Starting phenix.real_space_refine on Sun Jan 19 10:17:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2a_50143/01_2025/9f2a_50143.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2a_50143/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2a_50143/01_2025/9f2a_50143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2a_50143/01_2025/9f2a_50143.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2a_50143/01_2025/9f2a_50143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2a_50143/01_2025/9f2a_50143.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.05, per 1000 atoms: 0.59 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: 2.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.79 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: 5.15 Time building geometry restraints manager: 3.48 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.640 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- 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 13846 Z= 0.236 Angle : 0.549 7.228 18721 Z= 0.312 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), 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 TRP 0.010 0.001 TRP B 552 HIS 0.005 0.001 HIS A 562 PHE 0.021 0.002 PHE B 703 TYR 0.027 0.001 TYR B1022 ARG 0.004 0.000 ARG B 351 *********************** 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 : 1.448 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: 0.7283 (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: 0.7284 (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: 0.7927 (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: 0.7687 (mppt) REVERT: A 522 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7564 (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: 0.7920 (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: 0.6986 (mt0) REVERT: B 189 ASP cc_start: 0.7404 (t0) cc_final: 0.7162 (t0) REVERT: B 198 LEU cc_start: 0.8272 (mt) cc_final: 0.8055 (mp) REVERT: B 239 ASN cc_start: 0.8159 (m110) cc_final: 0.7958 (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: 0.8199 (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: 1.7412 time to fit residues: 665.5037 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 : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.115328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102040 restraints weight = 19144.813| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.84 r_work: 0.3180 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13846 Z= 0.196 Angle : 0.509 7.035 18721 Z= 0.270 Chirality : 0.045 0.160 2054 Planarity : 0.005 0.064 2417 Dihedral : 4.095 26.920 1861 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.50 % Allowed : 10.12 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1680 helix: 1.60 (0.21), residues: 618 sheet: 0.31 (0.37), residues: 220 loop : -0.54 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 609 HIS 0.003 0.001 HIS B 533 PHE 0.013 0.001 PHE B 362 TYR 0.022 0.001 TYR B 138 ARG 0.006 0.000 ARG A 366 *********************** 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 350 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 328 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8206 (mt) cc_final: 0.7555 (mp) REVERT: A 241 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7693 (ttp80) REVERT: A 248 GLU cc_start: 0.7947 (mp0) cc_final: 0.7733 (mp0) REVERT: A 286 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6729 (mt-10) REVERT: A 289 ASP cc_start: 0.7679 (t0) cc_final: 0.7435 (t0) REVERT: A 290 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8190 (ttpp) REVERT: A 298 LEU cc_start: 0.7920 (tt) cc_final: 0.7711 (tp) REVERT: A 499 ARG cc_start: 0.8586 (ttm170) cc_final: 0.8055 (ttp80) REVERT: A 502 GLU cc_start: 0.7765 (tp30) cc_final: 0.7052 (tp30) REVERT: A 522 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7840 (tp30) REVERT: A 536 LYS cc_start: 0.8498 (ptpp) cc_final: 0.8045 (pttp) REVERT: A 590 VAL cc_start: 0.7778 (m) cc_final: 0.7471 (p) REVERT: B 20 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8411 (ttpp) REVERT: B 79 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7755 (mmtp) REVERT: B 134 ASP cc_start: 0.7785 (t70) cc_final: 0.7101 (t0) REVERT: B 189 ASP cc_start: 0.7764 (t0) cc_final: 0.7475 (t0) REVERT: B 198 LEU cc_start: 0.8409 (mt) cc_final: 0.8185 (mp) REVERT: B 239 ASN cc_start: 0.8296 (m110) cc_final: 0.8079 (m-40) REVERT: B 241 LEU cc_start: 0.7537 (tp) cc_final: 0.7323 (tp) REVERT: B 256 LYS cc_start: 0.8449 (mmtp) cc_final: 0.8109 (mmtt) REVERT: B 259 LYS cc_start: 0.8306 (mppt) cc_final: 0.7620 (mppt) REVERT: B 428 GLU cc_start: 0.7251 (mp0) cc_final: 0.6675 (pm20) REVERT: B 491 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7379 (mm-30) REVERT: B 506 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: B 509 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7493 (mtm-85) REVERT: B 600 ASP cc_start: 0.8017 (t0) cc_final: 0.7525 (OUTLIER) REVERT: B 638 GLU cc_start: 0.8168 (tt0) cc_final: 0.7918 (tt0) REVERT: B 698 GLU cc_start: 0.7317 (tt0) cc_final: 0.6768 (tt0) REVERT: B 744 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 746 TYR cc_start: 0.8504 (m-10) cc_final: 0.8256 (m-80) REVERT: B 747 ASN cc_start: 0.8237 (t0) cc_final: 0.7815 (t0) REVERT: B 762 LYS cc_start: 0.8239 (tttp) cc_final: 0.7840 (tttp) REVERT: B 764 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8344 (mtmm) REVERT: B 963 MET cc_start: 0.8716 (ptp) cc_final: 0.8497 (ptp) REVERT: B 1118 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7668 (ptp-110) outliers start: 22 outliers final: 7 residues processed: 330 average time/residue: 1.7485 time to fit residues: 615.9027 Evaluate side-chains 318 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 311 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 10 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.114605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101369 restraints weight = 19379.288| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.83 r_work: 0.3169 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13846 Z= 0.211 Angle : 0.500 7.316 18721 Z= 0.264 Chirality : 0.044 0.175 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.070 27.076 1861 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.64 % Allowed : 12.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1680 helix: 1.55 (0.21), residues: 623 sheet: 0.34 (0.37), residues: 221 loop : -0.55 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 580 HIS 0.003 0.001 HIS A 489 PHE 0.012 0.001 PHE B 443 TYR 0.022 0.001 TYR B 138 ARG 0.010 0.000 ARG A 395 *********************** 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 337 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 313 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7955 (mp0) cc_final: 0.7728 (mp0) REVERT: A 286 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 290 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8195 (ttpp) REVERT: A 522 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7826 (tp30) REVERT: A 536 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8104 (pttp) REVERT: A 590 VAL cc_start: 0.7729 (m) cc_final: 0.7456 (p) REVERT: B 20 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8379 (ttpp) REVERT: B 71 TYR cc_start: 0.7710 (m-10) cc_final: 0.7443 (m-10) REVERT: B 79 LYS cc_start: 0.8071 (mmtp) cc_final: 0.7752 (mmtm) REVERT: B 134 ASP cc_start: 0.7867 (t70) cc_final: 0.7164 (t0) REVERT: B 189 ASP cc_start: 0.7720 (t0) cc_final: 0.7441 (t0) REVERT: B 198 LEU cc_start: 0.8400 (mt) cc_final: 0.8193 (mp) REVERT: B 239 ASN cc_start: 0.8244 (m-40) cc_final: 0.8040 (m110) REVERT: B 256 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8154 (mmtt) REVERT: B 259 LYS cc_start: 0.8321 (mppt) cc_final: 0.7615 (mppt) REVERT: B 428 GLU cc_start: 0.7182 (mp0) cc_final: 0.6708 (pm20) REVERT: B 438 ASP cc_start: 0.8277 (m-30) cc_final: 0.8076 (m-30) REVERT: B 491 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 506 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: B 509 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7482 (mtm-85) REVERT: B 600 ASP cc_start: 0.8017 (t0) cc_final: 0.7503 (OUTLIER) REVERT: B 638 GLU cc_start: 0.8180 (tt0) cc_final: 0.7928 (tt0) REVERT: B 692 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 746 TYR cc_start: 0.8506 (m-10) cc_final: 0.8217 (m-80) REVERT: B 747 ASN cc_start: 0.8249 (t0) cc_final: 0.7872 (t0) REVERT: B 762 LYS cc_start: 0.8218 (tttp) cc_final: 0.7995 (tttp) REVERT: B 764 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8362 (mtmm) REVERT: B 963 MET cc_start: 0.8736 (ptp) cc_final: 0.8491 (ptp) REVERT: B 1118 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7647 (ptp-110) outliers start: 24 outliers final: 6 residues processed: 319 average time/residue: 1.7755 time to fit residues: 606.8352 Evaluate side-chains 322 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 316 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 686 ASP 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 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.114129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100887 restraints weight = 19292.131| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.83 r_work: 0.3162 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13846 Z= 0.239 Angle : 0.515 7.224 18721 Z= 0.269 Chirality : 0.045 0.259 2054 Planarity : 0.005 0.066 2417 Dihedral : 4.115 27.294 1861 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.50 % Allowed : 13.68 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1680 helix: 1.49 (0.21), residues: 623 sheet: 0.26 (0.36), residues: 221 loop : -0.60 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 580 HIS 0.003 0.001 HIS B1104 PHE 0.014 0.001 PHE B 362 TYR 0.023 0.001 TYR B 138 ARG 0.008 0.000 ARG A 241 *********************** 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 351 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 329 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7975 (mp0) cc_final: 0.7725 (mp0) REVERT: A 286 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6917 (mt-10) REVERT: A 499 ARG cc_start: 0.8584 (ttm170) cc_final: 0.8150 (ttp-170) REVERT: A 522 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7820 (tp30) REVERT: A 590 VAL cc_start: 0.7677 (m) cc_final: 0.7423 (p) REVERT: B 79 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7756 (mmtm) REVERT: B 134 ASP cc_start: 0.7771 (t70) cc_final: 0.7097 (t0) REVERT: B 189 ASP cc_start: 0.7724 (t0) cc_final: 0.7449 (t0) REVERT: B 256 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8223 (mmtt) REVERT: B 259 LYS cc_start: 0.8314 (mppt) cc_final: 0.7609 (mppt) REVERT: B 320 PHE cc_start: 0.8128 (t80) cc_final: 0.7909 (t80) REVERT: B 428 GLU cc_start: 0.7180 (mp0) cc_final: 0.6699 (pm20) REVERT: B 491 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 506 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: B 509 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7566 (mtm-85) REVERT: B 556 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: B 600 ASP cc_start: 0.8010 (t0) cc_final: 0.7493 (OUTLIER) REVERT: B 667 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: B 692 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 744 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7871 (tm-30) REVERT: B 746 TYR cc_start: 0.8500 (m-10) cc_final: 0.8235 (m-80) REVERT: B 963 MET cc_start: 0.8737 (ptp) cc_final: 0.8515 (ptp) REVERT: B 1118 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7635 (ptp-110) outliers start: 22 outliers final: 9 residues processed: 335 average time/residue: 1.7655 time to fit residues: 631.6262 Evaluate side-chains 326 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 VAL 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 506 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain C residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 126 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 150 optimal weight: 0.3980 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 B 871 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101551 restraints weight = 19324.903| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.88 r_work: 0.3166 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13846 Z= 0.192 Angle : 0.498 10.367 18721 Z= 0.258 Chirality : 0.045 0.363 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.012 27.013 1861 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.50 % Allowed : 15.32 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1680 helix: 1.60 (0.21), residues: 617 sheet: 0.28 (0.35), residues: 231 loop : -0.60 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 580 HIS 0.004 0.001 HIS B1104 PHE 0.012 0.001 PHE B 443 TYR 0.023 0.001 TYR B 138 ARG 0.008 0.000 ARG A 395 *********************** 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 329 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 248 GLU cc_start: 0.7975 (mp0) cc_final: 0.7760 (mp0) REVERT: A 286 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 289 ASP cc_start: 0.7599 (t0) cc_final: 0.7246 (t0) REVERT: A 290 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8273 (ttpp) REVERT: A 522 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7849 (tp30) REVERT: B 71 TYR cc_start: 0.7664 (m-10) cc_final: 0.7357 (m-10) REVERT: B 79 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7642 (mmtm) REVERT: B 134 ASP cc_start: 0.7803 (t70) cc_final: 0.7105 (t0) REVERT: B 189 ASP cc_start: 0.7750 (t0) cc_final: 0.7475 (t0) REVERT: B 247 LEU cc_start: 0.7814 (mt) cc_final: 0.7513 (mp) REVERT: B 256 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8229 (mmtt) REVERT: B 259 LYS cc_start: 0.8328 (mppt) cc_final: 0.7621 (mppt) REVERT: B 320 PHE cc_start: 0.8122 (t80) cc_final: 0.7910 (t80) REVERT: B 428 GLU cc_start: 0.7179 (mp0) cc_final: 0.6696 (pm20) REVERT: B 491 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 506 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: B 509 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7569 (mtm-85) REVERT: B 556 LYS cc_start: 0.8089 (tppp) cc_final: 0.7791 (tptp) REVERT: B 600 ASP cc_start: 0.8023 (t0) cc_final: 0.7514 (OUTLIER) REVERT: B 667 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7508 (mtp) REVERT: B 746 TYR cc_start: 0.8484 (m-10) cc_final: 0.8232 (m-80) REVERT: B 747 ASN cc_start: 0.8237 (t0) cc_final: 0.7856 (t0) REVERT: B 963 MET cc_start: 0.8744 (ptp) cc_final: 0.8539 (ptp) REVERT: B 1118 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7641 (ptp-110) outliers start: 22 outliers final: 12 residues processed: 315 average time/residue: 1.7446 time to fit residues: 587.5614 Evaluate side-chains 315 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 302 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 506 GLU 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 851 THR 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 101 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 67 optimal weight: 0.0040 chunk 34 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 196 ASN A 450 ASN B 124 ASN B 871 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100655 restraints weight = 19532.200| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.84 r_work: 0.3160 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13846 Z= 0.248 Angle : 0.518 7.625 18721 Z= 0.269 Chirality : 0.045 0.211 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.088 27.371 1861 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.98 % Allowed : 15.39 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1680 helix: 1.58 (0.21), residues: 615 sheet: 0.28 (0.35), residues: 232 loop : -0.64 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 274 HIS 0.004 0.001 HIS B1104 PHE 0.028 0.002 PHE B 278 TYR 0.023 0.001 TYR B 138 ARG 0.009 0.001 ARG A 241 *********************** 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 342 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 313 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 248 GLU cc_start: 0.7986 (mp0) cc_final: 0.7770 (mp0) REVERT: A 286 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 290 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8259 (ttpp) REVERT: A 366 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8001 (tpp-160) REVERT: A 522 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7825 (tp30) REVERT: A 589 MET cc_start: 0.7048 (tmm) cc_final: 0.6739 (tmm) REVERT: A 590 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7474 (p) REVERT: B 79 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7730 (mmtm) REVERT: B 134 ASP cc_start: 0.7741 (t70) cc_final: 0.7075 (t0) REVERT: B 189 ASP cc_start: 0.7729 (t0) cc_final: 0.7483 (t0) REVERT: B 256 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8261 (mmtt) REVERT: B 259 LYS cc_start: 0.8320 (mppt) cc_final: 0.7619 (mppt) REVERT: B 320 PHE cc_start: 0.8113 (t80) cc_final: 0.7893 (t80) REVERT: B 428 GLU cc_start: 0.7196 (mp0) cc_final: 0.6708 (pm20) REVERT: B 491 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 506 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: B 519 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: B 556 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7792 (tptp) REVERT: B 600 ASP cc_start: 0.7996 (t0) cc_final: 0.7561 (t70) REVERT: B 667 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7573 (mtp) REVERT: B 746 TYR cc_start: 0.8512 (m-10) cc_final: 0.8240 (m-80) REVERT: B 760 TYR cc_start: 0.8644 (p90) cc_final: 0.8443 (p90) REVERT: B 963 MET cc_start: 0.8739 (ptp) cc_final: 0.8533 (ptp) REVERT: B 1118 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7648 (ptp-110) outliers start: 29 outliers final: 15 residues processed: 321 average time/residue: 1.7771 time to fit residues: 611.5848 Evaluate side-chains 333 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 313 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 A residue 590 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 617 LEU 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 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 24 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 124 ASN B 871 GLN B1127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100518 restraints weight = 19495.832| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.84 r_work: 0.3154 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13846 Z= 0.272 Angle : 0.546 11.416 18721 Z= 0.284 Chirality : 0.046 0.432 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.140 27.469 1861 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.92 % Allowed : 15.60 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1680 helix: 1.51 (0.21), residues: 615 sheet: 0.28 (0.35), residues: 227 loop : -0.67 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.004 0.001 HIS B1104 PHE 0.012 0.001 PHE B 467 TYR 0.024 0.001 TYR B 138 ARG 0.009 0.001 ARG A 241 *********************** 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 341 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 248 GLU cc_start: 0.8001 (mp0) cc_final: 0.7762 (mp0) REVERT: A 286 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 499 ARG cc_start: 0.8598 (ttm170) cc_final: 0.8107 (ttp-170) REVERT: A 522 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7849 (tp30) REVERT: A 589 MET cc_start: 0.7078 (tmm) cc_final: 0.6784 (tmm) REVERT: A 590 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7510 (p) REVERT: B 134 ASP cc_start: 0.7762 (t70) cc_final: 0.7040 (t0) REVERT: B 189 ASP cc_start: 0.7724 (t0) cc_final: 0.7479 (t0) REVERT: B 256 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8282 (mmtt) REVERT: B 259 LYS cc_start: 0.8306 (mppt) cc_final: 0.7606 (mppt) REVERT: B 491 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 506 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: B 519 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: B 556 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7785 (tptp) REVERT: B 600 ASP cc_start: 0.8001 (t0) cc_final: 0.7558 (t70) REVERT: B 667 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: B 746 TYR cc_start: 0.8505 (m-10) cc_final: 0.8236 (m-80) REVERT: B 762 LYS cc_start: 0.8348 (tttt) cc_final: 0.8100 (tttp) REVERT: B 963 MET cc_start: 0.8733 (ptp) cc_final: 0.8498 (ptp) REVERT: B 1070 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: B 1118 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7664 (ptp-110) outliers start: 28 outliers final: 16 residues processed: 322 average time/residue: 1.7971 time to fit residues: 616.6419 Evaluate side-chains 329 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 A residue 590 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 266 LYS 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 519 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 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 1033 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 B1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100617 restraints weight = 19534.214| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.84 r_work: 0.3160 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13846 Z= 0.223 Angle : 0.523 9.035 18721 Z= 0.271 Chirality : 0.045 0.327 2054 Planarity : 0.005 0.066 2417 Dihedral : 4.091 27.206 1861 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.71 % Allowed : 16.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1680 helix: 1.54 (0.21), residues: 615 sheet: 0.29 (0.35), residues: 232 loop : -0.66 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.004 0.001 HIS B1104 PHE 0.028 0.001 PHE B 278 TYR 0.023 0.001 TYR B 138 ARG 0.009 0.001 ARG A 366 *********************** 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 : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.8000 (mp0) cc_final: 0.7769 (mp0) REVERT: A 286 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6916 (mt-10) REVERT: A 290 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8310 (ttpp) REVERT: A 499 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8105 (ttp-170) REVERT: A 522 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7851 (tp30) REVERT: A 589 MET cc_start: 0.7072 (tmm) cc_final: 0.6778 (tmm) REVERT: A 590 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7498 (p) REVERT: B 134 ASP cc_start: 0.7738 (t70) cc_final: 0.7056 (t0) REVERT: B 189 ASP cc_start: 0.7721 (t0) cc_final: 0.7478 (t0) REVERT: B 256 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8282 (mmtt) REVERT: B 259 LYS cc_start: 0.8322 (mppt) cc_final: 0.7632 (mppt) REVERT: B 491 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 506 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: B 519 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: B 556 LYS cc_start: 0.8055 (tppp) cc_final: 0.7757 (tptp) REVERT: B 600 ASP cc_start: 0.7988 (t0) cc_final: 0.7560 (t70) REVERT: B 667 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7578 (mtp) REVERT: B 746 TYR cc_start: 0.8505 (m-10) cc_final: 0.8241 (m-80) REVERT: B 762 LYS cc_start: 0.8339 (tttt) cc_final: 0.8034 (tttp) REVERT: B 963 MET cc_start: 0.8731 (ptp) cc_final: 0.8504 (ptp) REVERT: B 1070 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: B 1118 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7655 (ptp-110) outliers start: 25 outliers final: 14 residues processed: 321 average time/residue: 1.7978 time to fit residues: 615.5968 Evaluate side-chains 329 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 310 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 A residue 590 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 519 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 B1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100688 restraints weight = 19292.050| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.87 r_work: 0.3155 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13846 Z= 0.262 Angle : 0.549 8.054 18721 Z= 0.285 Chirality : 0.046 0.299 2054 Planarity : 0.005 0.065 2417 Dihedral : 4.135 27.375 1861 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.57 % Allowed : 16.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1680 helix: 1.49 (0.21), residues: 615 sheet: 0.26 (0.35), residues: 227 loop : -0.70 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 184 HIS 0.005 0.001 HIS B1104 PHE 0.029 0.002 PHE B 278 TYR 0.023 0.001 TYR B 138 ARG 0.009 0.001 ARG A 366 *********************** 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 339 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 316 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7966 (mp0) cc_final: 0.7740 (mp0) REVERT: A 286 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 462 GLU cc_start: 0.8231 (pt0) cc_final: 0.8021 (pt0) REVERT: A 499 ARG cc_start: 0.8582 (ttm170) cc_final: 0.8080 (ttp-170) REVERT: A 522 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7830 (tp30) REVERT: A 589 MET cc_start: 0.7094 (tmm) cc_final: 0.6802 (tmm) REVERT: A 590 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7481 (p) REVERT: B 134 ASP cc_start: 0.7754 (t70) cc_final: 0.7065 (t0) REVERT: B 189 ASP cc_start: 0.7741 (t0) cc_final: 0.7504 (t0) REVERT: B 256 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8271 (mmtt) REVERT: B 259 LYS cc_start: 0.8316 (mppt) cc_final: 0.7621 (mppt) REVERT: B 320 PHE cc_start: 0.8078 (t80) cc_final: 0.7855 (t80) REVERT: B 491 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 506 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: B 556 LYS cc_start: 0.8065 (tppp) cc_final: 0.7777 (tptp) REVERT: B 600 ASP cc_start: 0.7991 (t0) cc_final: 0.7562 (t70) REVERT: B 667 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7485 (mtm) REVERT: B 746 TYR cc_start: 0.8491 (m-10) cc_final: 0.8223 (m-80) REVERT: B 1070 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: B 1118 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7681 (ptp-110) outliers start: 23 outliers final: 14 residues processed: 321 average time/residue: 1.8332 time to fit residues: 629.4000 Evaluate side-chains 325 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 307 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 A residue 590 VAL Chi-restraints excluded: chain B residue 13 MET 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 617 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 64 optimal weight: 0.0970 chunk 152 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 162 optimal weight: 0.0030 chunk 112 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.115582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102344 restraints weight = 19377.701| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.83 r_work: 0.3183 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13846 Z= 0.162 Angle : 0.516 13.373 18721 Z= 0.265 Chirality : 0.044 0.386 2054 Planarity : 0.005 0.063 2417 Dihedral : 3.942 26.766 1861 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.23 % Allowed : 16.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1680 helix: 1.69 (0.22), residues: 615 sheet: 0.29 (0.35), residues: 232 loop : -0.53 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.006 0.001 HIS B1104 PHE 0.029 0.001 PHE B 278 TYR 0.023 0.001 TYR B 138 ARG 0.010 0.000 ARG A 366 ********************** 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 330 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 312 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7990 (mp0) cc_final: 0.7764 (mp0) REVERT: A 286 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6899 (mt-10) REVERT: A 491 ARG cc_start: 0.8414 (mpt180) cc_final: 0.8036 (mpt180) REVERT: A 499 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8106 (ttp-170) REVERT: B 71 TYR cc_start: 0.7572 (m-10) cc_final: 0.7248 (m-10) REVERT: B 79 LYS cc_start: 0.7465 (mttm) cc_final: 0.7244 (mttp) REVERT: B 134 ASP cc_start: 0.7718 (t70) cc_final: 0.7040 (t0) REVERT: B 189 ASP cc_start: 0.7710 (t0) cc_final: 0.7475 (t0) REVERT: B 256 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8260 (mmtt) REVERT: B 259 LYS cc_start: 0.8300 (mppt) cc_final: 0.7636 (mppt) REVERT: B 320 PHE cc_start: 0.8110 (t80) cc_final: 0.7781 (t80) REVERT: B 415 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 491 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 506 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: B 556 LYS cc_start: 0.8086 (tppp) cc_final: 0.7797 (tptp) REVERT: B 573 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8287 (ttmm) REVERT: B 600 ASP cc_start: 0.7973 (t0) cc_final: 0.7543 (t70) REVERT: B 667 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7517 (mtp) REVERT: B 746 TYR cc_start: 0.8486 (m-10) cc_final: 0.8259 (m-80) REVERT: B 760 TYR cc_start: 0.8662 (p90) cc_final: 0.8457 (p90) REVERT: B 762 LYS cc_start: 0.8278 (tttt) cc_final: 0.7998 (tttp) REVERT: B 843 GLU cc_start: 0.7646 (mp0) cc_final: 0.7371 (mp0) REVERT: B 1118 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7619 (ptp-110) outliers start: 18 outliers final: 10 residues processed: 315 average time/residue: 1.7862 time to fit residues: 600.0427 Evaluate side-chains 319 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 306 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 A residue 590 VAL 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 617 LEU Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 908 LYS Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 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 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 = 0.3474 r_free = 0.3474 target = 0.114356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100887 restraints weight = 19404.328| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.87 r_work: 0.3158 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13846 Z= 0.251 Angle : 0.553 12.145 18721 Z= 0.284 Chirality : 0.046 0.358 2054 Planarity : 0.005 0.063 2417 Dihedral : 4.065 27.302 1861 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.09 % Allowed : 17.10 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1680 helix: 1.54 (0.21), residues: 615 sheet: 0.23 (0.35), residues: 232 loop : -0.67 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 184 HIS 0.005 0.001 HIS B1104 PHE 0.030 0.001 PHE B 278 TYR 0.023 0.001 TYR B 138 ARG 0.009 0.001 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11889.21 seconds wall clock time: 209 minutes 55.87 seconds (12595.87 seconds total)