Starting phenix.real_space_refine on Sun Jan 19 09:35:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f29_50140/01_2025/9f29_50140.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f29_50140/01_2025/9f29_50140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f29_50140/01_2025/9f29_50140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f29_50140/01_2025/9f29_50140.map" model { file = "/net/cci-nas-00/data/ceres_data/9f29_50140/01_2025/9f29_50140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f29_50140/01_2025/9f29_50140.cif" } resolution = 2.94 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 8685 2.51 5 N 2286 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13520 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 513 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "A" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3555 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 9448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9448 Classifications: {'peptide': 1181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1114} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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 9504 SG CYS B 706 57.750 10.812 89.318 1.00 70.75 S ATOM 9526 SG CYS B 709 60.620 10.094 91.692 1.00 87.39 S ATOM 9591 SG CYS B 718 61.172 12.448 88.800 1.00 70.59 S ATOM 9612 SG CYS B 721 60.777 8.651 88.273 1.00 83.58 S ATOM 9695 SG CYS B 731 42.821 20.273 106.274 1.00 85.38 S ATOM 9719 SG CYS B 734 44.262 17.375 108.000 1.00 81.51 S ATOM 9847 SG CYS B 750 41.097 16.935 105.812 1.00 79.83 S ATOM 9869 SG CYS B 753 40.879 18.680 109.202 1.00 98.63 S ATOM 12860 SG CYS B1123 67.265 52.477 113.233 1.00 75.26 S ATOM 12882 SG CYS B1126 64.568 50.029 113.234 1.00 69.63 S ATOM 12988 SG CYS B1139 65.803 51.198 116.599 1.00 76.33 S ATOM 13008 SG CYS B1142 67.423 48.548 114.171 1.00 88.32 S Time building chain proxies: 8.04, per 1000 atoms: 0.59 Number of scatterers: 13520 At special positions: 0 Unit cell: (85.44, 122.88, 160.32, 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 2496 8.00 N 2286 7.00 C 8685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 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 734 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " 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 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 14 sheets defined 42.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.681A pdb=" N GLU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.527A 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 240 through 255 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 219 through 244 removed outlier: 3.872A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 4.875A pdb=" N ASN A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.606A 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 435 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.658A pdb=" N ILE A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.723A pdb=" N VAL A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.658A pdb=" N MET A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'B' and resid 5 through 30 removed outlier: 3.757A pdb=" N GLU B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.739A 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 71 removed outlier: 4.578A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.867A pdb=" N ALA B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 removed outlier: 3.539A pdb=" N TYR B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) 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 170 removed outlier: 3.568A pdb=" N ALA B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.686A pdb=" N LYS B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 324 removed outlier: 3.542A pdb=" N SER B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.729A pdb=" N MET B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.508A pdb=" N ARG B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.862A 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 Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.669A pdb=" N VAL B 543 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 585 through 592 removed outlier: 3.578A pdb=" N LEU B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 615 removed outlier: 3.961A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.706A pdb=" N ASN B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 740 through 746 Processing helix chain 'B' and resid 766 through 779 removed outlier: 3.741A pdb=" N LEU B 770 " --> pdb=" O ARG B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.802A pdb=" N GLY B 805 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 Processing helix chain 'B' and resid 877 through 897 removed outlier: 3.658A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 913 removed outlier: 3.717A 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 removed outlier: 3.625A pdb=" N TYR B 976 " --> pdb=" O SER B 973 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 977 " --> pdb=" O ARG B 974 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 973 through 977' Processing helix chain 'B' and resid 996 through 1000 removed outlier: 3.952A pdb=" N VAL B1000 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1007 Processing helix chain 'B' and resid 1014 through 1022 removed outlier: 3.759A pdb=" N TYR B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1030 Processing helix chain 'B' and resid 1036 through 1041 Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.779A pdb=" N TYR B1047 " --> pdb=" O PRO B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1071 removed outlier: 3.778A pdb=" N LEU B1071 " --> pdb=" O TYR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 Processing helix chain 'B' and resid 1092 through 1104 Processing helix chain 'B' and resid 1105 through 1117 removed outlier: 4.410A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1156 removed outlier: 3.775A pdb=" N GLU B1156 " --> pdb=" O GLY B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1169 Processing helix chain 'B' and resid 1172 through 1190 removed outlier: 4.039A pdb=" N PHE B1190 " --> pdb=" O ILE B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1216 removed outlier: 3.616A pdb=" N ARG B1216 " --> pdb=" O LEU B1212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AA2, first strand: chain 'A' and resid 197 through 201 removed outlier: 6.618A pdb=" N VAL A 485 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 565 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 278 removed outlier: 6.614A pdb=" N GLU A 286 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 276 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 284 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU A 278 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 296 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N PHE A 329 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS A 295 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ALA A 331 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 297 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LYS A 333 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 12.379A pdb=" N TYR A 335 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS A 320 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A 334 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 318 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.207A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR A 354 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE A 400 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 356 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA A 402 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 358 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 357 " --> pdb=" O PRO A 600 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 599 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL A 612 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 601 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 608 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.847A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY B 941 " --> pdb=" O ASP B 824 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR B 826 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA B 943 " --> pdb=" O THR B 826 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA B 828 " --> pdb=" O ALA B 943 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL B 940 " --> pdb=" O SER B 876 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 876 " --> pdb=" O VAL B 940 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 875 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 935 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 129 removed outlier: 3.811A pdb=" N ASN B 124 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLU B 217 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 139 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 8.219A 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 224 through 227 removed outlier: 3.961A pdb=" N ASP B 224 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 241 " --> pdb=" O ASP B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.637A 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: 6.841A pdb=" N ILE B 406 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE B 433 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 408 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.771A pdb=" N GLU B 560 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 575 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 6.385A 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 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 832 through 833 Processing sheet with id=AB5, first strand: chain 'B' and resid 1129 through 1130 539 hydrogen bonds defined for protein. 1467 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: 5.05 Time building geometry restraints manager: 3.68 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: 4421 1.34 - 1.46: 2792 1.46 - 1.58: 6514 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 13807 Sorted by residual: bond pdb=" N GLU B 323 " pdb=" CA GLU B 323 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.33e-02 5.65e+03 5.94e+00 bond pdb=" CG LEU B1165 " pdb=" CD2 LEU B1165 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB THR B1021 " pdb=" CG2 THR B1021 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.30e-01 bond pdb=" CG LEU B1082 " pdb=" CD1 LEU B1082 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.49e-01 bond pdb=" CG PRO B 988 " pdb=" CD PRO B 988 " ideal model delta sigma weight residual 1.503 1.475 0.028 3.40e-02 8.65e+02 6.70e-01 ... (remaining 13802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 18389 1.59 - 3.19: 246 3.19 - 4.78: 23 4.78 - 6.38: 5 6.38 - 7.97: 3 Bond angle restraints: 18666 Sorted by residual: angle pdb=" N GLU C 256 " pdb=" CA GLU C 256 " pdb=" C GLU C 256 " ideal model delta sigma weight residual 114.64 107.99 6.65 1.52e+00 4.33e-01 1.91e+01 angle pdb=" C ASP B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 120.44 124.09 -3.65 1.30e+00 5.92e-01 7.88e+00 angle pdb=" CA GLU C 256 " pdb=" C GLU C 256 " pdb=" N ILE C 257 " ideal model delta sigma weight residual 119.58 115.75 3.83 1.39e+00 5.18e-01 7.59e+00 angle pdb=" CA VAL B 860 " pdb=" C VAL B 860 " pdb=" N SER B 861 " ideal model delta sigma weight residual 116.60 120.32 -3.72 1.45e+00 4.76e-01 6.57e+00 angle pdb=" CA LEU B1030 " pdb=" CB LEU B1030 " pdb=" CG LEU B1030 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 ... (remaining 18661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7645 17.63 - 35.26: 653 35.26 - 52.88: 105 52.88 - 70.51: 19 70.51 - 88.14: 10 Dihedral angle restraints: 8432 sinusoidal: 3533 harmonic: 4899 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 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+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 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LYS A 525 " pdb=" C LYS A 525 " pdb=" N MET A 526 " pdb=" CA MET A 526 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1095 0.027 - 0.054: 561 0.054 - 0.081: 201 0.081 - 0.109: 134 0.109 - 0.136: 58 Chirality restraints: 2049 Sorted by residual: chirality pdb=" CB VAL B 426 " pdb=" CA VAL B 426 " pdb=" CG1 VAL B 426 " pdb=" CG2 VAL B 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PRO B 870 " pdb=" N PRO B 870 " pdb=" C PRO B 870 " pdb=" CB PRO B 870 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 406 " pdb=" N ILE B 406 " pdb=" C ILE B 406 " pdb=" CB ILE B 406 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 2046 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 146 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 203 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 204 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 3 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 4 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 4 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 4 " -0.022 5.00e-02 4.00e+02 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2820 2.78 - 3.31: 11524 3.31 - 3.84: 20503 3.84 - 4.37: 24601 4.37 - 4.90: 44401 Nonbonded interactions: 103849 Sorted by model distance: nonbonded pdb=" OH TYR C 230 " pdb=" OE1 GLU B 476 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG B 822 " pdb=" OD1 ASP B 986 " model vdw 2.273 3.120 nonbonded pdb=" OD2 ASP B1008 " pdb=" OH TYR B1013 " model vdw 2.302 3.040 nonbonded pdb=" NH2 ARG B 846 " pdb=" O LEU B 859 " model vdw 2.346 3.120 nonbonded pdb=" O PRO B 455 " pdb=" OG SER B 650 " model vdw 2.357 3.040 ... (remaining 103844 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: 2.200 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.060 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13807 Z= 0.230 Angle : 0.488 7.974 18666 Z= 0.263 Chirality : 0.044 0.136 2049 Planarity : 0.005 0.049 2408 Dihedral : 13.451 88.138 5290 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.15 (0.20), residues: 1676 helix: 1.01 (0.22), residues: 593 sheet: -0.20 (0.35), residues: 227 loop : -0.85 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 622 HIS 0.003 0.001 HIS B 533 PHE 0.015 0.001 PHE B 854 TYR 0.022 0.001 TYR B 458 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7372 (mp0) cc_final: 0.7095 (mp0) REVERT: A 197 TYR cc_start: 0.8279 (p90) cc_final: 0.7844 (p90) REVERT: A 274 ASN cc_start: 0.8485 (m-40) cc_final: 0.8254 (m110) REVERT: A 339 VAL cc_start: 0.8489 (m) cc_final: 0.8228 (t) REVERT: A 352 LYS cc_start: 0.7626 (ttmm) cc_final: 0.7369 (ttmm) REVERT: A 365 SER cc_start: 0.8624 (t) cc_final: 0.8328 (m) REVERT: A 367 GLU cc_start: 0.7992 (mp0) cc_final: 0.7339 (mt-10) REVERT: A 374 LEU cc_start: 0.8541 (mm) cc_final: 0.8203 (mp) REVERT: A 444 MET cc_start: 0.8465 (mtp) cc_final: 0.8208 (mtm) REVERT: A 462 GLU cc_start: 0.7774 (pm20) cc_final: 0.7545 (pm20) REVERT: A 520 MET cc_start: 0.8577 (mtt) cc_final: 0.8367 (mtt) REVERT: A 590 VAL cc_start: 0.7845 (p) cc_final: 0.7601 (m) REVERT: B 19 ASP cc_start: 0.8213 (m-30) cc_final: 0.7886 (m-30) REVERT: B 67 LEU cc_start: 0.7878 (mt) cc_final: 0.7651 (mp) REVERT: B 73 LYS cc_start: 0.7526 (tttt) cc_final: 0.7322 (tmmm) REVERT: B 79 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7622 (mmmt) REVERT: B 124 ASN cc_start: 0.8288 (m-40) cc_final: 0.8059 (m-40) REVERT: B 134 ASP cc_start: 0.7551 (t70) cc_final: 0.7279 (t0) REVERT: B 178 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6415 (mm-30) REVERT: B 208 ARG cc_start: 0.8333 (mtt90) cc_final: 0.8127 (mtt-85) REVERT: B 225 ASP cc_start: 0.7809 (t0) cc_final: 0.7539 (t0) REVERT: B 247 LEU cc_start: 0.8293 (tp) cc_final: 0.8090 (tt) REVERT: B 425 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7622 (ttpt) REVERT: B 426 VAL cc_start: 0.7823 (p) cc_final: 0.7616 (m) REVERT: B 428 GLU cc_start: 0.7141 (mp0) cc_final: 0.6808 (mp0) REVERT: B 550 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7680 (mtpp) REVERT: B 602 ASN cc_start: 0.7464 (m-40) cc_final: 0.7232 (m-40) REVERT: B 661 LYS cc_start: 0.8315 (tttm) cc_final: 0.8044 (tttm) REVERT: B 663 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8123 (ttpt) REVERT: B 692 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6976 (mt-10) REVERT: B 704 PHE cc_start: 0.8583 (m-80) cc_final: 0.8349 (m-80) REVERT: B 766 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7606 (mtp-110) REVERT: B 841 SER cc_start: 0.7996 (m) cc_final: 0.7735 (p) REVERT: B 863 ASP cc_start: 0.8275 (m-30) cc_final: 0.8021 (m-30) REVERT: B 1028 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7847 (mmtt) REVERT: B 1132 ARG cc_start: 0.8294 (ptt90) cc_final: 0.8074 (ptt-90) REVERT: B 1155 ILE cc_start: 0.8263 (pt) cc_final: 0.8057 (mt) REVERT: B 1170 ASN cc_start: 0.8363 (t0) cc_final: 0.8082 (t0) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 1.7670 time to fit residues: 694.3265 Evaluate side-chains 315 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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: 2.9990 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.3980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 482 ASN A 557 GLN B 720 ASN B 735 ASN B 754 ASN B1104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101753 restraints weight = 19158.116| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.86 r_work: 0.3156 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13807 Z= 0.190 Angle : 0.494 6.718 18666 Z= 0.262 Chirality : 0.044 0.138 2049 Planarity : 0.005 0.045 2408 Dihedral : 3.931 25.436 1855 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.99 % Allowed : 10.71 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.17 (0.20), residues: 1676 helix: 1.26 (0.21), residues: 611 sheet: 0.12 (0.37), residues: 214 loop : -0.72 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 PHE 0.014 0.001 PHE A 309 TYR 0.012 0.001 TYR B 458 ARG 0.007 0.000 ARG B1079 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 317 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7725 (mp0) cc_final: 0.7458 (mp0) REVERT: A 197 TYR cc_start: 0.8333 (p90) cc_final: 0.7952 (p90) REVERT: A 225 VAL cc_start: 0.7587 (t) cc_final: 0.7363 (m) REVERT: A 284 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7750 (tt) REVERT: A 290 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8138 (ttpp) REVERT: A 335 TYR cc_start: 0.8362 (m-80) cc_final: 0.7756 (m-80) REVERT: A 365 SER cc_start: 0.8586 (t) cc_final: 0.8372 (m) REVERT: A 367 GLU cc_start: 0.8048 (mp0) cc_final: 0.7402 (mp0) REVERT: A 374 LEU cc_start: 0.8415 (mm) cc_final: 0.8122 (mp) REVERT: A 465 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7839 (tttp) REVERT: A 520 MET cc_start: 0.8539 (mtt) cc_final: 0.8322 (mtt) REVERT: B 17 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 19 ASP cc_start: 0.8272 (m-30) cc_final: 0.7975 (m-30) REVERT: B 67 LEU cc_start: 0.7879 (mt) cc_final: 0.7651 (mp) REVERT: B 73 LYS cc_start: 0.7238 (tttt) cc_final: 0.6974 (tmmm) REVERT: B 74 GLU cc_start: 0.7776 (mp0) cc_final: 0.7543 (mp0) REVERT: B 79 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7720 (mmmt) REVERT: B 124 ASN cc_start: 0.8286 (m-40) cc_final: 0.8076 (m-40) REVERT: B 134 ASP cc_start: 0.7694 (t70) cc_final: 0.7347 (t0) REVERT: B 225 ASP cc_start: 0.7977 (t0) cc_final: 0.7709 (t0) REVERT: B 226 VAL cc_start: 0.8437 (t) cc_final: 0.8143 (m) REVERT: B 266 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7768 (ttpp) REVERT: B 267 MET cc_start: 0.8440 (mtm) cc_final: 0.8227 (mtp) REVERT: B 425 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7642 (ttpt) REVERT: B 428 GLU cc_start: 0.7240 (mp0) cc_final: 0.6889 (mp0) REVERT: B 506 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7773 (mm-30) REVERT: B 554 LEU cc_start: 0.8055 (mt) cc_final: 0.7727 (mm) REVERT: B 573 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8199 (ttpp) REVERT: B 600 ASP cc_start: 0.7887 (t0) cc_final: 0.7661 (m-30) REVERT: B 625 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: B 754 ASN cc_start: 0.7391 (t0) cc_final: 0.6922 (t0) REVERT: B 841 SER cc_start: 0.7700 (m) cc_final: 0.7490 (p) REVERT: B 863 ASP cc_start: 0.8490 (m-30) cc_final: 0.8219 (m-30) REVERT: B 1079 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7353 (ttm-80) REVERT: B 1132 ARG cc_start: 0.8329 (ptt90) cc_final: 0.8093 (ptt-90) REVERT: B 1170 ASN cc_start: 0.8340 (t0) cc_final: 0.8052 (t0) outliers start: 29 outliers final: 12 residues processed: 322 average time/residue: 1.8344 time to fit residues: 631.1819 Evaluate side-chains 325 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 482 ASN A 557 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101315 restraints weight = 19255.099| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.86 r_work: 0.3149 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13807 Z= 0.224 Angle : 0.496 6.732 18666 Z= 0.262 Chirality : 0.045 0.134 2049 Planarity : 0.005 0.052 2408 Dihedral : 3.961 25.705 1855 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.99 % Allowed : 13.66 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.17 (0.20), residues: 1676 helix: 1.30 (0.21), residues: 612 sheet: 0.18 (0.37), residues: 212 loop : -0.78 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 PHE 0.016 0.001 PHE A 309 TYR 0.015 0.001 TYR B 458 ARG 0.005 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 310 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7750 (mp0) cc_final: 0.7482 (mp0) REVERT: A 197 TYR cc_start: 0.8347 (p90) cc_final: 0.7970 (p90) REVERT: A 225 VAL cc_start: 0.7643 (t) cc_final: 0.7377 (m) REVERT: A 244 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7769 (mmm160) REVERT: A 284 ILE cc_start: 0.8239 (mt) cc_final: 0.8017 (mm) REVERT: A 290 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7861 (ttpp) REVERT: A 335 TYR cc_start: 0.8346 (m-80) cc_final: 0.7777 (m-80) REVERT: A 365 SER cc_start: 0.8585 (t) cc_final: 0.8378 (m) REVERT: A 367 GLU cc_start: 0.8125 (mp0) cc_final: 0.7461 (mp0) REVERT: A 374 LEU cc_start: 0.8450 (mm) cc_final: 0.8158 (mp) REVERT: A 465 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7883 (tttm) REVERT: B 17 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7818 (mm-30) REVERT: B 67 LEU cc_start: 0.7888 (mt) cc_final: 0.7659 (mp) REVERT: B 73 LYS cc_start: 0.7191 (tttt) cc_final: 0.6958 (tmmm) REVERT: B 79 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7701 (mmmt) REVERT: B 124 ASN cc_start: 0.8288 (m-40) cc_final: 0.8076 (m-40) REVERT: B 134 ASP cc_start: 0.7706 (t70) cc_final: 0.7342 (t0) REVERT: B 168 LYS cc_start: 0.8796 (tppp) cc_final: 0.8555 (tppp) REVERT: B 225 ASP cc_start: 0.7972 (t0) cc_final: 0.7662 (t0) REVERT: B 226 VAL cc_start: 0.8353 (t) cc_final: 0.8027 (m) REVERT: B 267 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8237 (mtp) REVERT: B 425 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7628 (ttpt) REVERT: B 428 GLU cc_start: 0.7245 (mp0) cc_final: 0.6874 (mp0) REVERT: B 506 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7742 (mm-30) REVERT: B 573 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8211 (ttpp) REVERT: B 625 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7813 (mpp) REVERT: B 737 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 863 ASP cc_start: 0.8493 (m-30) cc_final: 0.8206 (m-30) REVERT: B 1019 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: B 1023 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: B 1141 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7413 (m) REVERT: B 1170 ASN cc_start: 0.8362 (t0) cc_final: 0.8053 (t0) outliers start: 29 outliers final: 15 residues processed: 321 average time/residue: 1.7801 time to fit residues: 609.6416 Evaluate side-chains 328 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 307 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 0.5980 chunk 136 optimal weight: 0.0970 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 482 ASN A 557 GLN B 602 ASN B 735 ASN B1104 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101102 restraints weight = 19195.015| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.86 r_work: 0.3141 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13807 Z= 0.224 Angle : 0.496 6.643 18666 Z= 0.262 Chirality : 0.045 0.133 2049 Planarity : 0.005 0.045 2408 Dihedral : 3.962 25.736 1855 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.95 % Allowed : 14.28 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.21 (0.20), residues: 1676 helix: 1.33 (0.21), residues: 618 sheet: 0.15 (0.36), residues: 215 loop : -0.76 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 PHE 0.013 0.001 PHE B 467 TYR 0.013 0.001 TYR B 458 ARG 0.009 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7756 (mp0) cc_final: 0.7503 (mp0) REVERT: A 197 TYR cc_start: 0.8354 (p90) cc_final: 0.8003 (p90) REVERT: A 225 VAL cc_start: 0.7677 (t) cc_final: 0.7380 (m) REVERT: A 244 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7927 (mmm-85) REVERT: A 335 TYR cc_start: 0.8386 (m-80) cc_final: 0.7787 (m-80) REVERT: A 367 GLU cc_start: 0.8152 (mp0) cc_final: 0.7453 (mt-10) REVERT: A 374 LEU cc_start: 0.8471 (mm) cc_final: 0.8159 (mp) REVERT: A 462 GLU cc_start: 0.7831 (pm20) cc_final: 0.7594 (pm20) REVERT: A 465 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7875 (tttm) REVERT: A 502 GLU cc_start: 0.7701 (mp0) cc_final: 0.7162 (mp0) REVERT: A 522 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 67 LEU cc_start: 0.7905 (mt) cc_final: 0.7688 (mp) REVERT: B 79 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7703 (mmmt) REVERT: B 83 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 124 ASN cc_start: 0.8304 (m-40) cc_final: 0.8083 (m-40) REVERT: B 126 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8308 (mtmp) REVERT: B 134 ASP cc_start: 0.7738 (t70) cc_final: 0.7371 (t0) REVERT: B 225 ASP cc_start: 0.7962 (t0) cc_final: 0.7657 (t0) REVERT: B 226 VAL cc_start: 0.8333 (t) cc_final: 0.7977 (m) REVERT: B 266 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7785 (ttpp) REVERT: B 425 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7743 (ttpt) REVERT: B 506 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 554 LEU cc_start: 0.8165 (mt) cc_final: 0.7877 (mm) REVERT: B 573 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8206 (ttpp) REVERT: B 625 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7832 (mpp) REVERT: B 685 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8062 (mmt180) REVERT: B 737 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 754 ASN cc_start: 0.7590 (t0) cc_final: 0.6962 (t0) REVERT: B 863 ASP cc_start: 0.8528 (m-30) cc_final: 0.8196 (m-30) REVERT: B 1019 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: B 1023 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 1079 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7388 (ttm-80) REVERT: B 1141 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7424 (m) REVERT: B 1170 ASN cc_start: 0.8360 (t0) cc_final: 0.8036 (t0) outliers start: 43 outliers final: 21 residues processed: 327 average time/residue: 1.8490 time to fit residues: 643.8266 Evaluate side-chains 331 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 302 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 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 415 GLN A 482 ASN A 557 GLN B1104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100637 restraints weight = 19280.578| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.87 r_work: 0.3131 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13807 Z= 0.243 Angle : 0.504 6.728 18666 Z= 0.265 Chirality : 0.045 0.134 2049 Planarity : 0.005 0.043 2408 Dihedral : 3.996 25.984 1855 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.54 % Allowed : 15.58 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.21 (0.20), residues: 1676 helix: 1.34 (0.21), residues: 618 sheet: 0.22 (0.36), residues: 215 loop : -0.78 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 PHE 0.014 0.002 PHE B 467 TYR 0.013 0.001 TYR B 458 ARG 0.008 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7737 (mp0) cc_final: 0.7476 (mp0) REVERT: A 197 TYR cc_start: 0.8350 (p90) cc_final: 0.7995 (p90) REVERT: A 225 VAL cc_start: 0.7713 (t) cc_final: 0.7388 (m) REVERT: A 335 TYR cc_start: 0.8410 (m-80) cc_final: 0.7823 (m-80) REVERT: A 367 GLU cc_start: 0.8175 (mp0) cc_final: 0.7490 (mt-10) REVERT: A 374 LEU cc_start: 0.8484 (mm) cc_final: 0.8176 (mp) REVERT: A 462 GLU cc_start: 0.7891 (pm20) cc_final: 0.7637 (pm20) REVERT: A 465 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7864 (tttm) REVERT: A 502 GLU cc_start: 0.7731 (mp0) cc_final: 0.7222 (mp0) REVERT: A 515 LYS cc_start: 0.8162 (mppt) cc_final: 0.7890 (mmmm) REVERT: B 67 LEU cc_start: 0.7904 (mt) cc_final: 0.7689 (mp) REVERT: B 79 LYS cc_start: 0.8130 (mmtp) cc_final: 0.7690 (mmmt) REVERT: B 83 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 126 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8298 (mtmp) REVERT: B 134 ASP cc_start: 0.7763 (t70) cc_final: 0.7404 (t0) REVERT: B 197 ARG cc_start: 0.7561 (mmp80) cc_final: 0.7308 (mmp80) REVERT: B 225 ASP cc_start: 0.7968 (t0) cc_final: 0.7669 (t0) REVERT: B 226 VAL cc_start: 0.8315 (t) cc_final: 0.7958 (m) REVERT: B 270 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: B 425 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7743 (ttpt) REVERT: B 505 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7951 (mtmt) REVERT: B 506 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 573 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8192 (ttpp) REVERT: B 576 VAL cc_start: 0.8845 (t) cc_final: 0.8581 (m) REVERT: B 625 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: B 685 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8134 (mmt180) REVERT: B 737 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: B 754 ASN cc_start: 0.7628 (t0) cc_final: 0.7038 (t0) REVERT: B 1019 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: B 1023 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: B 1141 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7434 (m) REVERT: B 1170 ASN cc_start: 0.8365 (t0) cc_final: 0.8038 (t0) outliers start: 37 outliers final: 20 residues processed: 320 average time/residue: 1.8979 time to fit residues: 646.8536 Evaluate side-chains 327 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1156 GLU Chi-restraints excluded: chain B residue 1213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 157 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 482 ASN A 557 GLN B 602 ASN B 720 ASN B1104 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100971 restraints weight = 19456.683| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.87 r_work: 0.3141 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13807 Z= 0.222 Angle : 0.496 6.454 18666 Z= 0.261 Chirality : 0.045 0.131 2049 Planarity : 0.005 0.044 2408 Dihedral : 3.963 25.842 1855 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.40 % Allowed : 16.40 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.25 (0.20), residues: 1676 helix: 1.39 (0.21), residues: 619 sheet: 0.20 (0.36), residues: 215 loop : -0.77 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 PHE 0.014 0.001 PHE A 322 TYR 0.010 0.001 TYR A 305 ARG 0.005 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 1.680 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7752 (mp0) cc_final: 0.7493 (mp0) REVERT: A 197 TYR cc_start: 0.8360 (p90) cc_final: 0.8016 (p90) REVERT: A 225 VAL cc_start: 0.7696 (t) cc_final: 0.7390 (m) REVERT: A 244 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7794 (mtp85) REVERT: A 335 TYR cc_start: 0.8409 (m-80) cc_final: 0.7802 (m-80) REVERT: A 367 GLU cc_start: 0.8190 (mp0) cc_final: 0.7471 (mt-10) REVERT: A 374 LEU cc_start: 0.8462 (mm) cc_final: 0.8157 (mp) REVERT: A 462 GLU cc_start: 0.7869 (pm20) cc_final: 0.7601 (pm20) REVERT: A 465 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7860 (tttm) REVERT: A 502 GLU cc_start: 0.7672 (mp0) cc_final: 0.7188 (mp0) REVERT: A 515 LYS cc_start: 0.8211 (mppt) cc_final: 0.7929 (mmmm) REVERT: A 522 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 67 LEU cc_start: 0.7901 (mt) cc_final: 0.7697 (mp) REVERT: B 79 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7678 (mmmt) REVERT: B 83 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 134 ASP cc_start: 0.7768 (t70) cc_final: 0.7389 (t0) REVERT: B 168 LYS cc_start: 0.8716 (tppp) cc_final: 0.8293 (tppt) REVERT: B 197 ARG cc_start: 0.7543 (mmp80) cc_final: 0.7305 (mmp80) REVERT: B 221 GLU cc_start: 0.7556 (mp0) cc_final: 0.7288 (pm20) REVERT: B 225 ASP cc_start: 0.7954 (t0) cc_final: 0.7650 (t0) REVERT: B 226 VAL cc_start: 0.8297 (t) cc_final: 0.7947 (m) REVERT: B 425 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7736 (ttpt) REVERT: B 506 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 554 LEU cc_start: 0.8160 (mt) cc_final: 0.7881 (mm) REVERT: B 573 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8183 (ttpp) REVERT: B 576 VAL cc_start: 0.8852 (t) cc_final: 0.8595 (m) REVERT: B 625 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7838 (mpp) REVERT: B 711 HIS cc_start: 0.8532 (t70) cc_final: 0.8210 (t70) REVERT: B 737 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: B 754 ASN cc_start: 0.7636 (t0) cc_final: 0.7097 (t0) REVERT: B 776 GLU cc_start: 0.8126 (tp30) cc_final: 0.7781 (tp30) REVERT: B 1019 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: B 1023 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 1079 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7383 (ttm-80) REVERT: B 1114 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7828 (ttm110) REVERT: B 1141 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7473 (m) REVERT: B 1170 ASN cc_start: 0.8361 (t0) cc_final: 0.8031 (t0) REVERT: B 1214 MET cc_start: 0.8362 (ttp) cc_final: 0.8052 (mmm) outliers start: 35 outliers final: 18 residues processed: 316 average time/residue: 1.8546 time to fit residues: 623.8765 Evaluate side-chains 316 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 139 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 16 optimal weight: 0.0270 chunk 41 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 557 GLN B 124 ASN B1104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101783 restraints weight = 19266.041| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.85 r_work: 0.3143 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13807 Z= 0.176 Angle : 0.475 5.977 18666 Z= 0.250 Chirality : 0.044 0.131 2049 Planarity : 0.004 0.044 2408 Dihedral : 3.858 25.295 1855 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.13 % Allowed : 17.23 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.32 (0.21), residues: 1676 helix: 1.48 (0.21), residues: 620 sheet: 0.12 (0.37), residues: 214 loop : -0.72 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 PHE 0.013 0.001 PHE A 322 TYR 0.009 0.001 TYR A 197 ARG 0.005 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7766 (mp0) cc_final: 0.7500 (mp0) REVERT: A 197 TYR cc_start: 0.8331 (p90) cc_final: 0.7975 (p90) REVERT: A 225 VAL cc_start: 0.7620 (t) cc_final: 0.7335 (m) REVERT: A 244 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7810 (mtp85) REVERT: A 284 ILE cc_start: 0.8227 (mt) cc_final: 0.7993 (mm) REVERT: A 335 TYR cc_start: 0.8392 (m-80) cc_final: 0.7749 (m-80) REVERT: A 365 SER cc_start: 0.8573 (t) cc_final: 0.8342 (m) REVERT: A 367 GLU cc_start: 0.8160 (mp0) cc_final: 0.7401 (mt-10) REVERT: A 374 LEU cc_start: 0.8442 (mm) cc_final: 0.8147 (mp) REVERT: A 465 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7838 (tttm) REVERT: A 502 GLU cc_start: 0.7674 (mp0) cc_final: 0.7172 (mp0) REVERT: A 515 LYS cc_start: 0.8203 (mppt) cc_final: 0.7930 (mmmm) REVERT: B 73 LYS cc_start: 0.6965 (tttt) cc_final: 0.6762 (ttpp) REVERT: B 79 LYS cc_start: 0.8105 (mmtp) cc_final: 0.7657 (mmmt) REVERT: B 83 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 134 ASP cc_start: 0.7783 (t70) cc_final: 0.7407 (t0) REVERT: B 168 LYS cc_start: 0.8709 (tppp) cc_final: 0.8289 (tppt) REVERT: B 197 ARG cc_start: 0.7558 (mmp80) cc_final: 0.7293 (mmp80) REVERT: B 221 GLU cc_start: 0.7560 (mp0) cc_final: 0.7285 (pm20) REVERT: B 225 ASP cc_start: 0.7929 (t0) cc_final: 0.7646 (t0) REVERT: B 425 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7683 (ttpt) REVERT: B 506 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 554 LEU cc_start: 0.8124 (mt) cc_final: 0.7834 (mm) REVERT: B 573 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8161 (ttpp) REVERT: B 576 VAL cc_start: 0.8845 (t) cc_final: 0.8579 (m) REVERT: B 625 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7829 (mpp) REVERT: B 711 HIS cc_start: 0.8534 (t70) cc_final: 0.8210 (t70) REVERT: B 737 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: B 754 ASN cc_start: 0.7624 (t0) cc_final: 0.7086 (t0) REVERT: B 757 LEU cc_start: 0.7974 (mp) cc_final: 0.7643 (mt) REVERT: B 776 GLU cc_start: 0.8077 (tp30) cc_final: 0.7725 (tp30) REVERT: B 1019 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: B 1023 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: B 1141 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7504 (m) REVERT: B 1170 ASN cc_start: 0.8329 (t0) cc_final: 0.8037 (t0) REVERT: B 1214 MET cc_start: 0.8374 (ttp) cc_final: 0.8070 (mmm) outliers start: 31 outliers final: 16 residues processed: 314 average time/residue: 1.8112 time to fit residues: 606.4342 Evaluate side-chains 316 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 294 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 557 GLN B 124 ASN B 602 ASN B1104 HIS 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 = 0.115206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101356 restraints weight = 19341.312| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.85 r_work: 0.3149 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.207 Angle : 0.494 7.001 18666 Z= 0.259 Chirality : 0.044 0.143 2049 Planarity : 0.005 0.049 2408 Dihedral : 3.901 25.445 1855 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.13 % Allowed : 18.05 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.30 (0.21), residues: 1676 helix: 1.48 (0.21), residues: 620 sheet: 0.08 (0.37), residues: 214 loop : -0.73 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 PHE 0.014 0.001 PHE A 322 TYR 0.010 0.001 TYR A 305 ARG 0.013 0.000 ARG B1079 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7728 (mp0) cc_final: 0.7479 (mp0) REVERT: A 197 TYR cc_start: 0.8330 (p90) cc_final: 0.7974 (p90) REVERT: A 284 ILE cc_start: 0.8255 (mt) cc_final: 0.8007 (mm) REVERT: A 335 TYR cc_start: 0.8409 (m-80) cc_final: 0.7760 (m-80) REVERT: A 366 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7130 (mtm-85) REVERT: A 367 GLU cc_start: 0.8166 (mp0) cc_final: 0.7445 (mp0) REVERT: A 374 LEU cc_start: 0.8454 (mm) cc_final: 0.8146 (mp) REVERT: A 465 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7851 (tttm) REVERT: A 502 GLU cc_start: 0.7644 (mp0) cc_final: 0.7142 (mp0) REVERT: A 515 LYS cc_start: 0.8212 (mppt) cc_final: 0.7945 (mmmm) REVERT: A 522 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 73 LYS cc_start: 0.6968 (tttt) cc_final: 0.6767 (ttpp) REVERT: B 79 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7700 (mmmt) REVERT: B 83 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: B 134 ASP cc_start: 0.7794 (t70) cc_final: 0.7393 (t0) REVERT: B 197 ARG cc_start: 0.7564 (mmp80) cc_final: 0.7273 (mmp80) REVERT: B 221 GLU cc_start: 0.7615 (mp0) cc_final: 0.7345 (pm20) REVERT: B 425 LYS cc_start: 0.7897 (ttmm) cc_final: 0.7635 (ttpt) REVERT: B 506 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 573 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8176 (ttpp) REVERT: B 576 VAL cc_start: 0.8850 (t) cc_final: 0.8576 (m) REVERT: B 625 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7807 (mpp) REVERT: B 711 HIS cc_start: 0.8520 (t70) cc_final: 0.8177 (t70) REVERT: B 737 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: B 754 ASN cc_start: 0.7640 (t0) cc_final: 0.7102 (t0) REVERT: B 776 GLU cc_start: 0.8078 (tp30) cc_final: 0.7715 (tp30) REVERT: B 1019 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 1023 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: B 1079 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7326 (ttm-80) REVERT: B 1141 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7486 (m) REVERT: B 1170 ASN cc_start: 0.8355 (t0) cc_final: 0.8042 (t0) REVERT: B 1214 MET cc_start: 0.8341 (ttp) cc_final: 0.8042 (mmm) outliers start: 31 outliers final: 20 residues processed: 306 average time/residue: 1.8348 time to fit residues: 599.7394 Evaluate side-chains 320 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 157 optimal weight: 0.8980 chunk 121 optimal weight: 0.1980 chunk 60 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 153 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 557 GLN B 124 ASN B 602 ASN B1104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102202 restraints weight = 19208.480| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.86 r_work: 0.3166 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.002 0.029 13807 Z= 0.162 Angle : 0.478 6.948 18666 Z= 0.250 Chirality : 0.043 0.130 2049 Planarity : 0.004 0.050 2408 Dihedral : 3.771 24.975 1855 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.92 % Allowed : 18.67 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.39 (0.21), residues: 1676 helix: 1.59 (0.21), residues: 615 sheet: 0.11 (0.36), residues: 213 loop : -0.69 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 PHE 0.014 0.001 PHE A 322 TYR 0.008 0.001 TYR A 305 ARG 0.011 0.000 ARG B1079 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7749 (mp0) cc_final: 0.7482 (mp0) REVERT: A 197 TYR cc_start: 0.8321 (p90) cc_final: 0.7979 (p90) REVERT: A 284 ILE cc_start: 0.8215 (mt) cc_final: 0.7997 (mm) REVERT: A 335 TYR cc_start: 0.8382 (m-80) cc_final: 0.7760 (m-80) REVERT: A 367 GLU cc_start: 0.8114 (mp0) cc_final: 0.7319 (mt-10) REVERT: A 374 LEU cc_start: 0.8420 (mm) cc_final: 0.8145 (mp) REVERT: A 465 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7825 (tttm) REVERT: A 502 GLU cc_start: 0.7672 (mp0) cc_final: 0.7177 (mp0) REVERT: A 515 LYS cc_start: 0.8190 (mppt) cc_final: 0.7932 (mmmm) REVERT: A 605 GLU cc_start: 0.7936 (tt0) cc_final: 0.7734 (tt0) REVERT: B 79 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7626 (mmmt) REVERT: B 83 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: B 134 ASP cc_start: 0.7784 (t70) cc_final: 0.7413 (t0) REVERT: B 168 LYS cc_start: 0.8665 (tppp) cc_final: 0.8372 (tppt) REVERT: B 197 ARG cc_start: 0.7511 (mmp80) cc_final: 0.7301 (mmp80) REVERT: B 221 GLU cc_start: 0.7594 (mp0) cc_final: 0.7328 (pm20) REVERT: B 266 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7804 (ttpp) REVERT: B 425 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7659 (ttpt) REVERT: B 506 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 550 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7848 (mtpp) REVERT: B 554 LEU cc_start: 0.8099 (mt) cc_final: 0.7811 (mm) REVERT: B 573 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8162 (ttpp) REVERT: B 576 VAL cc_start: 0.8840 (t) cc_final: 0.8583 (m) REVERT: B 625 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7834 (mpp) REVERT: B 711 HIS cc_start: 0.8516 (t70) cc_final: 0.8156 (t70) REVERT: B 737 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 754 ASN cc_start: 0.7639 (t0) cc_final: 0.7109 (t0) REVERT: B 757 LEU cc_start: 0.7962 (mp) cc_final: 0.7643 (mt) REVERT: B 776 GLU cc_start: 0.8066 (tp30) cc_final: 0.7684 (tp30) REVERT: B 1019 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: B 1023 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: B 1141 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7503 (m) REVERT: B 1170 ASN cc_start: 0.8329 (t0) cc_final: 0.8043 (t0) REVERT: B 1214 MET cc_start: 0.8404 (ttp) cc_final: 0.8094 (tpp) outliers start: 28 outliers final: 16 residues processed: 307 average time/residue: 1.8259 time to fit residues: 597.3419 Evaluate side-chains 317 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 557 GLN B 124 ASN B 602 ASN B1104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101457 restraints weight = 19263.496| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.86 r_work: 0.3153 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.203 Angle : 0.499 7.341 18666 Z= 0.260 Chirality : 0.044 0.130 2049 Planarity : 0.005 0.060 2408 Dihedral : 3.842 25.138 1855 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.78 % Allowed : 19.08 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.35 (0.21), residues: 1676 helix: 1.52 (0.21), residues: 621 sheet: 0.06 (0.36), residues: 214 loop : -0.70 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 PHE 0.014 0.001 PHE B 467 TYR 0.010 0.001 TYR A 305 ARG 0.014 0.000 ARG B1079 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7759 (mp0) cc_final: 0.7510 (mp0) REVERT: A 197 TYR cc_start: 0.8324 (p90) cc_final: 0.7985 (p90) REVERT: A 284 ILE cc_start: 0.8243 (mt) cc_final: 0.8010 (mm) REVERT: A 335 TYR cc_start: 0.8394 (m-80) cc_final: 0.7757 (m-80) REVERT: A 367 GLU cc_start: 0.8128 (mp0) cc_final: 0.7321 (mt-10) REVERT: A 374 LEU cc_start: 0.8451 (mm) cc_final: 0.8143 (mp) REVERT: A 417 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8103 (t) REVERT: A 465 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7824 (tttm) REVERT: A 502 GLU cc_start: 0.7668 (mp0) cc_final: 0.7168 (mp0) REVERT: A 515 LYS cc_start: 0.8184 (mppt) cc_final: 0.7888 (mmmm) REVERT: A 605 GLU cc_start: 0.7922 (tt0) cc_final: 0.7719 (tt0) REVERT: B 79 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7689 (mmmt) REVERT: B 83 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: B 134 ASP cc_start: 0.7792 (t70) cc_final: 0.7419 (t0) REVERT: B 168 LYS cc_start: 0.8654 (tppp) cc_final: 0.8293 (tppt) REVERT: B 197 ARG cc_start: 0.7508 (mmp80) cc_final: 0.7290 (mmp80) REVERT: B 266 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: B 425 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7676 (ttpt) REVERT: B 505 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7931 (mtmt) REVERT: B 506 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 554 LEU cc_start: 0.8164 (mt) cc_final: 0.7873 (mm) REVERT: B 573 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8176 (ttpp) REVERT: B 576 VAL cc_start: 0.8858 (t) cc_final: 0.8592 (m) REVERT: B 625 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: B 711 HIS cc_start: 0.8507 (t70) cc_final: 0.8156 (t70) REVERT: B 737 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 754 ASN cc_start: 0.7674 (t0) cc_final: 0.7144 (t0) REVERT: B 776 GLU cc_start: 0.8088 (tp30) cc_final: 0.7711 (tp30) REVERT: B 1019 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: B 1023 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 1132 ARG cc_start: 0.8489 (ptt90) cc_final: 0.8156 (ptt-90) REVERT: B 1141 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7464 (m) REVERT: B 1170 ASN cc_start: 0.8334 (t0) cc_final: 0.8033 (t0) REVERT: B 1214 MET cc_start: 0.8396 (ttp) cc_final: 0.8115 (mmm) outliers start: 26 outliers final: 18 residues processed: 305 average time/residue: 1.9492 time to fit residues: 636.2232 Evaluate side-chains 322 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 60 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 557 GLN B 124 ASN B 602 ASN B1104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102843 restraints weight = 19369.492| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.88 r_work: 0.3175 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13807 Z= 0.147 Angle : 0.475 6.960 18666 Z= 0.247 Chirality : 0.043 0.131 2049 Planarity : 0.004 0.059 2408 Dihedral : 3.671 24.441 1855 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.78 % Allowed : 19.08 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.47 (0.21), residues: 1676 helix: 1.68 (0.21), residues: 614 sheet: 0.12 (0.36), residues: 213 loop : -0.64 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.004 0.000 HIS B 478 PHE 0.013 0.001 PHE A 322 TYR 0.008 0.001 TYR A 197 ARG 0.013 0.000 ARG B1079 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12658.39 seconds wall clock time: 222 minutes 53.39 seconds (13373.39 seconds total)