residues processed: 208 average time/residue: 0.2546 time to fit residues: 76.9356 Evaluate side-chains 194 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1164 MET 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 1289 GLN 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 314 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 MET 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 277 THR Chi-restraints excluded: chain D residue 335 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 437 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 327 ILE 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 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG 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 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 534 ASN 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 = 0.208361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163102 restraints weight = 16869.760| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.49 r_work: 0.3731 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.7618 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= 0.150 Angle : 0.596 13.840 18509 Z= 0.309 Chirality : 0.042 0.192 1998 Planarity : 0.004 0.071 2351 Dihedral : 4.479 22.394 1769 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.25 % Allowed : 20.98 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1604 helix: 1.41 (0.18), residues: 824 sheet: -0.36 (0.54), residues: 104 loop : -1.06 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1151 HIS 0.009 0.001 HIS A 785 PHE 0.020 0.001 PHE F 326 TYR 0.013 0.001 TYR B 347 ARG 0.009 0.001 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 635) hydrogen bonds : angle 4.35026 ( 1812) metal coordination : bond 0.01120 ( 22) metal coordination : angle 4.32978 ( 15) covalent geometry : bond 0.00338 (13720) covalent geometry : angle 0.58304 (18494) *********************** 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 209 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 PHE cc_start: 0.5533 (m-80) cc_final: 0.5178 (m-80) REVERT: A 791 GLU cc_start: 0.6106 (mp0) cc_final: 0.5653 (mt-10) REVERT: A 860 MET cc_start: 0.5122 (mmt) cc_final: 0.4861 (tpt) REVERT: A 874 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.4268 (pt0) REVERT: A 983 ASN cc_start: 0.8071 (m110) cc_final: 0.7742 (m110) REVERT: A 986 TYR cc_start: 0.7169 (m-80) cc_final: 0.6823 (m-80) REVERT: A 1135 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 1304 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 62 GLU cc_start: 0.7878 (tp30) cc_final: 0.7600 (mt-10) REVERT: B 72 GLN cc_start: 0.8336 (tt0) cc_final: 0.7708 (mp10) REVERT: B 99 ARG cc_start: 0.7683 (mtp-110) cc_final: 0.7332 (ttm-80) REVERT: D 171 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.3796 (tp) REVERT: D 316 MET cc_start: 0.3517 (tmm) cc_final: 0.3153 (tmm) REVERT: D 553 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: D 559 LYS cc_start: 0.5823 (mttt) cc_final: 0.5478 (tttt) REVERT: F 332 ASN cc_start: 0.7187 (t0) cc_final: 0.6009 (p0) REVERT: F 552 PHE cc_start: 0.3250 (OUTLIER) cc_final: 0.2422 (m-80) REVERT: E 301 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6072 (pt) REVERT: E 351 SER cc_start: 0.6279 (m) cc_final: 0.6008 (t) REVERT: E 368 MET cc_start: 0.1882 (ttp) cc_final: 0.0577 (tpt) outliers start: 49 outliers final: 33 residues processed: 200 average time/residue: 0.2508 time to fit residues: 74.8281 Evaluate side-chains 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 874 GLU 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 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 GLU 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 370 ASP Chi-restraints excluded: chain B residue 373 MET 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 185 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 335 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 437 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 327 ILE 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 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG 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 117 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.0060 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN D 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.212599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.167618 restraints weight = 16721.926| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.32 r_work: 0.3800 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.7743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13742 Z= 0.108 Angle : 0.537 10.802 18509 Z= 0.281 Chirality : 0.041 0.198 1998 Planarity : 0.004 0.072 2351 Dihedral : 4.195 21.104 1769 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.52 % Allowed : 21.51 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1604 helix: 1.58 (0.18), residues: 823 sheet: 0.57 (0.58), residues: 92 loop : -1.03 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1151 HIS 0.009 0.001 HIS A 785 PHE 0.017 0.001 PHE F 326 TYR 0.011 0.001 TYR D 356 ARG 0.009 0.000 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 635) hydrogen bonds : angle 4.18231 ( 1812) metal coordination : bond 0.00939 ( 22) metal coordination : angle 3.41213 ( 15) covalent geometry : bond 0.00233 (13720) covalent geometry : angle 0.52813 (18494) *********************** 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 209 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 PHE cc_start: 0.5383 (m-80) cc_final: 0.5076 (m-80) REVERT: A 791 GLU cc_start: 0.5983 (mp0) cc_final: 0.5513 (mt-10) REVERT: A 860 MET cc_start: 0.5039 (mmt) cc_final: 0.4755 (tpt) REVERT: A 874 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4316 (pt0) REVERT: A 982 LYS cc_start: 0.6246 (mtmt) cc_final: 0.5309 (mtmt) REVERT: A 986 TYR cc_start: 0.7100 (m-80) cc_final: 0.6874 (m-80) REVERT: A 1135 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 1175 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6791 (mtt-85) REVERT: A 1300 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6888 (ttm) REVERT: A 1304 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 62 GLU cc_start: 0.7813 (tp30) cc_final: 0.7488 (mt-10) REVERT: B 72 GLN cc_start: 0.8291 (tt0) cc_final: 0.7505 (mp10) REVERT: B 99 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7321 (ttm-80) REVERT: D 171 LEU cc_start: 0.4072 (OUTLIER) cc_final: 0.3505 (tp) REVERT: D 316 MET cc_start: 0.3384 (tmm) cc_final: 0.3058 (tmm) REVERT: D 515 GLN cc_start: 0.8315 (tp40) cc_final: 0.8089 (tp40) REVERT: D 559 LYS cc_start: 0.5723 (mttt) cc_final: 0.5497 (tttt) REVERT: D 560 MET cc_start: 0.4082 (mmm) cc_final: 0.3716 (mmm) REVERT: F 332 ASN cc_start: 0.7201 (t0) cc_final: 0.6011 (p0) REVERT: E 256 MET cc_start: 0.3038 (ttp) cc_final: 0.2065 (mtt) REVERT: E 301 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6134 (pt) REVERT: E 351 SER cc_start: 0.6291 (m) cc_final: 0.5939 (t) REVERT: E 368 MET cc_start: 0.1766 (ttp) cc_final: 0.0309 (tpt) outliers start: 38 outliers final: 24 residues processed: 203 average time/residue: 0.2475 time to fit residues: 74.0940 Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 874 GLU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 213 GLU 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 B residue 373 MET 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 277 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG 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 104 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.210888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167868 restraints weight = 16518.122| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.47 r_work: 0.3779 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13742 Z= 0.114 Angle : 0.551 10.898 18509 Z= 0.288 Chirality : 0.041 0.206 1998 Planarity : 0.004 0.072 2351 Dihedral : 4.160 22.038 1769 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.32 % Allowed : 22.05 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1604 helix: 1.61 (0.18), residues: 824 sheet: 0.25 (0.56), residues: 102 loop : -0.98 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 261 HIS 0.008 0.001 HIS A 785 PHE 0.039 0.001 PHE F 326 TYR 0.011 0.001 TYR B 23 ARG 0.008 0.000 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 635) hydrogen bonds : angle 4.20088 ( 1812) metal coordination : bond 0.00909 ( 22) metal coordination : angle 3.52010 ( 15) covalent geometry : bond 0.00247 (13720) covalent geometry : angle 0.54174 (18494) ********************** 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 207 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 PHE cc_start: 0.5444 (m-80) cc_final: 0.5170 (m-80) REVERT: A 791 GLU cc_start: 0.6054 (mp0) cc_final: 0.5568 (mt-10) REVERT: A 860 MET cc_start: 0.5160 (mmt) cc_final: 0.4849 (tpt) REVERT: A 874 GLU cc_start: 0.4879 (OUTLIER) cc_final: 0.4339 (pt0) REVERT: A 982 LYS cc_start: 0.6332 (mtmt) cc_final: 0.5466 (mtmt) REVERT: A 983 ASN cc_start: 0.7950 (m110) cc_final: 0.7624 (m110) REVERT: A 986 TYR cc_start: 0.7049 (m-80) cc_final: 0.6836 (m-80) REVERT: A 1135 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 1175 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6798 (mtt-85) REVERT: A 1300 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6938 (ttm) REVERT: A 1304 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 62 GLU cc_start: 0.7819 (tp30) cc_final: 0.7546 (mt-10) REVERT: B 72 GLN cc_start: 0.8372 (tt0) cc_final: 0.7622 (mp10) REVERT: B 99 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7316 (ttm-80) REVERT: D 171 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3284 (tp) REVERT: D 316 MET cc_start: 0.3593 (tmm) cc_final: 0.3236 (tmm) REVERT: D 515 GLN cc_start: 0.8276 (tp40) cc_final: 0.8055 (tp40) REVERT: D 559 LYS cc_start: 0.5925 (mttt) cc_final: 0.5707 (tttt) REVERT: D 560 MET cc_start: 0.4064 (mmm) cc_final: 0.3713 (mmm) REVERT: F 560 MET cc_start: 0.5377 (ppp) cc_final: 0.4889 (ppp) REVERT: E 256 MET cc_start: 0.3112 (ttp) cc_final: 0.2094 (mtt) REVERT: E 301 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6092 (pt) REVERT: E 351 SER cc_start: 0.6342 (m) cc_final: 0.5991 (t) REVERT: E 368 MET cc_start: 0.1736 (ttp) cc_final: 0.0402 (tpt) outliers start: 35 outliers final: 27 residues processed: 200 average time/residue: 0.2581 time to fit residues: 75.5861 Evaluate side-chains 195 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 874 GLU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 213 GLU 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 B residue 373 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG 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 53 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.0030 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 0.2980 chunk 150 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN D 329 GLN F 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.213913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169787 restraints weight = 16661.558| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.47 r_work: 0.3802 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.7922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13742 Z= 0.109 Angle : 0.540 10.046 18509 Z= 0.284 Chirality : 0.041 0.206 1998 Planarity : 0.004 0.071 2351 Dihedral : 4.108 21.644 1769 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.39 % Allowed : 22.11 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1604 helix: 1.62 (0.18), residues: 827 sheet: 0.78 (0.60), residues: 92 loop : -0.99 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.008 0.001 HIS A 785 PHE 0.033 0.001 PHE F 326 TYR 0.016 0.001 TYR D 506 ARG 0.007 0.000 ARG C 381 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 635) hydrogen bonds : angle 4.15786 ( 1812) metal coordination : bond 0.00865 ( 22) metal coordination : angle 3.24723 ( 15) covalent geometry : bond 0.00231 (13720) covalent geometry : angle 0.53198 (18494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7125.77 seconds wall clock time: 124 minutes 1.18 seconds (7441.18 seconds total)