Starting phenix.real_space_refine on Thu Sep 18 03:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f29_50140/09_2025/9f29_50140.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f29_50140/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9f29_50140/09_2025/9f29_50140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f29_50140/09_2025/9f29_50140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f29_50140/09_2025/9f29_50140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f29_50140/09_2025/9f29_50140.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 3 6.06 5 S 49 5.16 5 C 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.39, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 598.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 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: 0.57 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: 2.69 Time building geometry restraints manager: 1.28 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: 2.720 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- 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 : 0.004 0.042 13819 Z= 0.143 Angle : 0.517 16.856 18684 Z= 0.265 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (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 ARG 0.003 0.000 ARG B 29 TYR 0.022 0.001 TYR B 458 PHE 0.015 0.001 PHE B 854 TRP 0.007 0.001 TRP B 622 HIS 0.003 0.001 HIS B 533 Details of bonding type rmsd covalent geometry : bond 0.00350 (13807) covalent geometry : angle 0.48775 (18666) hydrogen bonds : bond 0.20499 ( 539) hydrogen bonds : angle 6.19663 ( 1467) metal coordination : bond 0.00877 ( 12) metal coordination : angle 5.52552 ( 18) *********************** 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 : 0.532 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: 0.8163 time to fit residues: 320.7466 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 : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.114020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100218 restraints weight = 19278.164| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.86 r_work: 0.3128 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13819 Z= 0.188 Angle : 0.575 14.952 18684 Z= 0.290 Chirality : 0.047 0.141 2049 Planarity : 0.005 0.046 2408 Dihedral : 4.175 26.542 1855 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.33 % Allowed : 10.50 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.20), residues: 1676 helix: 1.09 (0.21), residues: 611 sheet: 0.11 (0.37), residues: 217 loop : -0.83 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1079 TYR 0.020 0.002 TYR B 458 PHE 0.015 0.002 PHE A 309 TRP 0.009 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00476 (13807) covalent geometry : angle 0.54477 (18666) hydrogen bonds : bond 0.05517 ( 539) hydrogen bonds : angle 4.69981 ( 1467) metal coordination : bond 0.00927 ( 12) metal coordination : angle 5.99583 ( 18) *********************** 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: 34 poor density : 312 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7739 (mp0) cc_final: 0.7464 (mp0) REVERT: A 225 VAL cc_start: 0.7709 (t) cc_final: 0.7399 (m) REVERT: A 284 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 290 LYS cc_start: 0.8358 (ttmm) cc_final: 0.8146 (ttpp) REVERT: A 335 TYR cc_start: 0.8403 (m-80) cc_final: 0.7864 (m-80) REVERT: A 339 VAL cc_start: 0.8565 (m) cc_final: 0.8270 (t) REVERT: A 367 GLU cc_start: 0.8104 (mp0) cc_final: 0.7453 (mp0) REVERT: A 374 LEU cc_start: 0.8460 (mm) cc_final: 0.8134 (mp) REVERT: A 465 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7875 (tttp) REVERT: B 17 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 19 ASP cc_start: 0.8289 (m-30) cc_final: 0.7996 (m-30) REVERT: B 67 LEU cc_start: 0.7897 (mt) cc_final: 0.7646 (mp) REVERT: B 73 LYS cc_start: 0.7401 (tttt) cc_final: 0.7115 (tmmm) REVERT: B 74 GLU cc_start: 0.7786 (mp0) cc_final: 0.7577 (mp0) REVERT: B 79 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7734 (mmmt) REVERT: B 97 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7879 (mtpp) REVERT: B 124 ASN cc_start: 0.8315 (m-40) cc_final: 0.8100 (m-40) REVERT: B 134 ASP cc_start: 0.7726 (t70) cc_final: 0.7379 (t0) REVERT: B 208 ARG cc_start: 0.8335 (mtt90) cc_final: 0.8107 (mtt-85) REVERT: B 225 ASP cc_start: 0.8000 (t0) cc_final: 0.7748 (t0) REVERT: B 226 VAL cc_start: 0.8470 (t) cc_final: 0.8160 (m) REVERT: B 266 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7849 (ttpp) REVERT: B 425 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7639 (ttpt) REVERT: B 428 GLU cc_start: 0.7252 (mp0) cc_final: 0.6905 (mp0) REVERT: B 506 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7778 (mm-30) REVERT: B 573 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8209 (ttpp) REVERT: B 600 ASP cc_start: 0.7969 (t0) cc_final: 0.7757 (m-30) REVERT: B 602 ASN cc_start: 0.7549 (m-40) cc_final: 0.7344 (m-40) REVERT: B 625 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7821 (mpp) REVERT: B 661 LYS cc_start: 0.8376 (tttm) cc_final: 0.8127 (tttm) REVERT: B 663 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8272 (ttpt) REVERT: B 754 ASN cc_start: 0.7446 (t0) cc_final: 0.6965 (t0) REVERT: B 766 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7837 (mtp-110) REVERT: B 863 ASP cc_start: 0.8505 (m-30) cc_final: 0.8232 (m-30) REVERT: B 1023 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: B 1079 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7401 (ttm-80) REVERT: B 1132 ARG cc_start: 0.8440 (ptt90) cc_final: 0.8176 (ptt-90) REVERT: B 1170 ASN cc_start: 0.8383 (t0) cc_final: 0.8039 (t0) outliers start: 34 outliers final: 13 residues processed: 321 average time/residue: 0.8788 time to fit residues: 300.6885 Evaluate side-chains 320 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 302 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 97 LYS 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 310 MET 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 723 THR Chi-restraints excluded: chain B residue 1023 GLU 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 116 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3464 r_free = 0.3464 target = 0.114405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100621 restraints weight = 19317.400| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.87 r_work: 0.3138 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13819 Z= 0.152 Angle : 0.533 12.427 18684 Z= 0.271 Chirality : 0.045 0.134 2049 Planarity : 0.005 0.051 2408 Dihedral : 4.093 26.263 1855 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.72 % Allowed : 14.07 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.20), residues: 1676 helix: 1.19 (0.21), residues: 611 sheet: 0.12 (0.36), residues: 218 loop : -0.85 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.013 0.001 TYR B 458 PHE 0.015 0.002 PHE A 309 TRP 0.009 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00381 (13807) covalent geometry : angle 0.50942 (18666) hydrogen bonds : bond 0.04802 ( 539) hydrogen bonds : angle 4.45319 ( 1467) metal coordination : bond 0.00699 ( 12) metal coordination : angle 5.09870 ( 18) *********************** 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 328 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7749 (mp0) cc_final: 0.7480 (mp0) REVERT: A 225 VAL cc_start: 0.7704 (t) cc_final: 0.7396 (m) REVERT: A 244 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7848 (mtp-110) REVERT: A 290 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7924 (ttpp) REVERT: A 335 TYR cc_start: 0.8368 (m-80) cc_final: 0.7802 (m-80) REVERT: A 367 GLU cc_start: 0.8134 (mp0) cc_final: 0.7498 (mp0) REVERT: A 374 LEU cc_start: 0.8463 (mm) cc_final: 0.8140 (mp) REVERT: A 515 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7876 (mmmm) REVERT: B 17 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 67 LEU cc_start: 0.7906 (mt) cc_final: 0.7662 (mp) REVERT: B 73 LYS cc_start: 0.7228 (tttt) cc_final: 0.6989 (tmmm) REVERT: B 79 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7690 (mmmt) REVERT: B 124 ASN cc_start: 0.8312 (m-40) cc_final: 0.8088 (m-40) REVERT: B 126 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8324 (mtmp) REVERT: B 134 ASP cc_start: 0.7736 (t70) cc_final: 0.7399 (t0) REVERT: B 168 LYS cc_start: 0.8749 (tppp) cc_final: 0.8239 (tppt) REVERT: B 225 ASP cc_start: 0.7977 (t0) cc_final: 0.7682 (t0) REVERT: B 226 VAL cc_start: 0.8383 (t) cc_final: 0.8044 (m) REVERT: B 425 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7645 (ttpt) REVERT: B 428 GLU cc_start: 0.7247 (mp0) cc_final: 0.6879 (mp0) REVERT: B 506 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7753 (mm-30) REVERT: B 554 LEU cc_start: 0.8156 (mt) cc_final: 0.7862 (mm) REVERT: B 573 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8222 (ttpp) REVERT: B 600 ASP cc_start: 0.7885 (t0) cc_final: 0.7672 (m-30) REVERT: B 625 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7842 (mpp) REVERT: B 661 LYS cc_start: 0.8355 (tttm) cc_final: 0.8123 (tttm) REVERT: B 737 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: B 754 ASN cc_start: 0.7507 (t0) cc_final: 0.7020 (t0) REVERT: B 757 LEU cc_start: 0.7998 (mp) cc_final: 0.7659 (mt) REVERT: B 863 ASP cc_start: 0.8511 (m-30) cc_final: 0.8229 (m-30) REVERT: B 1132 ARG cc_start: 0.8453 (ptt90) cc_final: 0.8150 (ptt-90) REVERT: B 1170 ASN cc_start: 0.8371 (t0) cc_final: 0.8023 (t0) outliers start: 25 outliers final: 16 residues processed: 313 average time/residue: 0.8366 time to fit residues: 279.9578 Evaluate side-chains 316 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 13 MET 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 246 ILE Chi-restraints excluded: chain B residue 261 VAL 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 737 GLU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 1030 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 B1104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100955 restraints weight = 19387.663| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.87 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13819 Z= 0.132 Angle : 0.515 11.243 18684 Z= 0.262 Chirality : 0.044 0.132 2049 Planarity : 0.005 0.044 2408 Dihedral : 3.996 25.909 1855 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.54 % Allowed : 15.17 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1676 helix: 1.30 (0.21), residues: 618 sheet: 0.12 (0.36), residues: 215 loop : -0.82 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 487 TYR 0.011 0.001 TYR B 458 PHE 0.013 0.001 PHE B 467 TRP 0.008 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00329 (13807) covalent geometry : angle 0.49495 (18666) hydrogen bonds : bond 0.04351 ( 539) hydrogen bonds : angle 4.31353 ( 1467) metal coordination : bond 0.00599 ( 12) metal coordination : angle 4.59867 ( 18) *********************** 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 344 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7745 (mp0) cc_final: 0.7488 (mp0) REVERT: A 197 TYR cc_start: 0.8344 (p90) cc_final: 0.7984 (p90) REVERT: A 225 VAL cc_start: 0.7664 (t) cc_final: 0.7372 (m) REVERT: A 244 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7750 (mmm160) REVERT: A 335 TYR cc_start: 0.8375 (m-80) cc_final: 0.7763 (m-80) REVERT: A 367 GLU cc_start: 0.8146 (mp0) cc_final: 0.7455 (mt-10) REVERT: A 374 LEU cc_start: 0.8459 (mm) cc_final: 0.8151 (mp) REVERT: A 462 GLU cc_start: 0.7816 (pm20) cc_final: 0.7608 (pm20) REVERT: A 502 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 515 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7856 (mmmm) REVERT: A 522 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 17 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 67 LEU cc_start: 0.7894 (mt) cc_final: 0.7664 (mp) REVERT: B 79 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7674 (mmmt) REVERT: B 97 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7827 (mtpp) REVERT: B 134 ASP cc_start: 0.7764 (t70) cc_final: 0.7397 (t0) REVERT: B 225 ASP cc_start: 0.7989 (t0) cc_final: 0.7679 (t0) REVERT: B 226 VAL cc_start: 0.8326 (t) cc_final: 0.7974 (m) REVERT: B 425 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7734 (ttpt) REVERT: B 506 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 573 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8204 (ttpp) REVERT: B 625 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: B 737 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: B 754 ASN cc_start: 0.7544 (t0) cc_final: 0.7062 (t0) REVERT: B 757 LEU cc_start: 0.8013 (mp) cc_final: 0.7692 (mt) REVERT: B 863 ASP cc_start: 0.8536 (m-30) cc_final: 0.8221 (m-30) REVERT: B 1019 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: B 1023 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: B 1079 ARG cc_start: 0.7743 (ttm110) cc_final: 0.7394 (ttm-80) REVERT: B 1099 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7832 (mtpt) REVERT: B 1114 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7833 (ttm110) REVERT: B 1132 ARG cc_start: 0.8421 (ptt90) cc_final: 0.8131 (ptt-90) REVERT: B 1141 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7474 (m) REVERT: B 1170 ASN cc_start: 0.8356 (t0) cc_final: 0.8024 (t0) outliers start: 37 outliers final: 19 residues processed: 326 average time/residue: 0.8674 time to fit residues: 301.7770 Evaluate side-chains 324 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 502 GLU 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 97 LYS 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 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 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 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 1099 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 557 GLN B 602 ASN B1104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100231 restraints weight = 19444.894| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.89 r_work: 0.3132 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13819 Z= 0.157 Angle : 0.532 11.956 18684 Z= 0.270 Chirality : 0.045 0.135 2049 Planarity : 0.005 0.044 2408 Dihedral : 4.057 26.218 1855 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.20 % Allowed : 16.06 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.20), residues: 1676 helix: 1.29 (0.21), residues: 618 sheet: 0.11 (0.36), residues: 218 loop : -0.84 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1079 TYR 0.011 0.001 TYR B 138 PHE 0.014 0.002 PHE B 467 TRP 0.009 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00398 (13807) covalent geometry : angle 0.51038 (18666) hydrogen bonds : bond 0.04664 ( 539) hydrogen bonds : angle 4.33487 ( 1467) metal coordination : bond 0.00666 ( 12) metal coordination : angle 4.83305 ( 18) *********************** 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 334 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7747 (mp0) cc_final: 0.7481 (mp0) REVERT: A 197 TYR cc_start: 0.8376 (p90) cc_final: 0.8010 (p90) REVERT: A 244 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7809 (mtp85) REVERT: A 335 TYR cc_start: 0.8419 (m-80) cc_final: 0.7809 (m-80) REVERT: A 367 GLU cc_start: 0.8220 (mp0) cc_final: 0.7507 (mt-10) REVERT: A 374 LEU cc_start: 0.8479 (mm) cc_final: 0.8149 (mp) REVERT: A 462 GLU cc_start: 0.7876 (pm20) cc_final: 0.7632 (pm20) REVERT: A 502 GLU cc_start: 0.7689 (mp0) cc_final: 0.7213 (mp0) REVERT: A 515 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7877 (mmmm) REVERT: A 570 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8576 (mtt180) REVERT: B 67 LEU cc_start: 0.7887 (mt) cc_final: 0.7660 (mp) REVERT: B 79 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7707 (mmmt) REVERT: B 97 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7871 (mtpp) REVERT: B 134 ASP cc_start: 0.7813 (t70) cc_final: 0.7452 (t0) REVERT: B 197 ARG cc_start: 0.7557 (mmp80) cc_final: 0.7338 (mmp80) REVERT: B 225 ASP cc_start: 0.7987 (t0) cc_final: 0.7682 (t0) REVERT: B 226 VAL cc_start: 0.8312 (t) cc_final: 0.7965 (m) REVERT: B 425 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7715 (ttpt) REVERT: B 506 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7785 (mt-10) REVERT: B 573 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8212 (ttpp) REVERT: B 576 VAL cc_start: 0.8853 (t) cc_final: 0.8583 (m) REVERT: B 625 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: B 737 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: B 754 ASN cc_start: 0.7560 (t0) cc_final: 0.7082 (t0) REVERT: B 757 LEU cc_start: 0.8014 (mp) cc_final: 0.7697 (mt) REVERT: B 1019 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: B 1023 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 1099 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: B 1132 ARG cc_start: 0.8464 (ptt90) cc_final: 0.8262 (ptt-90) REVERT: B 1141 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7471 (m) REVERT: B 1170 ASN cc_start: 0.8373 (t0) cc_final: 0.8021 (t0) REVERT: B 1214 MET cc_start: 0.8363 (ttp) cc_final: 0.8041 (mmm) outliers start: 32 outliers final: 18 residues processed: 315 average time/residue: 0.8513 time to fit residues: 285.7790 Evaluate side-chains 323 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 LYS Chi-restraints excluded: chain B residue 160 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 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 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 1099 LYS 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 127 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.115105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101267 restraints weight = 19223.304| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.86 r_work: 0.3147 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13819 Z= 0.118 Angle : 0.503 10.517 18684 Z= 0.256 Chirality : 0.044 0.131 2049 Planarity : 0.005 0.047 2408 Dihedral : 3.940 25.722 1855 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.61 % Allowed : 16.33 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1676 helix: 1.41 (0.21), residues: 618 sheet: 0.06 (0.36), residues: 214 loop : -0.80 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1079 TYR 0.011 0.001 TYR B 420 PHE 0.012 0.001 PHE B 467 TRP 0.008 0.001 TRP B 622 HIS 0.004 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00292 (13807) covalent geometry : angle 0.48553 (18666) hydrogen bonds : bond 0.04053 ( 539) hydrogen bonds : angle 4.22271 ( 1467) metal coordination : bond 0.00518 ( 12) metal coordination : angle 4.22187 ( 18) *********************** 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 339 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 301 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7747 (mp0) cc_final: 0.7483 (mp0) REVERT: A 197 TYR cc_start: 0.8353 (p90) cc_final: 0.8005 (p90) REVERT: A 244 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7886 (mtp-110) REVERT: A 284 ILE cc_start: 0.8104 (mt) cc_final: 0.7869 (mm) REVERT: A 335 TYR cc_start: 0.8403 (m-80) cc_final: 0.7739 (m-80) REVERT: A 365 SER cc_start: 0.8583 (t) cc_final: 0.8356 (m) REVERT: A 367 GLU cc_start: 0.8179 (mp0) cc_final: 0.7453 (mt-10) REVERT: A 374 LEU cc_start: 0.8438 (mm) cc_final: 0.8142 (mp) REVERT: A 502 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 515 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7878 (mmmm) REVERT: A 570 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8570 (mtp180) REVERT: B 67 LEU cc_start: 0.7891 (mt) cc_final: 0.7690 (mp) REVERT: B 79 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7686 (mmmt) REVERT: B 97 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7805 (mtpp) REVERT: B 134 ASP cc_start: 0.7771 (t70) cc_final: 0.7383 (t0) REVERT: B 168 LYS cc_start: 0.8761 (tppp) cc_final: 0.8278 (tppt) REVERT: B 197 ARG cc_start: 0.7526 (mmp80) cc_final: 0.7260 (mmp80) REVERT: B 225 ASP cc_start: 0.7953 (t0) cc_final: 0.7657 (t0) REVERT: B 266 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7880 (ttpp) REVERT: B 415 LEU cc_start: 0.8306 (mp) cc_final: 0.8099 (mt) REVERT: B 425 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7719 (ttpt) REVERT: B 506 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 554 LEU cc_start: 0.8158 (mt) cc_final: 0.7876 (mm) REVERT: B 573 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8173 (ttpp) REVERT: B 576 VAL cc_start: 0.8843 (t) cc_final: 0.8581 (m) REVERT: B 625 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7830 (mpp) REVERT: B 737 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: B 754 ASN cc_start: 0.7577 (t0) cc_final: 0.7088 (t0) REVERT: B 757 LEU cc_start: 0.8008 (mp) cc_final: 0.7709 (mt) REVERT: B 762 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8250 (mtpt) REVERT: B 1019 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: B 1023 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 1079 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7357 (ttm-80) REVERT: B 1099 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7814 (mtpt) REVERT: B 1141 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7474 (m) REVERT: B 1170 ASN cc_start: 0.8343 (t0) cc_final: 0.8020 (t0) REVERT: B 1214 MET cc_start: 0.8354 (ttp) cc_final: 0.8047 (mmm) outliers start: 38 outliers final: 19 residues processed: 319 average time/residue: 0.8520 time to fit residues: 289.8476 Evaluate side-chains 324 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 466 GLU Chi-restraints excluded: chain A residue 502 GLU 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 97 LYS 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 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 1082 LEU Chi-restraints excluded: chain B residue 1099 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 139 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.114550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100738 restraints weight = 19210.931| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.86 r_work: 0.3139 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13819 Z= 0.144 Angle : 0.523 11.148 18684 Z= 0.266 Chirality : 0.045 0.133 2049 Planarity : 0.005 0.044 2408 Dihedral : 4.005 25.949 1855 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.61 % Allowed : 16.82 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.20), residues: 1676 helix: 1.36 (0.21), residues: 620 sheet: 0.02 (0.36), residues: 217 loop : -0.80 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1079 TYR 0.011 0.001 TYR A 305 PHE 0.015 0.001 PHE B 467 TRP 0.008 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00365 (13807) covalent geometry : angle 0.50390 (18666) hydrogen bonds : bond 0.04407 ( 539) hydrogen bonds : angle 4.24755 ( 1467) metal coordination : bond 0.00624 ( 12) metal coordination : angle 4.50802 ( 18) *********************** 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 335 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 297 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7726 (mp0) cc_final: 0.7478 (mp0) REVERT: A 197 TYR cc_start: 0.8358 (p90) cc_final: 0.8007 (p90) REVERT: A 244 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7896 (mtp-110) REVERT: A 335 TYR cc_start: 0.8425 (m-80) cc_final: 0.7829 (m-80) REVERT: A 367 GLU cc_start: 0.8193 (mp0) cc_final: 0.7351 (mt-10) REVERT: A 374 LEU cc_start: 0.8444 (mm) cc_final: 0.8132 (mp) REVERT: A 502 GLU cc_start: 0.7650 (mp0) cc_final: 0.7146 (mp0) REVERT: A 515 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7878 (mmmm) REVERT: A 570 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8531 (mtp180) REVERT: B 67 LEU cc_start: 0.7850 (mt) cc_final: 0.7640 (mp) REVERT: B 79 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7670 (mmmt) REVERT: B 97 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7848 (mtpp) REVERT: B 134 ASP cc_start: 0.7812 (t70) cc_final: 0.7425 (t0) REVERT: B 197 ARG cc_start: 0.7564 (mmp80) cc_final: 0.7287 (mmp80) REVERT: B 425 LYS cc_start: 0.7914 (ttmm) cc_final: 0.7641 (ttpt) REVERT: B 506 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7758 (mt-10) REVERT: B 573 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8182 (ttpp) REVERT: B 576 VAL cc_start: 0.8859 (t) cc_final: 0.8583 (m) REVERT: B 625 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7810 (mpp) REVERT: B 711 HIS cc_start: 0.8531 (t70) cc_final: 0.8170 (t70) REVERT: B 737 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: B 754 ASN cc_start: 0.7590 (t0) cc_final: 0.7125 (t0) REVERT: B 757 LEU cc_start: 0.7988 (mp) cc_final: 0.7691 (mt) REVERT: B 776 GLU cc_start: 0.8187 (tp30) cc_final: 0.7805 (tp30) REVERT: B 1019 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: B 1023 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 1079 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7388 (ttm-80) REVERT: B 1099 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7834 (mtpt) REVERT: B 1141 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7435 (m) REVERT: B 1170 ASN cc_start: 0.8358 (t0) cc_final: 0.8019 (t0) REVERT: B 1214 MET cc_start: 0.8348 (ttp) cc_final: 0.8049 (mmm) outliers start: 38 outliers final: 23 residues processed: 313 average time/residue: 0.8513 time to fit residues: 283.5969 Evaluate side-chains 322 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 466 GLU 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 78 LEU Chi-restraints excluded: chain B residue 97 LYS 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 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 1099 LYS 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 156 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 0.0000 chunk 145 optimal weight: 0.0870 chunk 48 optimal weight: 0.0970 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 0.1760 ------------------------------------------------------------------------------- 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 A 573 GLN B 124 ASN B1104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103401 restraints weight = 19138.076| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.86 r_work: 0.3182 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13819 Z= 0.086 Angle : 0.464 7.387 18684 Z= 0.238 Chirality : 0.042 0.131 2049 Planarity : 0.004 0.044 2408 Dihedral : 3.674 24.479 1855 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 18.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.21), residues: 1676 helix: 1.57 (0.21), residues: 620 sheet: 0.08 (0.36), residues: 213 loop : -0.65 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 487 TYR 0.009 0.001 TYR B1169 PHE 0.011 0.001 PHE B 443 TRP 0.008 0.001 TRP B 609 HIS 0.004 0.000 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00196 (13807) covalent geometry : angle 0.45346 (18666) hydrogen bonds : bond 0.03149 ( 539) hydrogen bonds : angle 4.03781 ( 1467) metal coordination : bond 0.00380 ( 12) metal coordination : angle 3.24950 ( 18) *********************** 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 334 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 0.511 Fit side-chains REVERT: A 173 GLU cc_start: 0.7739 (mp0) cc_final: 0.7474 (mp0) REVERT: A 197 TYR cc_start: 0.8327 (p90) cc_final: 0.7995 (p90) REVERT: A 244 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7799 (mtp-110) REVERT: A 335 TYR cc_start: 0.8357 (m-80) cc_final: 0.7682 (m-80) REVERT: A 367 GLU cc_start: 0.8051 (mp0) cc_final: 0.7154 (mt-10) REVERT: A 374 LEU cc_start: 0.8363 (mm) cc_final: 0.8117 (mp) REVERT: A 417 SER cc_start: 0.8341 (p) cc_final: 0.8103 (t) REVERT: A 487 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7284 (ttm-80) REVERT: A 502 GLU cc_start: 0.7653 (mp0) cc_final: 0.7128 (mp0) REVERT: A 515 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7793 (mmmm) REVERT: A 522 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 79 LYS cc_start: 0.8064 (mmtp) cc_final: 0.7815 (mmmt) REVERT: B 134 ASP cc_start: 0.7770 (t70) cc_final: 0.7382 (t0) REVERT: B 168 LYS cc_start: 0.8697 (tppp) cc_final: 0.8318 (tppt) REVERT: B 197 ARG cc_start: 0.7532 (mmp80) cc_final: 0.7239 (mmp80) REVERT: B 425 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7610 (ttpt) REVERT: B 506 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 554 LEU cc_start: 0.8017 (mt) cc_final: 0.7746 (mm) REVERT: B 573 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8156 (ttpp) REVERT: B 576 VAL cc_start: 0.8827 (t) cc_final: 0.8591 (m) REVERT: B 625 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: B 711 HIS cc_start: 0.8488 (t70) cc_final: 0.8155 (t70) REVERT: B 754 ASN cc_start: 0.7540 (t0) cc_final: 0.7090 (t0) REVERT: B 757 LEU cc_start: 0.7966 (mp) cc_final: 0.7674 (mt) REVERT: B 762 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8255 (mtpt) REVERT: B 776 GLU cc_start: 0.8188 (tp30) cc_final: 0.7809 (tp30) REVERT: B 1019 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: B 1023 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: B 1079 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7357 (ttm-80) REVERT: B 1141 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7468 (m) REVERT: B 1170 ASN cc_start: 0.8287 (t0) cc_final: 0.7981 (t0) REVERT: B 1214 MET cc_start: 0.8319 (ttp) cc_final: 0.8037 (tpp) outliers start: 24 outliers final: 12 residues processed: 320 average time/residue: 0.7862 time to fit residues: 269.4372 Evaluate side-chains 318 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 302 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU 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 150 SER 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 841 SER 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 151 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 128 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 = 0.3465 r_free = 0.3465 target = 0.114563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100810 restraints weight = 19327.125| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.86 r_work: 0.3141 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13819 Z= 0.154 Angle : 0.537 11.271 18684 Z= 0.271 Chirality : 0.045 0.134 2049 Planarity : 0.005 0.044 2408 Dihedral : 3.927 25.638 1855 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.78 % Allowed : 18.67 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.21), residues: 1676 helix: 1.47 (0.21), residues: 621 sheet: 0.07 (0.36), residues: 217 loop : -0.74 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 487 TYR 0.013 0.001 TYR A 305 PHE 0.016 0.002 PHE B 467 TRP 0.007 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00392 (13807) covalent geometry : angle 0.51876 (18666) hydrogen bonds : bond 0.04449 ( 539) hydrogen bonds : angle 4.18318 ( 1467) metal coordination : bond 0.00639 ( 12) metal coordination : angle 4.47547 ( 18) *********************** 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: 26 poor density : 301 time to evaluate : 0.504 Fit side-chains REVERT: A 173 GLU cc_start: 0.7770 (mp0) cc_final: 0.7527 (mp0) REVERT: A 197 TYR cc_start: 0.8346 (p90) cc_final: 0.7979 (p90) REVERT: A 244 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7865 (mtp-110) REVERT: A 335 TYR cc_start: 0.8432 (m-80) cc_final: 0.7848 (m-80) REVERT: A 367 GLU cc_start: 0.8148 (mp0) cc_final: 0.7172 (mt-10) REVERT: A 374 LEU cc_start: 0.8465 (mm) cc_final: 0.8143 (mp) REVERT: A 417 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8104 (t) REVERT: A 462 GLU cc_start: 0.7826 (pm20) cc_final: 0.7605 (pm20) REVERT: A 502 GLU cc_start: 0.7683 (mp0) cc_final: 0.7152 (mp0) REVERT: A 515 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7856 (mmmm) REVERT: A 522 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 79 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7716 (mmmt) REVERT: B 83 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: B 134 ASP cc_start: 0.7822 (t70) cc_final: 0.7452 (t0) REVERT: B 168 LYS cc_start: 0.8718 (tppp) cc_final: 0.8278 (tppt) REVERT: B 197 ARG cc_start: 0.7500 (mmp80) cc_final: 0.7296 (mmp80) REVERT: B 425 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7682 (ttpt) REVERT: B 505 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7940 (mtmt) REVERT: B 506 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 573 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8175 (ttpp) REVERT: B 576 VAL cc_start: 0.8878 (t) cc_final: 0.8610 (m) REVERT: B 625 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: B 711 HIS cc_start: 0.8524 (t70) cc_final: 0.8160 (t70) REVERT: B 737 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: B 754 ASN cc_start: 0.7627 (t0) cc_final: 0.7152 (t0) REVERT: B 757 LEU cc_start: 0.8005 (mp) cc_final: 0.7717 (mt) REVERT: B 776 GLU cc_start: 0.8183 (tp30) cc_final: 0.7792 (tp30) REVERT: B 1019 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: B 1023 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 1079 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7409 (ttm-80) REVERT: B 1099 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7834 (mtpt) REVERT: B 1141 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7458 (m) REVERT: B 1170 ASN cc_start: 0.8359 (t0) cc_final: 0.8008 (t0) outliers start: 26 outliers final: 14 residues processed: 311 average time/residue: 0.8131 time to fit residues: 270.0347 Evaluate side-chains 324 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 302 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 SER 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 83 GLU Chi-restraints excluded: chain B residue 150 SER 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 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1099 LYS 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 8 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 98 optimal weight: 0.0670 chunk 106 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.115419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101668 restraints weight = 19189.246| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.86 r_work: 0.3157 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13819 Z= 0.113 Angle : 0.506 9.421 18684 Z= 0.256 Chirality : 0.044 0.131 2049 Planarity : 0.004 0.044 2408 Dihedral : 3.842 25.542 1855 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 19.22 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.21), residues: 1676 helix: 1.54 (0.21), residues: 620 sheet: 0.03 (0.36), residues: 214 loop : -0.70 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.009 0.001 TYR A 197 PHE 0.013 0.001 PHE A 334 TRP 0.008 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00277 (13807) covalent geometry : angle 0.49016 (18666) hydrogen bonds : bond 0.03871 ( 539) hydrogen bonds : angle 4.11679 ( 1467) metal coordination : bond 0.00556 ( 12) metal coordination : angle 4.03662 ( 18) ********************** 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 325 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.476 Fit side-chains REVERT: A 173 GLU cc_start: 0.7748 (mp0) cc_final: 0.7508 (mp0) REVERT: A 197 TYR cc_start: 0.8328 (p90) cc_final: 0.7980 (p90) REVERT: A 244 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7884 (mtp-110) REVERT: A 335 TYR cc_start: 0.8390 (m-80) cc_final: 0.7791 (m-80) REVERT: A 367 GLU cc_start: 0.8125 (mp0) cc_final: 0.7122 (mt-10) REVERT: A 374 LEU cc_start: 0.8431 (mm) cc_final: 0.8143 (mp) REVERT: A 417 SER cc_start: 0.8368 (p) cc_final: 0.8113 (t) REVERT: A 462 GLU cc_start: 0.7776 (pm20) cc_final: 0.7561 (pm20) REVERT: A 502 GLU cc_start: 0.7647 (mp0) cc_final: 0.7122 (mp0) REVERT: A 515 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7846 (mmmm) REVERT: A 522 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 79 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7774 (mmmt) REVERT: B 134 ASP cc_start: 0.7802 (t70) cc_final: 0.7411 (t0) REVERT: B 168 LYS cc_start: 0.8711 (tppp) cc_final: 0.8286 (tppt) REVERT: B 197 ARG cc_start: 0.7512 (mmp80) cc_final: 0.7278 (mmp80) REVERT: B 211 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: B 425 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7632 (ttpt) REVERT: B 429 ASP cc_start: 0.7874 (m-30) cc_final: 0.7619 (m-30) REVERT: B 505 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7896 (mtmt) REVERT: B 506 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 554 LEU cc_start: 0.8090 (mt) cc_final: 0.7805 (mm) REVERT: B 573 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8170 (ttpp) REVERT: B 576 VAL cc_start: 0.8857 (t) cc_final: 0.8596 (m) REVERT: B 625 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7805 (mpp) REVERT: B 711 HIS cc_start: 0.8495 (t70) cc_final: 0.8123 (t70) REVERT: B 737 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: B 754 ASN cc_start: 0.7594 (t0) cc_final: 0.7136 (t0) REVERT: B 757 LEU cc_start: 0.7980 (mp) cc_final: 0.7694 (mt) REVERT: B 762 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8279 (mtpt) REVERT: B 776 GLU cc_start: 0.8177 (tp30) cc_final: 0.7767 (tp30) REVERT: B 1019 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: B 1023 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: B 1079 ARG cc_start: 0.7701 (ttm110) cc_final: 0.7359 (ttm-80) REVERT: B 1141 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7469 (m) REVERT: B 1170 ASN cc_start: 0.8328 (t0) cc_final: 0.7990 (t0) outliers start: 22 outliers final: 15 residues processed: 315 average time/residue: 0.8364 time to fit residues: 281.3501 Evaluate side-chains 322 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 301 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 211 MET 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 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 790 MET Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1082 LEU 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 75 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 154 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 A 573 GLN B 124 ASN B 602 ASN B1104 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100196 restraints weight = 19345.298| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.86 r_work: 0.3129 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13819 Z= 0.169 Angle : 0.562 11.170 18684 Z= 0.282 Chirality : 0.046 0.137 2049 Planarity : 0.005 0.044 2408 Dihedral : 4.045 26.338 1855 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 19.01 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.21), residues: 1676 helix: 1.42 (0.21), residues: 621 sheet: -0.02 (0.36), residues: 220 loop : -0.77 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 487 TYR 0.013 0.001 TYR A 428 PHE 0.017 0.002 PHE B 467 TRP 0.007 0.001 TRP B 622 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00432 (13807) covalent geometry : angle 0.54167 (18666) hydrogen bonds : bond 0.04733 ( 539) hydrogen bonds : angle 4.23969 ( 1467) metal coordination : bond 0.00730 ( 12) metal coordination : angle 4.84052 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6333.45 seconds wall clock time: 108 minutes 13.37 seconds (6493.37 seconds total)