Starting phenix.real_space_refine on Sat Aug 23 17:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2a_50143/08_2025/9f2a_50143.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2a_50143/08_2025/9f2a_50143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f2a_50143/08_2025/9f2a_50143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2a_50143/08_2025/9f2a_50143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f2a_50143/08_2025/9f2a_50143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2a_50143/08_2025/9f2a_50143.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 3 6.06 5 S 49 5.16 5 C 8708 2.51 5 N 2294 2.21 5 O 2502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13557 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3573 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 416} Chain breaks: 1 Chain: "B" Number of atoms: 9458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9458 Classifications: {'peptide': 1182} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1114} Chain breaks: 2 Chain: "C" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9009 SG CYS B 706 58.712 10.852 92.109 1.00 71.40 S ATOM 9031 SG CYS B 709 61.580 10.085 94.373 1.00 87.05 S ATOM 9096 SG CYS B 718 62.186 12.518 91.619 1.00 73.36 S ATOM 9117 SG CYS B 721 61.852 8.854 90.833 1.00 82.70 S ATOM 9200 SG CYS B 731 43.647 20.403 108.969 1.00 89.25 S ATOM 9224 SG CYS B 734 45.398 17.611 110.607 1.00 76.71 S ATOM 9352 SG CYS B 750 42.187 16.938 108.580 1.00 82.80 S ATOM 9374 SG CYS B 753 42.043 18.710 112.005 1.00 97.97 S ATOM 12365 SG CYS B1123 68.392 52.234 115.752 1.00 83.46 S ATOM 12387 SG CYS B1126 65.582 49.966 115.357 1.00 79.71 S ATOM 12493 SG CYS B1139 66.651 51.200 118.946 1.00 70.37 S ATOM 12513 SG CYS B1142 68.221 48.344 116.783 1.00 74.41 S Time building chain proxies: 2.76, per 1000 atoms: 0.20 Number of scatterers: 13557 At special positions: 0 Unit cell: (86.4, 122.88, 163.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Fe 1 26.01 S 49 16.00 O 2502 8.00 N 2294 7.00 C 8708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 575.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 734 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1126 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1139 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1142 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1123 " Number of angles added : 18 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3150 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 43.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.554A pdb=" N VAL A 206 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.751A pdb=" N PHE A 373 " --> pdb=" O CYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.556A pdb=" N SER A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.677A pdb=" N TYR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.676A pdb=" N VAL A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.624A pdb=" N GLU B 8 " --> pdb=" O PRO B 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 59 through 72 removed outlier: 4.531A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.044A pdb=" N LEU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 151 through 169 removed outlier: 3.696A pdb=" N GLN B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.566A pdb=" N ILE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.610A pdb=" N LYS B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 368 through 375 removed outlier: 3.768A pdb=" N MET B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.811A pdb=" N PHE B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.523A pdb=" N THR B 537 " --> pdb=" O PRO B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.828A pdb=" N VAL B 543 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.578A pdb=" N VAL B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 585 through 592 removed outlier: 3.512A pdb=" N LEU B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 615 removed outlier: 3.922A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.666A pdb=" N LEU B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.749A pdb=" N ASN B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 removed outlier: 3.640A pdb=" N ALA B 680 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 681 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 677 through 682' Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 739 through 746 Processing helix chain 'B' and resid 766 through 779 removed outlier: 3.635A pdb=" N LEU B 770 " --> pdb=" O ARG B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.789A pdb=" N GLY B 805 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.819A pdb=" N ILE B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 Processing helix chain 'B' and resid 877 through 897 removed outlier: 3.632A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 913 removed outlier: 3.789A pdb=" N ILE B 913 " --> pdb=" O GLU B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 950 Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 973 through 977 Processing helix chain 'B' and resid 996 through 1000 removed outlier: 3.907A pdb=" N VAL B1000 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1007 Processing helix chain 'B' and resid 1014 through 1022 removed outlier: 3.737A pdb=" N TYR B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.783A pdb=" N VAL B1031 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1041 Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.576A pdb=" N MET B1046 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR B1047 " --> pdb=" O PRO B1044 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1043 through 1047' Processing helix chain 'B' and resid 1066 through 1070 removed outlier: 3.560A pdb=" N LYS B1069 " --> pdb=" O SER B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 Processing helix chain 'B' and resid 1092 through 1104 removed outlier: 3.542A pdb=" N LEU B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1117 removed outlier: 4.374A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1157 removed outlier: 3.721A pdb=" N ILE B1155 " --> pdb=" O SER B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1169 Processing helix chain 'B' and resid 1172 through 1190 removed outlier: 3.919A pdb=" N PHE B1190 " --> pdb=" O ILE B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1216 removed outlier: 3.853A pdb=" N ARG B1216 " --> pdb=" O LEU B1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 222 removed outlier: 3.795A pdb=" N LYS C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 255 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 removed outlier: 6.579A pdb=" N VAL A 485 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 556 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 565 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 278 removed outlier: 5.553A pdb=" N VAL A 273 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 288 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 275 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N PHE A 329 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS A 295 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA A 331 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 297 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS A 333 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N TYR A 335 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS A 320 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 334 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA A 318 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.440A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A 354 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 398 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 402 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 357 " --> pdb=" O PRO A 600 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 599 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL A 612 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 601 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 608 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.890A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 875 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE B 935 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY B 941 " --> pdb=" O ASP B 824 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 826 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA B 943 " --> pdb=" O THR B 826 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA B 828 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.890A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 129 removed outlier: 3.937A pdb=" N ASN B 124 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N GLU B 217 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 139 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR B 219 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 141 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 437 through 441 Processing sheet with id=AA8, first strand: chain 'B' and resid 393 through 395 removed outlier: 3.536A pdb=" N GLN B 384 " --> pdb=" O GLY B 657 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 414 through 416 removed outlier: 6.772A pdb=" N ILE B 406 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 433 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS B 408 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 559 through 566 removed outlier: 6.743A pdb=" N GLU B 560 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 575 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU B 562 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 697 through 701 removed outlier: 3.522A pdb=" N ALA B 697 " --> pdb=" O ILE B 765 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 761 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AB5, first strand: chain 'B' and resid 832 through 833 Processing sheet with id=AB6, first strand: chain 'B' and resid 1129 through 1130 Processing sheet with id=AB7, first strand: chain 'C' and resid 226 through 227 545 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4432 1.34 - 1.46: 2911 1.46 - 1.58: 6423 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 13846 Sorted by residual: bond pdb=" N HIS A 362 " pdb=" CA HIS A 362 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.41e-02 5.03e+03 4.74e+00 bond pdb=" N GLU B 519 " pdb=" CA GLU B 519 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.28e-02 6.10e+03 4.21e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.332 0.022 1.10e-02 8.26e+03 4.00e+00 bond pdb=" CG HIS A 562 " pdb=" CD2 HIS A 562 " ideal model delta sigma weight residual 1.354 1.332 0.022 1.10e-02 8.26e+03 3.87e+00 bond pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.41e-02 5.03e+03 2.94e+00 ... (remaining 13841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 18208 1.45 - 2.89: 425 2.89 - 4.34: 74 4.34 - 5.78: 12 5.78 - 7.23: 2 Bond angle restraints: 18721 Sorted by residual: angle pdb=" C HIS A 562 " pdb=" CA HIS A 562 " pdb=" CB HIS A 562 " ideal model delta sigma weight residual 111.39 117.90 -6.51 1.55e+00 4.16e-01 1.76e+01 angle pdb=" CA HIS A 562 " pdb=" CB HIS A 562 " pdb=" CG HIS A 562 " ideal model delta sigma weight residual 113.80 117.96 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CA ASP A 404 " pdb=" C ASP A 404 " pdb=" O ASP A 404 " ideal model delta sigma weight residual 121.84 117.39 4.45 1.16e+00 7.43e-01 1.47e+01 angle pdb=" CA ASP A 360 " pdb=" C ASP A 360 " pdb=" O ASP A 360 " ideal model delta sigma weight residual 122.45 117.86 4.59 1.30e+00 5.92e-01 1.24e+01 angle pdb=" C ALA B 194 " pdb=" N VAL B 195 " pdb=" CA VAL B 195 " ideal model delta sigma weight residual 122.63 118.64 3.99 1.19e+00 7.06e-01 1.13e+01 ... (remaining 18716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 7733 17.49 - 34.97: 610 34.97 - 52.46: 67 52.46 - 69.94: 44 69.94 - 87.43: 6 Dihedral angle restraints: 8460 sinusoidal: 3549 harmonic: 4911 Sorted by residual: dihedral pdb=" CA LYS B 668 " pdb=" C LYS B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ALA B 194 " pdb=" C ALA B 194 " pdb=" N VAL B 195 " pdb=" CA VAL B 195 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU B 388 " pdb=" C GLU B 388 " pdb=" N ARG B 389 " pdb=" CA ARG B 389 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1475 0.043 - 0.086: 408 0.086 - 0.129: 160 0.129 - 0.172: 8 0.172 - 0.215: 3 Chirality restraints: 2054 Sorted by residual: chirality pdb=" CA ASP A 404 " pdb=" N ASP A 404 " pdb=" C ASP A 404 " pdb=" CB ASP A 404 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASP A 360 " pdb=" N ASP A 360 " pdb=" C ASP A 360 " pdb=" CB ASP A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA HIS A 562 " pdb=" N HIS A 562 " pdb=" C HIS A 562 " pdb=" CB HIS A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 2051 not shown) Planarity restraints: 2417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " 0.045 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO B 146 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 668 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO B 669 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 669 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 669 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 669 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 670 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " -0.029 5.00e-02 4.00e+02 ... (remaining 2414 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1852 2.75 - 3.29: 12008 3.29 - 3.83: 20725 3.83 - 4.36: 25009 4.36 - 4.90: 44967 Nonbonded interactions: 104561 Sorted by model distance: nonbonded pdb=" OD2 ASP A 404 " pdb="FE FE A 701 " model vdw 2.218 2.260 nonbonded pdb=" OD2 ASP A 360 " pdb="FE FE A 701 " model vdw 2.272 2.260 nonbonded pdb=" NE2 HIS A 362 " pdb="FE FE A 701 " model vdw 2.273 2.340 nonbonded pdb=" OD1 ASN A 185 " pdb=" ND1 HIS A 383 " model vdw 2.292 3.120 nonbonded pdb=" OD1 ASP A 542 " pdb=" ND2 ASN B1192 " model vdw 2.313 3.120 ... (remaining 104556 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.190 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.004 0.034 13858 Z= 0.160 Angle : 0.575 15.025 18739 Z= 0.314 Chirality : 0.045 0.215 2054 Planarity : 0.005 0.069 2417 Dihedral : 12.979 87.430 5310 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.20), residues: 1680 helix: 1.27 (0.21), residues: 626 sheet: -0.00 (0.38), residues: 211 loop : -0.62 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.027 0.001 TYR B1022 PHE 0.021 0.002 PHE B 703 TRP 0.010 0.001 TRP B 552 HIS 0.005 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00356 (13846) covalent geometry : angle 0.54895 (18721) hydrogen bonds : bond 0.19109 ( 542) hydrogen bonds : angle 6.29164 ( 1506) metal coordination : bond 0.00493 ( 12) metal coordination : angle 5.51109 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8240 (mt) cc_final: 0.7816 (mp) REVERT: A 178 GLU cc_start: 0.7223 (tp30) cc_final: 0.7007 (tp30) REVERT: A 241 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7158 (ttp80) REVERT: A 248 GLU cc_start: 0.7523 (mp0) cc_final: 0.7284 (mp0) REVERT: A 286 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6550 (mt-10) REVERT: A 289 ASP cc_start: 0.7495 (t0) cc_final: 0.7283 (t0) REVERT: A 297 PHE cc_start: 0.7805 (t80) cc_final: 0.7574 (t80) REVERT: A 395 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7649 (mtt-85) REVERT: A 499 ARG cc_start: 0.8385 (ttm170) cc_final: 0.7928 (ttp80) REVERT: A 502 GLU cc_start: 0.7614 (tp30) cc_final: 0.7081 (tp30) REVERT: A 515 LYS cc_start: 0.7954 (mppt) cc_final: 0.7686 (mppt) REVERT: A 522 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7563 (tp30) REVERT: B 38 ASP cc_start: 0.7916 (p0) cc_final: 0.7637 (p0) REVERT: B 62 LYS cc_start: 0.7068 (mtpt) cc_final: 0.6852 (mtpt) REVERT: B 79 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7923 (mmtm) REVERT: B 134 ASP cc_start: 0.7733 (t70) cc_final: 0.7064 (t0) REVERT: B 155 GLN cc_start: 0.7262 (mt0) cc_final: 0.6987 (mt0) REVERT: B 189 ASP cc_start: 0.7404 (t0) cc_final: 0.7160 (t0) REVERT: B 198 LEU cc_start: 0.8272 (mt) cc_final: 0.8054 (mp) REVERT: B 239 ASN cc_start: 0.8159 (m110) cc_final: 0.7957 (m-40) REVERT: B 259 LYS cc_start: 0.8150 (mppt) cc_final: 0.7724 (mppt) REVERT: B 428 GLU cc_start: 0.7136 (mp0) cc_final: 0.6646 (pm20) REVERT: B 469 LYS cc_start: 0.8470 (tttm) cc_final: 0.8236 (tttp) REVERT: B 491 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 509 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.6987 (mtm-85) REVERT: B 600 ASP cc_start: 0.7847 (t0) cc_final: 0.7372 (OUTLIER) REVERT: B 638 GLU cc_start: 0.7964 (tt0) cc_final: 0.7749 (tt0) REVERT: B 746 TYR cc_start: 0.8481 (m-10) cc_final: 0.8198 (m-80) REVERT: B 747 ASN cc_start: 0.8119 (t0) cc_final: 0.7739 (t0) REVERT: B 764 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8095 (mtmm) REVERT: B 812 ASP cc_start: 0.7593 (t0) cc_final: 0.7332 (t70) REVERT: B 963 MET cc_start: 0.8782 (ptp) cc_final: 0.8553 (ptp) REVERT: B 1118 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7692 (ptp-110) outliers start: 0 outliers final: 1 residues processed: 358 average time/residue: 0.9000 time to fit residues: 343.7009 Evaluate side-chains 328 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 450 ASN A 591 ASN B 124 ASN B 720 ASN B 948 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101123 restraints weight = 19490.100| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.84 r_work: 0.3165 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13858 Z= 0.143 Angle : 0.548 13.257 18739 Z= 0.279 Chirality : 0.045 0.168 2054 Planarity : 0.005 0.064 2417 Dihedral : 4.159 27.138 1861 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.71 % Allowed : 9.99 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.21), residues: 1680 helix: 1.55 (0.21), residues: 618 sheet: 0.30 (0.37), residues: 220 loop : -0.57 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 366 TYR 0.022 0.001 TYR B 138 PHE 0.015 0.001 PHE B 362 TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00348 (13846) covalent geometry : angle 0.52266 (18721) hydrogen bonds : bond 0.05141 ( 542) hydrogen bonds : angle 4.85456 ( 1506) metal coordination : bond 0.00448 ( 12) metal coordination : angle 5.36713 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 329 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8184 (mt) cc_final: 0.7585 (mp) REVERT: A 241 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7682 (ttp80) REVERT: A 248 GLU cc_start: 0.7937 (mp0) cc_final: 0.7726 (mp0) REVERT: A 286 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6742 (mt-10) REVERT: A 290 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8193 (ttpp) REVERT: A 298 LEU cc_start: 0.7938 (tt) cc_final: 0.7729 (tp) REVERT: A 499 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8163 (ttp80) REVERT: A 502 GLU cc_start: 0.7792 (tp30) cc_final: 0.7068 (tp30) REVERT: A 522 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7850 (tp30) REVERT: A 536 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8045 (pttp) REVERT: A 590 VAL cc_start: 0.7952 (m) cc_final: 0.7602 (p) REVERT: B 20 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8388 (ttpp) REVERT: B 134 ASP cc_start: 0.7841 (t70) cc_final: 0.7160 (t0) REVERT: B 189 ASP cc_start: 0.7733 (t0) cc_final: 0.7446 (t0) REVERT: B 198 LEU cc_start: 0.8418 (mt) cc_final: 0.8209 (mp) REVERT: B 239 ASN cc_start: 0.8268 (m110) cc_final: 0.8044 (m-40) REVERT: B 241 LEU cc_start: 0.7536 (tp) cc_final: 0.7210 (tp) REVERT: B 256 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8140 (mmtt) REVERT: B 259 LYS cc_start: 0.8318 (mppt) cc_final: 0.7620 (mppt) REVERT: B 428 GLU cc_start: 0.7219 (mp0) cc_final: 0.6755 (pm20) REVERT: B 491 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 506 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 509 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7492 (mtm-85) REVERT: B 600 ASP cc_start: 0.8011 (t0) cc_final: 0.7507 (OUTLIER) REVERT: B 638 GLU cc_start: 0.8180 (tt0) cc_final: 0.7917 (tt0) REVERT: B 698 GLU cc_start: 0.7323 (tt0) cc_final: 0.6784 (tt0) REVERT: B 744 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 746 TYR cc_start: 0.8525 (m-10) cc_final: 0.8238 (m-80) REVERT: B 747 ASN cc_start: 0.8241 (t0) cc_final: 0.7813 (t0) REVERT: B 762 LYS cc_start: 0.8249 (tttp) cc_final: 0.7855 (tttp) REVERT: B 764 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8335 (mtmm) REVERT: B 963 MET cc_start: 0.8725 (ptp) cc_final: 0.8504 (ptp) REVERT: B 1118 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7671 (ptp-110) outliers start: 25 outliers final: 8 residues processed: 331 average time/residue: 0.9007 time to fit residues: 318.6088 Evaluate side-chains 319 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 311 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 165 optimal weight: 0.0770 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 147 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101304 restraints weight = 19514.388| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.84 r_work: 0.3167 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13858 Z= 0.135 Angle : 0.533 12.869 18739 Z= 0.268 Chirality : 0.045 0.155 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.117 27.093 1861 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.57 % Allowed : 12.18 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1680 helix: 1.51 (0.21), residues: 623 sheet: 0.30 (0.37), residues: 221 loop : -0.57 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 395 TYR 0.023 0.001 TYR B 138 PHE 0.013 0.001 PHE B 362 TRP 0.006 0.001 TRP A 580 HIS 0.004 0.001 HIS B 533 Details of bonding type rmsd covalent geometry : bond 0.00331 (13846) covalent geometry : angle 0.50365 (18721) hydrogen bonds : bond 0.04705 ( 542) hydrogen bonds : angle 4.61585 ( 1506) metal coordination : bond 0.00509 ( 12) metal coordination : angle 5.66038 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7962 (mp0) cc_final: 0.7733 (mp0) REVERT: A 286 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 298 LEU cc_start: 0.7912 (tt) cc_final: 0.7703 (tp) REVERT: A 462 GLU cc_start: 0.8066 (pt0) cc_final: 0.7848 (pm20) REVERT: A 522 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7825 (tp30) REVERT: A 590 VAL cc_start: 0.7871 (m) cc_final: 0.7558 (p) REVERT: B 20 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8365 (ttpp) REVERT: B 134 ASP cc_start: 0.7813 (t70) cc_final: 0.7116 (t0) REVERT: B 189 ASP cc_start: 0.7720 (t0) cc_final: 0.7445 (t0) REVERT: B 198 LEU cc_start: 0.8416 (mt) cc_final: 0.8208 (mp) REVERT: B 256 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8173 (mmtt) REVERT: B 259 LYS cc_start: 0.8331 (mppt) cc_final: 0.7626 (mppt) REVERT: B 428 GLU cc_start: 0.7186 (mp0) cc_final: 0.6711 (pm20) REVERT: B 491 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 506 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: B 509 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7476 (mtm-85) REVERT: B 556 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7784 (tptp) REVERT: B 600 ASP cc_start: 0.8008 (t0) cc_final: 0.7495 (OUTLIER) REVERT: B 638 GLU cc_start: 0.8177 (tt0) cc_final: 0.7925 (tt0) REVERT: B 692 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 698 GLU cc_start: 0.7370 (tt0) cc_final: 0.7074 (tt0) REVERT: B 744 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 746 TYR cc_start: 0.8515 (m-10) cc_final: 0.8228 (m-80) REVERT: B 747 ASN cc_start: 0.8244 (t0) cc_final: 0.7860 (t0) REVERT: B 762 LYS cc_start: 0.8233 (tttp) cc_final: 0.8011 (tttp) REVERT: B 764 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8378 (mtmm) REVERT: B 963 MET cc_start: 0.8734 (ptp) cc_final: 0.8482 (ptp) REVERT: B 1118 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7650 (ptp-110) outliers start: 23 outliers final: 7 residues processed: 328 average time/residue: 0.8837 time to fit residues: 310.0401 Evaluate side-chains 331 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1141 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 144 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101785 restraints weight = 19516.604| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.84 r_work: 0.3175 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13858 Z= 0.113 Angle : 0.513 11.822 18739 Z= 0.256 Chirality : 0.044 0.277 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.002 26.738 1861 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.09 % Allowed : 14.50 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.21), residues: 1680 helix: 1.58 (0.21), residues: 623 sheet: 0.29 (0.36), residues: 221 loop : -0.54 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 241 TYR 0.022 0.001 TYR B 138 PHE 0.012 0.001 PHE B 443 TRP 0.005 0.001 TRP A 580 HIS 0.003 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00272 (13846) covalent geometry : angle 0.48853 (18721) hydrogen bonds : bond 0.04157 ( 542) hydrogen bonds : angle 4.44101 ( 1506) metal coordination : bond 0.00477 ( 12) metal coordination : angle 5.07959 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 331 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7979 (mp0) cc_final: 0.7729 (mp0) REVERT: A 286 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6875 (mt-10) REVERT: A 366 ARG cc_start: 0.8366 (tpp80) cc_final: 0.8087 (ttm-80) REVERT: A 499 ARG cc_start: 0.8581 (ttm170) cc_final: 0.8169 (ttp-170) REVERT: A 522 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7842 (tp30) REVERT: A 590 VAL cc_start: 0.7823 (m) cc_final: 0.7550 (p) REVERT: B 134 ASP cc_start: 0.7812 (t70) cc_final: 0.7125 (t0) REVERT: B 189 ASP cc_start: 0.7700 (t0) cc_final: 0.7414 (t0) REVERT: B 198 LEU cc_start: 0.8363 (mt) cc_final: 0.8153 (mp) REVERT: B 206 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 256 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8192 (mmtt) REVERT: B 259 LYS cc_start: 0.8318 (mppt) cc_final: 0.7613 (mppt) REVERT: B 320 PHE cc_start: 0.8125 (t80) cc_final: 0.7910 (t80) REVERT: B 428 GLU cc_start: 0.7166 (mp0) cc_final: 0.6676 (pm20) REVERT: B 491 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 506 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: B 509 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7536 (mtm-85) REVERT: B 556 LYS cc_start: 0.8103 (tppp) cc_final: 0.7776 (tptp) REVERT: B 600 ASP cc_start: 0.8007 (t0) cc_final: 0.7484 (OUTLIER) REVERT: B 638 GLU cc_start: 0.8160 (tt0) cc_final: 0.7910 (tt0) REVERT: B 667 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7492 (mtp) REVERT: B 744 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 746 TYR cc_start: 0.8497 (m-10) cc_final: 0.8193 (m-80) REVERT: B 747 ASN cc_start: 0.8259 (t0) cc_final: 0.7863 (t0) REVERT: B 764 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8431 (mtmm) REVERT: B 1118 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7616 (ptp-110) outliers start: 16 outliers final: 11 residues processed: 333 average time/residue: 0.8093 time to fit residues: 288.0640 Evaluate side-chains 327 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 315 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain C residue 218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 450 ASN B 124 ASN B 871 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100885 restraints weight = 19381.877| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.87 r_work: 0.3154 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13858 Z= 0.150 Angle : 0.538 13.650 18739 Z= 0.269 Chirality : 0.045 0.141 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.085 27.344 1861 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.78 % Allowed : 14.36 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.20), residues: 1680 helix: 1.55 (0.21), residues: 617 sheet: 0.26 (0.35), residues: 231 loop : -0.63 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 241 TYR 0.023 0.001 TYR B 138 PHE 0.012 0.001 PHE B 443 TRP 0.005 0.001 TRP A 580 HIS 0.003 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00377 (13846) covalent geometry : angle 0.51174 (18721) hydrogen bonds : bond 0.04652 ( 542) hydrogen bonds : angle 4.48348 ( 1506) metal coordination : bond 0.00504 ( 12) metal coordination : angle 5.40968 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7111 (mm-30) REVERT: A 248 GLU cc_start: 0.7973 (mp0) cc_final: 0.7734 (mp0) REVERT: A 286 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6944 (mt-10) REVERT: A 499 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8137 (ttp-170) REVERT: A 522 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7838 (tp30) REVERT: A 590 VAL cc_start: 0.7738 (m) cc_final: 0.7480 (p) REVERT: B 20 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8440 (ttpp) REVERT: B 134 ASP cc_start: 0.7806 (t70) cc_final: 0.7128 (t0) REVERT: B 189 ASP cc_start: 0.7746 (t0) cc_final: 0.7498 (t0) REVERT: B 206 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 256 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8272 (mmtt) REVERT: B 259 LYS cc_start: 0.8338 (mppt) cc_final: 0.7632 (mppt) REVERT: B 320 PHE cc_start: 0.8108 (t80) cc_final: 0.7891 (t80) REVERT: B 461 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 491 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 506 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: B 509 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7533 (mtm-85) REVERT: B 556 LYS cc_start: 0.8087 (tppp) cc_final: 0.7790 (tptp) REVERT: B 600 ASP cc_start: 0.8030 (t0) cc_final: 0.7524 (OUTLIER) REVERT: B 638 GLU cc_start: 0.8128 (tt0) cc_final: 0.7885 (tt0) REVERT: B 667 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: B 744 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 746 TYR cc_start: 0.8511 (m-10) cc_final: 0.8214 (m-80) REVERT: B 764 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8429 (mtmm) REVERT: B 1118 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7666 (ptp-110) outliers start: 26 outliers final: 13 residues processed: 323 average time/residue: 0.8605 time to fit residues: 297.0018 Evaluate side-chains 321 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 306 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain C residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 0.0570 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 450 ASN B 124 ASN B1127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099761 restraints weight = 19650.936| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.84 r_work: 0.3139 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13858 Z= 0.206 Angle : 0.594 15.820 18739 Z= 0.294 Chirality : 0.047 0.210 2054 Planarity : 0.006 0.066 2417 Dihedral : 4.277 27.901 1861 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.57 % Allowed : 15.32 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.20), residues: 1680 helix: 1.37 (0.21), residues: 622 sheet: 0.20 (0.35), residues: 221 loop : -0.74 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 487 TYR 0.022 0.002 TYR B 138 PHE 0.012 0.002 PHE B 467 TRP 0.007 0.001 TRP B 552 HIS 0.005 0.001 HIS B 533 Details of bonding type rmsd covalent geometry : bond 0.00525 (13846) covalent geometry : angle 0.56399 (18721) hydrogen bonds : bond 0.05309 ( 542) hydrogen bonds : angle 4.60064 ( 1506) metal coordination : bond 0.00606 ( 12) metal coordination : angle 6.03071 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 317 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 248 GLU cc_start: 0.8000 (mp0) cc_final: 0.7742 (mp0) REVERT: A 286 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 522 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7829 (tp30) REVERT: A 590 VAL cc_start: 0.7897 (m) cc_final: 0.7580 (p) REVERT: B 20 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8437 (ttpp) REVERT: B 134 ASP cc_start: 0.7723 (t70) cc_final: 0.7097 (t0) REVERT: B 189 ASP cc_start: 0.7734 (t0) cc_final: 0.7471 (t0) REVERT: B 256 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8292 (mmtt) REVERT: B 259 LYS cc_start: 0.8342 (mppt) cc_final: 0.7643 (mppt) REVERT: B 461 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: B 491 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 506 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: B 509 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7669 (ttp-170) REVERT: B 556 LYS cc_start: 0.8094 (tppp) cc_final: 0.7782 (tptp) REVERT: B 600 ASP cc_start: 0.8000 (t0) cc_final: 0.7566 (t70) REVERT: B 638 GLU cc_start: 0.8150 (tt0) cc_final: 0.7909 (tt0) REVERT: B 667 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7520 (mtm) REVERT: B 744 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 746 TYR cc_start: 0.8545 (m-10) cc_final: 0.8257 (m-80) REVERT: B 764 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8441 (mtmm) REVERT: B 1118 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7696 (ptp-110) outliers start: 23 outliers final: 13 residues processed: 323 average time/residue: 0.8292 time to fit residues: 286.5778 Evaluate side-chains 329 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 313 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 908 LYS Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain C residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.0170 chunk 145 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100538 restraints weight = 19561.737| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.83 r_work: 0.3155 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13858 Z= 0.148 Angle : 0.558 13.982 18739 Z= 0.278 Chirality : 0.045 0.234 2054 Planarity : 0.005 0.064 2417 Dihedral : 4.179 27.573 1861 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.78 % Allowed : 16.21 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1680 helix: 1.47 (0.21), residues: 617 sheet: 0.18 (0.35), residues: 221 loop : -0.68 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 241 TYR 0.023 0.001 TYR B 138 PHE 0.012 0.001 PHE B 443 TRP 0.010 0.001 TRP A 184 HIS 0.004 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00370 (13846) covalent geometry : angle 0.53176 (18721) hydrogen bonds : bond 0.04620 ( 542) hydrogen bonds : angle 4.48717 ( 1506) metal coordination : bond 0.00505 ( 12) metal coordination : angle 5.49752 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 321 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 248 GLU cc_start: 0.8005 (mp0) cc_final: 0.7774 (mp0) REVERT: A 286 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6951 (mt-10) REVERT: A 499 ARG cc_start: 0.8597 (ttm170) cc_final: 0.8116 (ttp-170) REVERT: A 522 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7846 (tp30) REVERT: A 590 VAL cc_start: 0.7845 (m) cc_final: 0.7557 (p) REVERT: A 605 GLU cc_start: 0.8109 (tt0) cc_final: 0.7847 (tt0) REVERT: B 20 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8436 (ttpp) REVERT: B 79 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7610 (mmtp) REVERT: B 134 ASP cc_start: 0.7773 (t70) cc_final: 0.7098 (t0) REVERT: B 189 ASP cc_start: 0.7714 (t0) cc_final: 0.7478 (t0) REVERT: B 206 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7432 (mm-30) REVERT: B 256 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8286 (mmtt) REVERT: B 259 LYS cc_start: 0.8315 (mppt) cc_final: 0.7631 (mppt) REVERT: B 461 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 491 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 506 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: B 509 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7531 (mtm-85) REVERT: B 556 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7740 (tptp) REVERT: B 600 ASP cc_start: 0.7981 (t0) cc_final: 0.7547 (t70) REVERT: B 638 GLU cc_start: 0.8144 (tt0) cc_final: 0.7900 (tt0) REVERT: B 667 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7586 (mtp) REVERT: B 744 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 746 TYR cc_start: 0.8534 (m-10) cc_final: 0.8243 (m-80) REVERT: B 764 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8421 (mtmm) REVERT: B 1070 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: B 1118 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7678 (ptp-110) outliers start: 26 outliers final: 18 residues processed: 326 average time/residue: 0.7409 time to fit residues: 258.1600 Evaluate side-chains 334 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 908 LYS Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1070 GLN Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain C residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 chunk 161 optimal weight: 0.4980 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 196 ASN A 450 ASN B 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100813 restraints weight = 19146.463| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.86 r_work: 0.3156 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13858 Z= 0.136 Angle : 0.553 13.345 18739 Z= 0.274 Chirality : 0.045 0.255 2054 Planarity : 0.005 0.064 2417 Dihedral : 4.127 27.307 1861 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.71 % Allowed : 16.35 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.20), residues: 1680 helix: 1.51 (0.21), residues: 617 sheet: 0.21 (0.35), residues: 227 loop : -0.66 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 395 TYR 0.023 0.001 TYR B 138 PHE 0.012 0.001 PHE B 443 TRP 0.013 0.001 TRP A 184 HIS 0.004 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00337 (13846) covalent geometry : angle 0.52776 (18721) hydrogen bonds : bond 0.04422 ( 542) hydrogen bonds : angle 4.43494 ( 1506) metal coordination : bond 0.00487 ( 12) metal coordination : angle 5.33371 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 317 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7045 (mm-30) REVERT: A 248 GLU cc_start: 0.7946 (mp0) cc_final: 0.7723 (mp0) REVERT: A 286 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6962 (mt-10) REVERT: A 298 LEU cc_start: 0.7973 (tt) cc_final: 0.7765 (tp) REVERT: A 499 ARG cc_start: 0.8585 (ttm170) cc_final: 0.8100 (ttp-170) REVERT: A 522 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7836 (tp30) REVERT: A 590 VAL cc_start: 0.7775 (m) cc_final: 0.7516 (p) REVERT: A 605 GLU cc_start: 0.8166 (tt0) cc_final: 0.7885 (tt0) REVERT: B 134 ASP cc_start: 0.7711 (t70) cc_final: 0.7083 (t0) REVERT: B 189 ASP cc_start: 0.7720 (t0) cc_final: 0.7481 (t0) REVERT: B 206 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7359 (mm-30) REVERT: B 256 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8294 (mmtt) REVERT: B 259 LYS cc_start: 0.8311 (mppt) cc_final: 0.7625 (mppt) REVERT: B 461 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: B 491 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 506 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: B 509 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7522 (mtm-85) REVERT: B 556 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7734 (tptp) REVERT: B 600 ASP cc_start: 0.7994 (t0) cc_final: 0.7554 (t70) REVERT: B 638 GLU cc_start: 0.8148 (tt0) cc_final: 0.7905 (tt0) REVERT: B 667 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7567 (mtp) REVERT: B 744 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 746 TYR cc_start: 0.8505 (m-10) cc_final: 0.8207 (m-80) REVERT: B 764 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8407 (mtmm) REVERT: B 1070 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: B 1118 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7687 (ptp-110) outliers start: 25 outliers final: 15 residues processed: 323 average time/residue: 0.9092 time to fit residues: 313.1714 Evaluate side-chains 332 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1070 GLN Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain C residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 89 optimal weight: 0.1980 chunk 163 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 23 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102065 restraints weight = 19540.565| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.85 r_work: 0.3187 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13858 Z= 0.098 Angle : 0.521 11.315 18739 Z= 0.258 Chirality : 0.044 0.269 2054 Planarity : 0.005 0.064 2417 Dihedral : 3.915 26.561 1861 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 16.42 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.21), residues: 1680 helix: 1.70 (0.22), residues: 618 sheet: 0.27 (0.35), residues: 232 loop : -0.49 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 366 TYR 0.023 0.001 TYR B 138 PHE 0.026 0.001 PHE B 278 TRP 0.012 0.001 TRP A 184 HIS 0.005 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00229 (13846) covalent geometry : angle 0.50119 (18721) hydrogen bonds : bond 0.03621 ( 542) hydrogen bonds : angle 4.26240 ( 1506) metal coordination : bond 0.00406 ( 12) metal coordination : angle 4.65418 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7994 (mp0) cc_final: 0.7765 (mp0) REVERT: A 286 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 350 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 499 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8136 (ttp-170) REVERT: A 590 VAL cc_start: 0.7758 (m) cc_final: 0.7503 (p) REVERT: A 605 GLU cc_start: 0.8119 (tt0) cc_final: 0.7845 (tt0) REVERT: B 134 ASP cc_start: 0.7764 (t70) cc_final: 0.7046 (t0) REVERT: B 189 ASP cc_start: 0.7694 (t0) cc_final: 0.7454 (t0) REVERT: B 206 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7317 (mm-30) REVERT: B 256 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8259 (mmtt) REVERT: B 259 LYS cc_start: 0.8288 (mppt) cc_final: 0.7628 (mppt) REVERT: B 415 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 491 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 506 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: B 509 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7521 (mtm-85) REVERT: B 556 LYS cc_start: 0.8086 (tppp) cc_final: 0.7769 (tptp) REVERT: B 600 ASP cc_start: 0.7965 (t0) cc_final: 0.7533 (t70) REVERT: B 638 GLU cc_start: 0.8140 (tt0) cc_final: 0.7900 (tt0) REVERT: B 667 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7497 (mtp) REVERT: B 746 TYR cc_start: 0.8502 (m-10) cc_final: 0.8238 (m-80) REVERT: B 760 TYR cc_start: 0.8650 (p90) cc_final: 0.8430 (p90) REVERT: B 764 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8423 (mtmm) REVERT: B 1070 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: B 1118 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7608 (ptp-110) outliers start: 22 outliers final: 10 residues processed: 318 average time/residue: 0.9184 time to fit residues: 311.9103 Evaluate side-chains 317 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 303 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1070 GLN Chi-restraints excluded: chain B residue 1141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 154 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 155 optimal weight: 0.6980 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 450 ASN B 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101196 restraints weight = 19277.278| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.87 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13858 Z= 0.136 Angle : 0.564 12.713 18739 Z= 0.281 Chirality : 0.045 0.290 2054 Planarity : 0.005 0.086 2417 Dihedral : 4.004 26.842 1861 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.03 % Allowed : 17.51 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.21), residues: 1680 helix: 1.67 (0.21), residues: 611 sheet: 0.27 (0.35), residues: 232 loop : -0.54 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 395 TYR 0.023 0.001 TYR B 138 PHE 0.027 0.001 PHE B 278 TRP 0.014 0.001 TRP A 184 HIS 0.005 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00340 (13846) covalent geometry : angle 0.54176 (18721) hydrogen bonds : bond 0.04226 ( 542) hydrogen bonds : angle 4.33520 ( 1506) metal coordination : bond 0.00458 ( 12) metal coordination : angle 5.08693 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 314 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7968 (mp0) cc_final: 0.7742 (mp0) REVERT: A 286 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A 350 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7298 (tm-30) REVERT: A 476 ASN cc_start: 0.8564 (p0) cc_final: 0.8232 (p0) REVERT: A 499 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8094 (ttp-170) REVERT: A 590 VAL cc_start: 0.7743 (m) cc_final: 0.7505 (p) REVERT: A 605 GLU cc_start: 0.8175 (tt0) cc_final: 0.7899 (tt0) REVERT: B 134 ASP cc_start: 0.7705 (t70) cc_final: 0.7046 (t0) REVERT: B 189 ASP cc_start: 0.7740 (t0) cc_final: 0.7502 (t0) REVERT: B 206 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7290 (mm-30) REVERT: B 256 LYS cc_start: 0.8526 (mmtp) cc_final: 0.8289 (mmtt) REVERT: B 259 LYS cc_start: 0.8298 (mppt) cc_final: 0.7633 (mppt) REVERT: B 491 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7302 (mp0) REVERT: B 509 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7549 (mtm-85) REVERT: B 556 LYS cc_start: 0.8033 (tppp) cc_final: 0.7752 (tptp) REVERT: B 600 ASP cc_start: 0.7990 (t0) cc_final: 0.7566 (t70) REVERT: B 638 GLU cc_start: 0.8119 (tt0) cc_final: 0.7890 (tt0) REVERT: B 667 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7522 (mtp) REVERT: B 746 TYR cc_start: 0.8484 (m-10) cc_final: 0.8197 (m-80) REVERT: B 760 TYR cc_start: 0.8662 (p90) cc_final: 0.8451 (p90) REVERT: B 764 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8406 (mtmm) REVERT: B 1070 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: B 1118 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7653 (ptp-110) outliers start: 15 outliers final: 9 residues processed: 316 average time/residue: 0.9063 time to fit residues: 305.9560 Evaluate side-chains 320 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 309 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1070 GLN Chi-restraints excluded: chain B residue 1141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 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 381 ASN A 450 ASN A 482 ASN B 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101341 restraints weight = 19302.996| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.88 r_work: 0.3163 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13858 Z= 0.138 Angle : 0.571 12.988 18739 Z= 0.284 Chirality : 0.045 0.299 2054 Planarity : 0.005 0.077 2417 Dihedral : 4.024 27.048 1861 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.89 % Allowed : 17.65 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.21), residues: 1680 helix: 1.64 (0.21), residues: 611 sheet: 0.28 (0.35), residues: 232 loop : -0.55 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 395 TYR 0.023 0.001 TYR B 138 PHE 0.026 0.001 PHE B 278 TRP 0.014 0.001 TRP A 184 HIS 0.005 0.001 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00343 (13846) covalent geometry : angle 0.54833 (18721) hydrogen bonds : bond 0.04271 ( 542) hydrogen bonds : angle 4.36415 ( 1506) metal coordination : bond 0.00465 ( 12) metal coordination : angle 5.12796 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6526.80 seconds wall clock time: 111 minutes 43.81 seconds (6703.81 seconds total)