Starting phenix.real_space_refine on Tue Aug 26 10:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxt_38760/08_2025/8xxt_38760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxt_38760/08_2025/8xxt_38760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxt_38760/08_2025/8xxt_38760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxt_38760/08_2025/8xxt_38760.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxt_38760/08_2025/8xxt_38760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxt_38760/08_2025/8xxt_38760.cif" } resolution = 2.85 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= -0.000 sd= 0.072 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 Zn 7 6.06 5 Mg 1 5.21 5 S 198 5.16 5 C 22804 2.51 5 N 6119 2.21 5 O 6654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35783 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 11244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1415, 11244 Classifications: {'peptide': 1415} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1348} Chain breaks: 3 Chain: "B" Number of atoms: 9701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1226, 9701 Classifications: {'peptide': 1226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1172} Chain breaks: 1 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2907 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "E" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2687 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 553 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Chain: "I" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5177 Classifications: {'peptide': 638} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 605} Chain breaks: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 107.808 71.655 67.821 1.00 96.79 S ATOM 471 SG CYS A 62 106.237 70.743 64.569 1.00 86.79 S ATOM 531 SG CYS A 69 104.902 73.685 66.700 1.00 86.39 S ATOM 775 SG CYS A 99 91.303 51.790 107.062 1.00118.54 S ATOM 797 SG CYS A 102 91.863 48.543 105.070 1.00136.13 S ATOM 1049 SG CYS A 134 89.289 48.539 107.640 1.00141.58 S ATOM 1074 SG CYS A 137 92.885 48.794 108.764 1.00143.53 S ATOM 20464 SG CYS B1180 99.044 56.557 66.969 1.00 93.78 S ATOM 20489 SG CYS B1183 98.319 57.630 70.419 1.00 77.39 S ATOM 20605 SG CYS B1198 101.936 57.724 68.976 1.00 84.05 S ATOM 20627 SG CYS B1201 100.482 54.414 69.722 1.00 88.51 S ATOM 29260 SG CYS G 4 62.330 92.802 137.794 1.00114.33 S ATOM 29414 SG CYS G 24 63.888 90.587 135.166 1.00111.40 S ATOM 29426 SG CYS G 26 64.678 90.216 138.616 1.00130.76 S ATOM 29796 SG CYS G 73 33.111 124.509 107.346 1.00101.74 S ATOM 29817 SG CYS G 76 34.730 127.920 107.851 1.00 99.93 S ATOM 29974 SG CYS G 96 36.855 125.243 106.598 1.00 94.45 S ATOM 29991 SG CYS G 98 35.421 124.982 110.208 1.00 96.08 S ATOM 30096 SG CYS H 7 71.329 129.661 47.557 1.00 88.29 S ATOM 30120 SG CYS H 10 70.290 130.146 43.927 1.00 83.84 S ATOM 30461 SG CYS H 65 67.660 129.721 46.666 1.00 66.49 S ATOM 30467 SG CYS H 66 69.703 132.938 46.225 1.00 73.29 S Time building chain proxies: 7.37, per 1000 atoms: 0.21 Number of scatterers: 35783 At special positions: 0 Unit cell: (150.88, 164.82, 171.38, 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 7 29.99 S 198 16.00 Mg 1 11.99 O 6654 8.00 N 6119 7.00 C 22804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS I 937 " - pdb=" SG CYS I 950 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 4 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " Number of angles added : 27 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8480 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 46 sheets defined 43.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.630A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.526A pdb=" N VAL A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.586A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.506A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.683A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.860A pdb=" N LEU A 393 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.159A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.527A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.718A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 648 Proline residue: A 626 - end of helix removed outlier: 3.786A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.900A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.627A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 865 removed outlier: 3.962A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.838A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.618A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1040 through 1061 removed outlier: 3.540A pdb=" N GLU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Proline residue: A1052 - end of helix removed outlier: 3.879A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1102 through 1105 Processing helix chain 'A' and resid 1106 through 1118 Processing helix chain 'A' and resid 1137 through 1141 removed outlier: 3.773A pdb=" N LYS A1140 " --> pdb=" O SER A1137 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A1141 " --> pdb=" O SER A1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1137 through 1141' Processing helix chain 'A' and resid 1146 through 1150 removed outlier: 4.259A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 4.024A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1189 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1229 through 1234 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.784A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A1356 " --> pdb=" O HIS A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.505A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.831A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.992A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Proline residue: B 56 - end of helix Processing helix chain 'B' and resid 76 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.971A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 300 through 315 Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.501A pdb=" N HIS B 325 " --> pdb=" O GLN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 349 through 352 removed outlier: 3.589A pdb=" N SER B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 421 through 452 removed outlier: 4.099A pdb=" N ALA B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.528A pdb=" N ILE B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.829A pdb=" N LYS B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 removed outlier: 3.509A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 742 through 747 removed outlier: 3.846A pdb=" N GLU B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.595A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.863A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.951A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1162 through 1169 Processing helix chain 'B' and resid 1201 through 1205 Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.677A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.649A pdb=" N SER C 212 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 259 removed outlier: 3.577A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.565A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 358 Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.703A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.875A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.595A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.802A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.693A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.641A pdb=" N LEU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 194 Processing helix chain 'F' and resid 196 through 207 removed outlier: 3.875A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 Processing helix chain 'F' and resid 288 through 314 Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.863A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 removed outlier: 4.050A pdb=" N TRP F 327 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'H' and resid 14 through 31 removed outlier: 4.583A pdb=" N ALA H 19 " --> pdb=" O GLY H 15 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.508A pdb=" N GLY H 59 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.540A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.706A pdb=" N TYR H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.778A pdb=" N PHE I 142 " --> pdb=" O SER I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 167 through 175 removed outlier: 4.220A pdb=" N CYS I 175 " --> pdb=" O VAL I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 211 Processing helix chain 'I' and resid 212 through 234 Processing helix chain 'I' and resid 678 through 683 removed outlier: 3.788A pdb=" N LEU I 683 " --> pdb=" O THR I 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 684 through 698 removed outlier: 3.773A pdb=" N ASP I 688 " --> pdb=" O ASP I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 790 Processing helix chain 'I' and resid 794 through 818 removed outlier: 3.719A pdb=" N THR I 804 " --> pdb=" O ALA I 800 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN I 812 " --> pdb=" O ALA I 808 " (cutoff:3.500A) Processing helix chain 'I' and resid 845 through 849 Processing helix chain 'I' and resid 882 through 887 Processing helix chain 'I' and resid 907 through 911 Processing helix chain 'I' and resid 912 through 933 Processing helix chain 'I' and resid 956 through 961 removed outlier: 4.089A pdb=" N TYR I 961 " --> pdb=" O THR I 957 " (cutoff:3.500A) Processing helix chain 'I' and resid 966 through 974 removed outlier: 3.708A pdb=" N ASP I 972 " --> pdb=" O GLU I 968 " (cutoff:3.500A) Processing helix chain 'I' and resid 974 through 986 Processing helix chain 'I' and resid 1016 through 1027 removed outlier: 4.400A pdb=" N ILE I1020 " --> pdb=" O ASP I1016 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE I1021 " --> pdb=" O TYR I1017 " (cutoff:3.500A) Processing helix chain 'I' and resid 1030 through 1036 removed outlier: 3.575A pdb=" N ILE I1034 " --> pdb=" O SER I1030 " (cutoff:3.500A) Processing helix chain 'I' and resid 1044 through 1051 Processing helix chain 'I' and resid 1063 through 1085 removed outlier: 3.920A pdb=" N MET I1067 " --> pdb=" O ASP I1063 " (cutoff:3.500A) Processing helix chain 'I' and resid 1093 through 1098 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 4.371A pdb=" N HIS I1102 " --> pdb=" O LEU I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1104 through 1115 removed outlier: 4.338A pdb=" N GLU I1112 " --> pdb=" O LYS I1108 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS I1113 " --> pdb=" O GLU I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1121 through 1133 removed outlier: 3.518A pdb=" N HIS I1128 " --> pdb=" O THR I1124 " (cutoff:3.500A) Processing helix chain 'I' and resid 1133 through 1154 removed outlier: 3.639A pdb=" N LEU I1138 " --> pdb=" O PRO I1134 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU I1139 " --> pdb=" O ALA I1135 " (cutoff:3.500A) Processing helix chain 'I' and resid 1158 through 1182 removed outlier: 3.913A pdb=" N ASN I1163 " --> pdb=" O SER I1159 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I1164 " --> pdb=" O TRP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1190 through 1194 removed outlier: 3.525A pdb=" N PHE I1194 " --> pdb=" O PHE I1191 " (cutoff:3.500A) Processing helix chain 'I' and resid 1209 through 1214 removed outlier: 3.742A pdb=" N TYR I1213 " --> pdb=" O ASP I1209 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER I1214 " --> pdb=" O ILE I1210 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1209 through 1214' Processing helix chain 'I' and resid 1240 through 1247 removed outlier: 4.184A pdb=" N ASP I1244 " --> pdb=" O ASP I1241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 4.433A pdb=" N ASP B1211 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.574A pdb=" N LEU A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.108A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.486A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.707A pdb=" N SER A 325 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 4.077A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.551A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 836 through 838 removed outlier: 6.456A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB4, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 3.637A pdb=" N ASN A1267 " --> pdb=" O ASN A1296 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A1290 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG A1275 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP A1288 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A1277 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A1286 " --> pdb=" O ARG A1277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB6, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.387A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 40 " --> pdb=" O LEU A1131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.598A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 145 through 151 Processing sheet with id=AB9, first strand: chain 'B' and resid 145 through 151 removed outlier: 4.387A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC2, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 420 Processing sheet with id=AC4, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.976A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.611A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 597 removed outlier: 5.342A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 5.979A pdb=" N VAL B 865 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B1009 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL B 867 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AD4, first strand: chain 'B' and resid 932 through 933 Processing sheet with id=AD5, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD6, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 12 removed outlier: 4.981A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 46 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 67 through 73 removed outlier: 4.034A pdb=" N ASP C 162 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE C 111 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 removed outlier: 4.342A pdb=" N GLY C 150 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.534A pdb=" N HIS C 325 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.323A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 88 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR D 121 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU D 90 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.870A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET D 162 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 10 removed outlier: 7.294A pdb=" N HIS F 71 " --> pdb=" O GLN F 53 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN F 53 " --> pdb=" O HIS F 71 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG F 73 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL F 51 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER F 75 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 86 through 87 removed outlier: 4.605A pdb=" N VAL F 110 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 93 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 237 through 238 removed outlier: 3.702A pdb=" N ILE F 285 " --> pdb=" O VAL F 163 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AE8, first strand: chain 'I' and resid 100 through 101 removed outlier: 4.466A pdb=" N GLY I 129 " --> pdb=" O ILE I 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=AF1, first strand: chain 'I' and resid 875 through 878 removed outlier: 3.651A pdb=" N ILE I 876 " --> pdb=" O TYR I 864 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP I 859 " --> pdb=" O CYS I 898 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS I 898 " --> pdb=" O TRP I 859 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE I 861 " --> pdb=" O LEU I 896 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU I 896 " --> pdb=" O ILE I 861 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL I 863 " --> pdb=" O ALA I 894 " (cutoff:3.500A) 1552 hydrogen bonds defined for protein. 4323 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: 8.90 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8435 1.33 - 1.45: 7456 1.45 - 1.58: 20281 1.58 - 1.70: 2 1.70 - 1.82: 323 Bond restraints: 36497 Sorted by residual: bond pdb=" CB PRO A1204 " pdb=" CG PRO A1204 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.25e+01 bond pdb=" CB PRO I 124 " pdb=" CG PRO I 124 " ideal model delta sigma weight residual 1.492 1.657 -0.165 5.00e-02 4.00e+02 1.09e+01 bond pdb=" C PRO I 103 " pdb=" O PRO I 103 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.06e-02 8.90e+03 6.94e+00 bond pdb=" N ARG I 102 " pdb=" CA ARG I 102 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.58e-02 4.01e+03 5.41e+00 bond pdb=" CA SER I 104 " pdb=" CB SER I 104 " ideal model delta sigma weight residual 1.529 1.493 0.036 1.64e-02 3.72e+03 4.73e+00 ... (remaining 36492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 48953 2.78 - 5.56: 409 5.56 - 8.34: 31 8.34 - 11.12: 8 11.12 - 13.90: 3 Bond angle restraints: 49404 Sorted by residual: angle pdb=" CA PRO I 124 " pdb=" N PRO I 124 " pdb=" CD PRO I 124 " ideal model delta sigma weight residual 112.00 99.01 12.99 1.40e+00 5.10e-01 8.61e+01 angle pdb=" CA PRO A1204 " pdb=" N PRO A1204 " pdb=" CD PRO A1204 " ideal model delta sigma weight residual 112.00 99.92 12.08 1.40e+00 5.10e-01 7.44e+01 angle pdb=" CA PRO B 440 " pdb=" N PRO B 440 " pdb=" CD PRO B 440 " ideal model delta sigma weight residual 112.00 103.68 8.32 1.40e+00 5.10e-01 3.53e+01 angle pdb=" C GLU E 16 " pdb=" CA GLU E 16 " pdb=" CB GLU E 16 " ideal model delta sigma weight residual 115.89 109.51 6.38 1.32e+00 5.74e-01 2.34e+01 angle pdb=" N PRO A1204 " pdb=" CD PRO A1204 " pdb=" CG PRO A1204 " ideal model delta sigma weight residual 103.20 96.17 7.03 1.50e+00 4.44e-01 2.20e+01 ... (remaining 49399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 19314 17.86 - 35.73: 2158 35.73 - 53.59: 581 53.59 - 71.45: 135 71.45 - 89.31: 55 Dihedral angle restraints: 22243 sinusoidal: 9123 harmonic: 13120 Sorted by residual: dihedral pdb=" CA ILE A1422 " pdb=" C ILE A1422 " pdb=" N GLY A1423 " pdb=" CA GLY A1423 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ILE E 123 " pdb=" C ILE E 123 " pdb=" N LYS E 124 " pdb=" CA LYS E 124 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR I 822 " pdb=" C TYR I 822 " pdb=" N ASN I 823 " pdb=" CA ASN I 823 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 22240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5054 0.080 - 0.160: 523 0.160 - 0.240: 5 0.240 - 0.320: 1 0.320 - 0.400: 2 Chirality restraints: 5585 Sorted by residual: chirality pdb=" CG LEU H 47 " pdb=" CB LEU H 47 " pdb=" CD1 LEU H 47 " pdb=" CD2 LEU H 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB ILE A1074 " pdb=" CA ILE A1074 " pdb=" CG1 ILE A1074 " pdb=" CG2 ILE A1074 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE B 442 " pdb=" CA ILE B 442 " pdb=" CG1 ILE B 442 " pdb=" CG2 ILE B 442 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5582 not shown) Planarity restraints: 6361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 439 " -0.091 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO B 440 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 119 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO I 120 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO I 120 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO I 120 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 123 " -0.080 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO I 124 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO I 124 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO I 124 " -0.061 5.00e-02 4.00e+02 ... (remaining 6358 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 344 2.56 - 3.14: 29198 3.14 - 3.73: 58091 3.73 - 4.31: 83588 4.31 - 4.90: 139172 Nonbonded interactions: 310393 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.973 2.170 nonbonded pdb=" O MET D 192 " pdb=" ND1 HIS D 193 " model vdw 2.083 3.120 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1503 " model vdw 2.099 2.170 nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 2.107 2.170 nonbonded pdb=" OH TYR A 824 " pdb=" OG SER I1232 " model vdw 2.114 3.040 ... (remaining 310388 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: 11.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 34.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:8.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.005 0.176 36521 Z= 0.189 Angle : 0.645 13.897 49433 Z= 0.342 Chirality : 0.046 0.400 5585 Planarity : 0.005 0.132 6361 Dihedral : 16.865 89.315 13760 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.90 % Favored : 93.70 % Rotamer: Outliers : 2.76 % Allowed : 21.23 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % 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: -0.32 (0.13), residues: 4443 helix: 0.44 (0.13), residues: 1701 sheet: -0.34 (0.22), residues: 575 loop : -0.61 (0.14), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 305 TYR 0.025 0.001 TYR D 16 PHE 0.037 0.002 PHE B 304 TRP 0.051 0.002 TRP B 701 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00455 (36497) covalent geometry : angle 0.63984 (49404) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.28243 ( 2) hydrogen bonds : bond 0.20381 ( 1544) hydrogen bonds : angle 7.31949 ( 4323) metal coordination : bond 0.00794 ( 23) metal coordination : angle 3.59794 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 366 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1087 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: I 226 MET cc_start: 0.6126 (mtp) cc_final: 0.5877 (mtm) outliers start: 110 outliers final: 92 residues processed: 465 average time/residue: 0.5309 time to fit residues: 304.7838 Evaluate side-chains 458 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 365 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1137 ASP Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 801 GLU Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 847 SER Chi-restraints excluded: chain I residue 876 ILE Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1218 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 667 GLN A 959 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 325 HIS B 497 GLN B 840 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN E 51 GLN F 47 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN G 59 ASN G 83 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 HIS I 164 ASN I 819 GLN I 905 GLN I 912 ASN I1085 HIS I1174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098717 restraints weight = 61407.377| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.09 r_work: 0.3248 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 36521 Z= 0.269 Angle : 0.668 10.178 49433 Z= 0.351 Chirality : 0.048 0.216 5585 Planarity : 0.005 0.075 6361 Dihedral : 7.653 85.794 5030 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.26 % Favored : 93.29 % Rotamer: Outliers : 5.22 % Allowed : 18.30 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.30 (0.13), residues: 4443 helix: 0.56 (0.12), residues: 1737 sheet: -0.56 (0.21), residues: 607 loop : -0.64 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 302 TYR 0.021 0.002 TYR F 69 PHE 0.026 0.002 PHE A 918 TRP 0.022 0.002 TRP A 155 HIS 0.006 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00635 (36497) covalent geometry : angle 0.66212 (49404) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.60114 ( 2) hydrogen bonds : bond 0.05304 ( 1544) hydrogen bonds : angle 5.48723 ( 4323) metal coordination : bond 0.01073 ( 23) metal coordination : angle 3.93403 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 388 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8371 (tm) REVERT: A 245 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: A 1094 MET cc_start: 0.8466 (mtp) cc_final: 0.8254 (mtm) REVERT: A 1253 LYS cc_start: 0.8058 (pttp) cc_final: 0.7766 (tptp) REVERT: B 96 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8449 (mm) REVERT: B 146 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6269 (tp30) REVERT: B 225 ASN cc_start: 0.7989 (p0) cc_final: 0.7738 (t0) REVERT: B 269 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8041 (mtm-85) REVERT: B 334 GLN cc_start: 0.8047 (tt0) cc_final: 0.7821 (tt0) REVERT: B 582 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: B 823 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7672 (mmt-90) REVERT: B 861 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: B 970 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6875 (mmt180) REVERT: C 27 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7769 (pttm) REVERT: C 236 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8007 (mtm110) REVERT: C 266 GLU cc_start: 0.7964 (mp0) cc_final: 0.7683 (mp0) REVERT: C 275 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6976 (tm-30) REVERT: D 125 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8919 (tt) REVERT: D 180 ASP cc_start: 0.8464 (t70) cc_final: 0.8165 (m-30) REVERT: F 145 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7535 (mpt180) REVERT: F 245 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6691 (p0) REVERT: G 89 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: H 27 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6903 (mp0) REVERT: H 47 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.4321 (tm) REVERT: H 60 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8679 (mm) REVERT: I 686 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6550 (pmt) REVERT: I 778 TYR cc_start: 0.5187 (t80) cc_final: 0.4659 (t80) REVERT: I 831 ARG cc_start: 0.5382 (mtm110) cc_final: 0.5178 (ptp90) REVERT: I 885 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7155 (mptt) outliers start: 208 outliers final: 93 residues processed: 553 average time/residue: 0.5235 time to fit residues: 357.1288 Evaluate side-chains 474 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 363 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 861 GLN Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 970 ARG Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1137 ASP Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 876 ILE Chi-restraints excluded: chain I residue 879 THR Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 114 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 417 optimal weight: 0.0980 chunk 319 optimal weight: 10.0000 chunk 441 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN A 814 ASN A 980 GLN A1062 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 216 HIS B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 33 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN E 51 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN H 48 GLN I 164 ASN I 819 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.135239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103268 restraints weight = 60978.474| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.10 r_work: 0.3321 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36521 Z= 0.118 Angle : 0.567 12.509 49433 Z= 0.297 Chirality : 0.044 0.176 5585 Planarity : 0.004 0.062 6361 Dihedral : 6.583 84.208 4954 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.58 % Favored : 94.01 % Rotamer: Outliers : 4.12 % Allowed : 19.28 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.06 (0.13), residues: 4443 helix: 0.86 (0.12), residues: 1743 sheet: -0.43 (0.22), residues: 579 loop : -0.62 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.021 0.001 TYR D 16 PHE 0.022 0.001 PHE A 918 TRP 0.026 0.001 TRP B 701 HIS 0.004 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00250 (36497) covalent geometry : angle 0.56230 (49404) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.41739 ( 2) hydrogen bonds : bond 0.04221 ( 1544) hydrogen bonds : angle 5.09220 ( 4323) metal coordination : bond 0.00532 ( 23) metal coordination : angle 3.08835 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 423 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8419 (tt0) cc_final: 0.8201 (tt0) REVERT: A 27 MET cc_start: 0.8597 (ppp) cc_final: 0.8380 (ptt) REVERT: A 119 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6979 (tttt) REVERT: A 242 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8088 (mtpm) REVERT: A 257 ASP cc_start: 0.8158 (t0) cc_final: 0.7866 (m-30) REVERT: A 259 ASN cc_start: 0.7772 (t0) cc_final: 0.7490 (t0) REVERT: A 1087 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: A 1181 ASN cc_start: 0.8000 (t0) cc_final: 0.7623 (t0) REVERT: A 1253 LYS cc_start: 0.7953 (pttp) cc_final: 0.7705 (tttp) REVERT: B 77 GLU cc_start: 0.7465 (pm20) cc_final: 0.7043 (tp30) REVERT: B 102 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7668 (mtt-85) REVERT: B 146 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6189 (tp30) REVERT: B 225 ASN cc_start: 0.7911 (p0) cc_final: 0.7648 (t0) REVERT: B 266 SER cc_start: 0.8138 (m) cc_final: 0.7422 (p) REVERT: B 269 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8308 (mpt-90) REVERT: B 582 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: B 703 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7912 (ptmm) REVERT: B 823 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7732 (mmt-90) REVERT: B 956 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7538 (tpp) REVERT: B 969 MET cc_start: 0.7382 (pmm) cc_final: 0.7177 (pmm) REVERT: C 266 GLU cc_start: 0.7942 (mp0) cc_final: 0.7626 (mp0) REVERT: C 275 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6767 (tm-30) REVERT: D 113 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: D 125 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8909 (tt) REVERT: D 157 GLN cc_start: 0.8525 (mp-120) cc_final: 0.8132 (mp10) REVERT: D 180 ASP cc_start: 0.8386 (t70) cc_final: 0.8163 (m-30) REVERT: F 117 SER cc_start: 0.6745 (p) cc_final: 0.6360 (m) REVERT: F 145 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7211 (mpt180) REVERT: H 27 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6745 (mp0) REVERT: H 47 LEU cc_start: 0.4470 (OUTLIER) cc_final: 0.3957 (tm) REVERT: I 173 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.4727 (tpp) REVERT: I 686 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6720 (pmt) REVERT: I 778 TYR cc_start: 0.5030 (t80) cc_final: 0.4615 (t80) REVERT: I 885 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7392 (mptt) REVERT: I 912 ASN cc_start: 0.7199 (t0) cc_final: 0.6938 (t0) REVERT: I 1029 ILE cc_start: 0.7872 (pp) cc_final: 0.7428 (pp) outliers start: 164 outliers final: 60 residues processed: 549 average time/residue: 0.5126 time to fit residues: 349.0083 Evaluate side-chains 441 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 366 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 956 MET Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 369 optimal weight: 0.9990 chunk 311 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 392 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 721 ASN A1405 ASN B 451 GLN B 840 ASN B 912 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN E 51 GLN E 90 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN I 164 ASN I 906 HIS ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099690 restraints weight = 61147.597| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.09 r_work: 0.3265 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 36521 Z= 0.225 Angle : 0.623 9.209 49433 Z= 0.323 Chirality : 0.047 0.193 5585 Planarity : 0.004 0.058 6361 Dihedral : 6.401 84.342 4927 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.99 % Favored : 93.59 % Rotamer: Outliers : 4.62 % Allowed : 19.60 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.11 (0.13), residues: 4443 helix: 0.84 (0.12), residues: 1742 sheet: -0.55 (0.21), residues: 579 loop : -0.64 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 503 TYR 0.021 0.002 TYR A 824 PHE 0.025 0.002 PHE A 918 TRP 0.024 0.002 TRP B 701 HIS 0.006 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00533 (36497) covalent geometry : angle 0.61666 (49404) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.40179 ( 2) hydrogen bonds : bond 0.04443 ( 1544) hydrogen bonds : angle 5.08253 ( 4323) metal coordination : bond 0.00978 ( 23) metal coordination : angle 3.84979 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 370 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8486 (tt0) cc_final: 0.8276 (tt0) REVERT: A 23 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6965 (ptt180) REVERT: A 92 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7200 (ttt90) REVERT: A 119 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6955 (tttt) REVERT: A 242 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8116 (mtpm) REVERT: A 690 MET cc_start: 0.8985 (mmm) cc_final: 0.8446 (mpp) REVERT: A 1087 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: A 1096 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 1102 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: A 1144 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5128 (mtp) REVERT: A 1181 ASN cc_start: 0.8105 (t0) cc_final: 0.7736 (t0) REVERT: A 1253 LYS cc_start: 0.7958 (pttp) cc_final: 0.7747 (tttm) REVERT: B 96 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 146 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6297 (tp30) REVERT: B 263 THR cc_start: 0.6470 (m) cc_final: 0.6152 (p) REVERT: B 266 SER cc_start: 0.8210 (m) cc_final: 0.7532 (p) REVERT: B 269 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8054 (mtm-85) REVERT: B 289 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: B 582 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: B 823 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7821 (mmt-90) REVERT: C 27 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7800 (pttm) REVERT: C 275 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6858 (tm-30) REVERT: D 113 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: D 125 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8939 (tt) REVERT: D 157 GLN cc_start: 0.8568 (mp-120) cc_final: 0.8248 (mp10) REVERT: D 180 ASP cc_start: 0.8419 (t70) cc_final: 0.8139 (m-30) REVERT: F 145 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7222 (mpt180) REVERT: F 171 THR cc_start: 0.5369 (OUTLIER) cc_final: 0.4970 (m) REVERT: H 27 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6893 (mp0) REVERT: H 47 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4043 (tm) REVERT: I 778 TYR cc_start: 0.5125 (t80) cc_final: 0.4663 (t80) REVERT: I 885 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7376 (mptt) REVERT: I 912 ASN cc_start: 0.7231 (t0) cc_final: 0.6970 (t0) outliers start: 184 outliers final: 97 residues processed: 511 average time/residue: 0.5094 time to fit residues: 321.5940 Evaluate side-chains 471 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 354 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1137 ASP Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 876 ILE Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 234 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 336 optimal weight: 0.3980 chunk 271 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 306 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 346 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A 646 ASN A 721 ASN B 451 GLN B 704 HIS B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN E 51 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN I 164 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102404 restraints weight = 60795.634| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.10 r_work: 0.3311 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36521 Z= 0.127 Angle : 0.563 8.885 49433 Z= 0.293 Chirality : 0.044 0.192 5585 Planarity : 0.004 0.057 6361 Dihedral : 6.132 84.036 4923 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.67 % Favored : 93.92 % Rotamer: Outliers : 4.19 % Allowed : 20.51 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.03 (0.13), residues: 4443 helix: 1.00 (0.12), residues: 1746 sheet: -0.39 (0.22), residues: 566 loop : -0.63 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 543 TYR 0.024 0.001 TYR D 16 PHE 0.023 0.001 PHE A 918 TRP 0.024 0.001 TRP B 701 HIS 0.004 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00285 (36497) covalent geometry : angle 0.55833 (49404) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.31628 ( 2) hydrogen bonds : bond 0.03915 ( 1544) hydrogen bonds : angle 4.94404 ( 4323) metal coordination : bond 0.00488 ( 23) metal coordination : angle 3.27304 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 384 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6803 (ptt180) REVERT: A 92 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7163 (ttt90) REVERT: A 119 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7022 (tttt) REVERT: A 242 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (mtpm) REVERT: A 257 ASP cc_start: 0.8142 (t0) cc_final: 0.7848 (m-30) REVERT: A 259 ASN cc_start: 0.7850 (t0) cc_final: 0.7497 (t0) REVERT: A 372 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: A 1087 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: A 1181 ASN cc_start: 0.8112 (t0) cc_final: 0.7684 (t0) REVERT: A 1207 TYR cc_start: 0.7880 (t80) cc_final: 0.7426 (t80) REVERT: B 77 GLU cc_start: 0.7456 (pm20) cc_final: 0.7192 (tp30) REVERT: B 80 LYS cc_start: 0.7862 (mttt) cc_final: 0.7628 (mptp) REVERT: B 146 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6208 (tp30) REVERT: B 201 VAL cc_start: 0.8883 (t) cc_final: 0.8664 (p) REVERT: B 263 THR cc_start: 0.6612 (m) cc_final: 0.6326 (p) REVERT: B 266 SER cc_start: 0.8141 (m) cc_final: 0.7427 (p) REVERT: B 269 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8027 (mtm-85) REVERT: B 300 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6963 (tp) REVERT: B 494 MET cc_start: 0.6795 (ptp) cc_final: 0.6440 (ptm) REVERT: B 541 MET cc_start: 0.8448 (mmm) cc_final: 0.8188 (mmm) REVERT: B 823 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7694 (mmt-90) REVERT: B 956 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7548 (tpp) REVERT: C 275 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6729 (tm-30) REVERT: C 301 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8031 (ttm) REVERT: D 5 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6359 (mtpp) REVERT: D 113 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8117 (m-40) REVERT: D 125 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8937 (tt) REVERT: F 145 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7223 (mpt180) REVERT: F 292 MET cc_start: 0.7232 (mmt) cc_final: 0.7017 (mmt) REVERT: G 101 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7423 (tmm) REVERT: H 27 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6786 (mp0) REVERT: H 47 LEU cc_start: 0.4671 (OUTLIER) cc_final: 0.3972 (tm) REVERT: I 116 HIS cc_start: 0.3904 (OUTLIER) cc_final: 0.3566 (m-70) REVERT: I 686 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6301 (pmm) REVERT: I 778 TYR cc_start: 0.5025 (t80) cc_final: 0.4668 (t80) REVERT: I 885 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7475 (mptt) REVERT: I 912 ASN cc_start: 0.7242 (t0) cc_final: 0.6979 (t0) REVERT: I 1210 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8218 (pt) outliers start: 167 outliers final: 73 residues processed: 510 average time/residue: 0.5081 time to fit residues: 319.4482 Evaluate side-chains 445 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 351 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 956 MET Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 182 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 389 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 807 ASN B 225 ASN B 451 GLN B 598 GLN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 341 GLN D 33 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN I 116 HIS I 164 ASN ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097725 restraints weight = 61500.195| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.08 r_work: 0.3232 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 36521 Z= 0.305 Angle : 0.687 15.181 49433 Z= 0.354 Chirality : 0.049 0.287 5585 Planarity : 0.005 0.055 6361 Dihedral : 6.368 84.910 4917 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.55 % Favored : 93.09 % Rotamer: Outliers : 4.99 % Allowed : 20.51 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.24 (0.13), residues: 4443 helix: 0.75 (0.12), residues: 1732 sheet: -0.75 (0.21), residues: 591 loop : -0.68 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 305 TYR 0.022 0.002 TYR D 16 PHE 0.028 0.002 PHE A 912 TRP 0.031 0.002 TRP B 701 HIS 0.007 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00727 (36497) covalent geometry : angle 0.67971 (49404) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.38504 ( 2) hydrogen bonds : bond 0.04713 ( 1544) hydrogen bonds : angle 5.15520 ( 4323) metal coordination : bond 0.01330 ( 23) metal coordination : angle 4.27463 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 368 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6867 (ptt180) REVERT: A 92 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7256 (ttt90) REVERT: A 119 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6937 (tttt) REVERT: A 147 ASP cc_start: 0.7826 (t0) cc_final: 0.6862 (t0) REVERT: A 242 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8140 (mtpm) REVERT: A 378 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7302 (mtp85) REVERT: A 690 MET cc_start: 0.8987 (mmm) cc_final: 0.8454 (mpp) REVERT: A 1087 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: A 1096 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8213 (mm) REVERT: A 1144 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5098 (mtp) REVERT: A 1181 ASN cc_start: 0.8067 (t0) cc_final: 0.7643 (t0) REVERT: A 1207 TYR cc_start: 0.7841 (t80) cc_final: 0.7508 (t80) REVERT: B 104 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5385 (p90) REVERT: B 146 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6308 (tp30) REVERT: B 149 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7349 (mtt90) REVERT: B 225 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7775 (p0) REVERT: B 266 SER cc_start: 0.8244 (m) cc_final: 0.7596 (p) REVERT: B 269 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7990 (mtm-85) REVERT: B 413 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.8564 (t80) REVERT: B 541 MET cc_start: 0.8615 (mmm) cc_final: 0.8392 (mmm) REVERT: B 582 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: B 823 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7774 (mmt-90) REVERT: C 275 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6881 (tm-30) REVERT: D 5 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.5918 (mtpp) REVERT: D 113 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8150 (m-40) REVERT: D 125 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8940 (tt) REVERT: F 145 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7636 (mpt180) REVERT: F 245 ASP cc_start: 0.7226 (p0) cc_final: 0.6750 (p0) REVERT: F 274 ASP cc_start: 0.7793 (m-30) cc_final: 0.7298 (t70) REVERT: F 292 MET cc_start: 0.7121 (mmt) cc_final: 0.6920 (mmt) REVERT: F 304 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8032 (tt) REVERT: G 101 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7474 (tmm) REVERT: H 27 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6935 (mp0) REVERT: H 47 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4202 (tm) REVERT: I 128 TYR cc_start: 0.5339 (p90) cc_final: 0.4931 (p90) REVERT: I 189 VAL cc_start: 0.5616 (OUTLIER) cc_final: 0.5353 (t) REVERT: I 686 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6301 (pmm) REVERT: I 778 TYR cc_start: 0.5183 (t80) cc_final: 0.4719 (t80) REVERT: I 885 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7459 (mptt) REVERT: I 912 ASN cc_start: 0.7345 (t0) cc_final: 0.7035 (t0) REVERT: I 1029 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7450 (pp) outliers start: 199 outliers final: 97 residues processed: 518 average time/residue: 0.5494 time to fit residues: 350.2707 Evaluate side-chains 477 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 355 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1137 ASP Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 684 ASP Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 876 ILE Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1198 PHE Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 265 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 433 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 214 optimal weight: 0.6980 chunk 379 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A 721 ASN A 814 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 451 GLN B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN I 164 ASN ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.135192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103849 restraints weight = 60517.106| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.04 r_work: 0.3356 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36521 Z= 0.123 Angle : 0.585 12.754 49433 Z= 0.303 Chirality : 0.045 0.246 5585 Planarity : 0.004 0.052 6361 Dihedral : 6.057 84.792 4917 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.49 % Favored : 94.10 % Rotamer: Outliers : 3.51 % Allowed : 22.36 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.01 (0.13), residues: 4443 helix: 1.00 (0.12), residues: 1744 sheet: -0.57 (0.22), residues: 564 loop : -0.60 (0.14), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.026 0.001 TYR D 16 PHE 0.022 0.001 PHE A 918 TRP 0.038 0.001 TRP B 701 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00274 (36497) covalent geometry : angle 0.58063 (49404) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.32545 ( 2) hydrogen bonds : bond 0.03836 ( 1544) hydrogen bonds : angle 4.93755 ( 4323) metal coordination : bond 0.00505 ( 23) metal coordination : angle 3.27363 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 379 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6841 (ptt180) REVERT: A 31 ILE cc_start: 0.7990 (pt) cc_final: 0.7752 (pp) REVERT: A 92 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7254 (ttt90) REVERT: A 119 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7073 (tttt) REVERT: A 242 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8154 (mtpm) REVERT: A 257 ASP cc_start: 0.8144 (t0) cc_final: 0.7874 (m-30) REVERT: A 259 ASN cc_start: 0.7788 (t0) cc_final: 0.7530 (t0) REVERT: A 1087 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: A 1181 ASN cc_start: 0.8232 (t0) cc_final: 0.7795 (t0) REVERT: A 1207 TYR cc_start: 0.7811 (t80) cc_final: 0.7367 (t80) REVERT: B 69 TYR cc_start: 0.6733 (m-80) cc_final: 0.6383 (m-80) REVERT: B 102 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7555 (mtt-85) REVERT: B 269 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8120 (mtm-85) REVERT: B 300 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7033 (tp) REVERT: B 413 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8439 (t80) REVERT: B 494 MET cc_start: 0.6818 (ptp) cc_final: 0.6484 (ptm) REVERT: B 541 MET cc_start: 0.8524 (mmm) cc_final: 0.8240 (mmm) REVERT: B 823 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7714 (mmt-90) REVERT: B 861 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: C 275 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7092 (tm-30) REVERT: D 5 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6565 (mtpp) REVERT: D 109 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7950 (mm-40) REVERT: D 113 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8113 (m-40) REVERT: D 157 GLN cc_start: 0.8585 (mp-120) cc_final: 0.8206 (mp10) REVERT: F 145 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7393 (mpt180) REVERT: F 235 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5407 (ptpp) REVERT: F 274 ASP cc_start: 0.7802 (m-30) cc_final: 0.6920 (t0) REVERT: F 292 MET cc_start: 0.7452 (mmt) cc_final: 0.7236 (mmt) REVERT: F 304 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8068 (tt) REVERT: G 101 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: H 27 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6914 (mp0) REVERT: H 47 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4043 (tm) REVERT: I 128 TYR cc_start: 0.5137 (p90) cc_final: 0.4557 (p90) REVERT: I 686 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6308 (pmm) REVERT: I 778 TYR cc_start: 0.5254 (t80) cc_final: 0.4825 (t80) REVERT: I 885 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7541 (mptt) REVERT: I 912 ASN cc_start: 0.7380 (t0) cc_final: 0.7152 (t0) REVERT: I 1029 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7467 (pp) outliers start: 140 outliers final: 67 residues processed: 482 average time/residue: 0.5305 time to fit residues: 314.7906 Evaluate side-chains 434 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1240 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 861 GLN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 684 ASP Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 346 optimal weight: 0.7980 chunk 311 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 293 optimal weight: 0.1980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 814 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 451 GLN B 829 ASN B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN E 90 ASN F 95 ASN G 83 GLN I 116 HIS I 164 ASN ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.134653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103291 restraints weight = 60464.019| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.03 r_work: 0.3348 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36521 Z= 0.142 Angle : 0.593 12.340 49433 Z= 0.306 Chirality : 0.045 0.305 5585 Planarity : 0.004 0.050 6361 Dihedral : 5.920 84.283 4915 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.92 % Favored : 93.68 % Rotamer: Outliers : 3.31 % Allowed : 22.69 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.13), residues: 4443 helix: 1.08 (0.12), residues: 1744 sheet: -0.56 (0.22), residues: 578 loop : -0.57 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 694 TYR 0.042 0.001 TYR F 244 PHE 0.025 0.001 PHE D 126 TRP 0.041 0.001 TRP B 701 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00328 (36497) covalent geometry : angle 0.58833 (49404) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.23352 ( 2) hydrogen bonds : bond 0.03849 ( 1544) hydrogen bonds : angle 4.88907 ( 4323) metal coordination : bond 0.00583 ( 23) metal coordination : angle 3.23434 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 374 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6846 (ptt180) REVERT: A 31 ILE cc_start: 0.8085 (pt) cc_final: 0.7865 (pp) REVERT: A 92 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7336 (ttt90) REVERT: A 147 ASP cc_start: 0.7650 (t0) cc_final: 0.7403 (t0) REVERT: A 242 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8166 (mtpm) REVERT: A 257 ASP cc_start: 0.8215 (t0) cc_final: 0.7951 (m-30) REVERT: A 259 ASN cc_start: 0.7791 (t0) cc_final: 0.7471 (t0) REVERT: A 690 MET cc_start: 0.8996 (mmm) cc_final: 0.8535 (mpp) REVERT: A 1087 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: A 1181 ASN cc_start: 0.8278 (t0) cc_final: 0.7826 (t0) REVERT: A 1207 TYR cc_start: 0.7826 (t80) cc_final: 0.7384 (t80) REVERT: B 102 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7571 (mtt-85) REVERT: B 269 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8149 (mtm-85) REVERT: B 300 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7076 (tp) REVERT: B 413 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.8458 (t80) REVERT: B 494 MET cc_start: 0.6861 (ptp) cc_final: 0.6579 (ptm) REVERT: B 523 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8745 (m) REVERT: B 541 MET cc_start: 0.8536 (mmm) cc_final: 0.8261 (mmm) REVERT: B 823 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7772 (mmt-90) REVERT: C 275 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6861 (tm-30) REVERT: D 5 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6698 (mtpp) REVERT: D 109 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7955 (mm-40) REVERT: D 113 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8132 (m-40) REVERT: E 125 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7365 (m) REVERT: F 145 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7394 (mpt180) REVERT: F 274 ASP cc_start: 0.7762 (m-30) cc_final: 0.6933 (t0) REVERT: F 304 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8082 (tt) REVERT: G 101 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7426 (tmm) REVERT: H 27 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7055 (mp0) REVERT: H 47 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4184 (tm) REVERT: I 128 TYR cc_start: 0.5088 (p90) cc_final: 0.4389 (p90) REVERT: I 189 VAL cc_start: 0.5797 (m) cc_final: 0.5554 (t) REVERT: I 686 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6384 (pmm) REVERT: I 778 TYR cc_start: 0.5334 (t80) cc_final: 0.4850 (t80) REVERT: I 885 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7574 (mptt) REVERT: I 912 ASN cc_start: 0.7389 (t0) cc_final: 0.7168 (t0) REVERT: I 1029 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7482 (pp) outliers start: 132 outliers final: 76 residues processed: 471 average time/residue: 0.5609 time to fit residues: 325.6583 Evaluate side-chains 447 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 353 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1173 ASN Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 905 LYS Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 684 ASP Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 876 ILE Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1034 ILE Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 386 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 419 optimal weight: 0.0570 chunk 286 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 378 optimal weight: 0.8980 chunk 401 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 273 optimal weight: 0.2980 chunk 371 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 77 GLN A 814 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 33 GLN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN F 167 GLN ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.135648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104442 restraints weight = 60376.431| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.03 r_work: 0.3367 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36521 Z= 0.128 Angle : 0.589 12.782 49433 Z= 0.304 Chirality : 0.045 0.209 5585 Planarity : 0.004 0.049 6361 Dihedral : 5.802 83.765 4914 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.83 % Favored : 93.81 % Rotamer: Outliers : 3.26 % Allowed : 22.94 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.13), residues: 4443 helix: 1.11 (0.12), residues: 1750 sheet: -0.49 (0.22), residues: 574 loop : -0.53 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.032 0.001 TYR A 824 PHE 0.023 0.001 PHE A 918 TRP 0.048 0.001 TRP B 701 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00291 (36497) covalent geometry : angle 0.58499 (49404) SS BOND : bond 0.00118 ( 1) SS BOND : angle 0.30223 ( 2) hydrogen bonds : bond 0.03693 ( 1544) hydrogen bonds : angle 4.85843 ( 4323) metal coordination : bond 0.00484 ( 23) metal coordination : angle 3.03234 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 379 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.8020 (pt) cc_final: 0.7791 (pp) REVERT: A 92 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7358 (ttt90) REVERT: A 147 ASP cc_start: 0.7590 (t0) cc_final: 0.7330 (t0) REVERT: A 242 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8136 (mtpm) REVERT: A 257 ASP cc_start: 0.8202 (t0) cc_final: 0.7947 (m-30) REVERT: A 259 ASN cc_start: 0.7759 (t0) cc_final: 0.7408 (t0) REVERT: A 690 MET cc_start: 0.8969 (mmm) cc_final: 0.8518 (mpp) REVERT: A 1087 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: A 1181 ASN cc_start: 0.8313 (t0) cc_final: 0.7849 (t0) REVERT: A 1207 TYR cc_start: 0.7832 (t80) cc_final: 0.7425 (t80) REVERT: B 102 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7519 (mtt-85) REVERT: B 104 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5544 (p90) REVERT: B 225 ASN cc_start: 0.7755 (t0) cc_final: 0.7352 (p0) REVERT: B 269 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8102 (mtm-85) REVERT: B 300 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7055 (tp) REVERT: B 413 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 480 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7298 (ttm-80) REVERT: B 523 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 541 MET cc_start: 0.8574 (mmm) cc_final: 0.8236 (mmm) REVERT: B 823 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7710 (mmt-90) REVERT: B 863 ASP cc_start: 0.8167 (p0) cc_final: 0.7340 (m-30) REVERT: C 275 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6856 (tm-30) REVERT: D 5 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6702 (mtpp) REVERT: D 78 THR cc_start: 0.7629 (p) cc_final: 0.7113 (m) REVERT: D 109 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7809 (mm-40) REVERT: D 113 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: D 157 GLN cc_start: 0.8582 (mp-120) cc_final: 0.8198 (mt0) REVERT: F 145 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7339 (mpt180) REVERT: F 235 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5418 (ptpp) REVERT: F 274 ASP cc_start: 0.7720 (m-30) cc_final: 0.6938 (t0) REVERT: F 304 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8103 (tt) REVERT: H 27 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7008 (mp0) REVERT: H 47 LEU cc_start: 0.4990 (OUTLIER) cc_final: 0.4202 (tm) REVERT: I 128 TYR cc_start: 0.5068 (p90) cc_final: 0.4365 (p90) REVERT: I 189 VAL cc_start: 0.5924 (m) cc_final: 0.5659 (t) REVERT: I 686 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6431 (pmm) REVERT: I 778 TYR cc_start: 0.5337 (t80) cc_final: 0.4880 (t80) REVERT: I 885 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7643 (mptt) REVERT: I 912 ASN cc_start: 0.7373 (t0) cc_final: 0.7158 (t0) REVERT: I 1029 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7505 (pp) outliers start: 130 outliers final: 70 residues processed: 476 average time/residue: 0.5558 time to fit residues: 326.6542 Evaluate side-chains 443 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 356 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 684 ASP Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 836 THR Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 406 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 721 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN B 451 GLN B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 80 ASN F 95 ASN I 116 HIS I 164 ASN ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100081 restraints weight = 61044.585| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.03 r_work: 0.3299 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 36521 Z= 0.265 Angle : 0.677 11.027 49433 Z= 0.349 Chirality : 0.049 0.275 5585 Planarity : 0.005 0.048 6361 Dihedral : 5.970 84.325 4906 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.27 % Rotamer: Outliers : 2.99 % Allowed : 23.47 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.09 (0.13), residues: 4443 helix: 0.88 (0.12), residues: 1736 sheet: -0.67 (0.21), residues: 596 loop : -0.60 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 229 TYR 0.031 0.002 TYR F 244 PHE 0.026 0.002 PHE A 912 TRP 0.050 0.002 TRP B 701 HIS 0.008 0.001 HIS F 165 Details of bonding type rmsd covalent geometry : bond 0.00628 (36497) covalent geometry : angle 0.67104 (49404) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.40882 ( 2) hydrogen bonds : bond 0.04389 ( 1544) hydrogen bonds : angle 5.01853 ( 4323) metal coordination : bond 0.01131 ( 23) metal coordination : angle 3.89725 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8886 Ramachandran restraints generated. 4443 Oldfield, 0 Emsley, 4443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 362 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.8149 (pt) cc_final: 0.7919 (pp) REVERT: A 92 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7332 (ttt90) REVERT: A 147 ASP cc_start: 0.7606 (t0) cc_final: 0.7348 (t0) REVERT: A 242 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8179 (mtpm) REVERT: A 257 ASP cc_start: 0.8247 (t0) cc_final: 0.7951 (m-30) REVERT: A 1087 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: A 1181 ASN cc_start: 0.8242 (t0) cc_final: 0.7805 (t0) REVERT: A 1207 TYR cc_start: 0.7885 (t80) cc_final: 0.7411 (t80) REVERT: B 104 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5524 (p90) REVERT: B 225 ASN cc_start: 0.7817 (t0) cc_final: 0.7336 (p0) REVERT: B 269 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8085 (mtm-85) REVERT: B 300 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6976 (tp) REVERT: B 413 TYR cc_start: 0.9273 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 487 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 541 MET cc_start: 0.8600 (mmm) cc_final: 0.8275 (mmm) REVERT: B 823 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7795 (mmt-90) REVERT: B 863 ASP cc_start: 0.8332 (p0) cc_final: 0.7422 (m-30) REVERT: C 266 GLU cc_start: 0.8105 (mp0) cc_final: 0.7779 (mp0) REVERT: C 275 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6904 (tm-30) REVERT: D 5 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6751 (mtpp) REVERT: D 78 THR cc_start: 0.7692 (p) cc_final: 0.7206 (m) REVERT: D 109 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7884 (mm-40) REVERT: D 113 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8122 (m-40) REVERT: F 145 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7598 (mpt180) REVERT: F 235 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5521 (ptpp) REVERT: F 274 ASP cc_start: 0.7773 (m-30) cc_final: 0.6957 (t0) REVERT: H 27 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7027 (mp0) REVERT: H 47 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4307 (tm) REVERT: I 128 TYR cc_start: 0.5093 (p90) cc_final: 0.4471 (p90) REVERT: I 189 VAL cc_start: 0.5865 (m) cc_final: 0.5649 (t) REVERT: I 686 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6437 (pmm) REVERT: I 778 TYR cc_start: 0.5399 (t80) cc_final: 0.4901 (t80) REVERT: I 885 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7615 (mptt) REVERT: I 912 ASN cc_start: 0.7506 (t0) cc_final: 0.7274 (t0) REVERT: I 1029 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7106 (pp) outliers start: 119 outliers final: 63 residues processed: 456 average time/residue: 0.5837 time to fit residues: 327.9384 Evaluate side-chains 432 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 353 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1200 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 684 ASP Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 775 THR Chi-restraints excluded: chain I residue 794 ASN Chi-restraints excluded: chain I residue 876 ILE Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 28 optimal weight: 0.9990 chunk 106 optimal weight: 0.0070 chunk 239 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 417 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 300 optimal weight: 4.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN A 814 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN B 840 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN F 95 ASN I 164 ASN ** I 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.134899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103597 restraints weight = 60160.143| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.03 r_work: 0.3349 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36521 Z= 0.138 Angle : 0.608 10.784 49433 Z= 0.314 Chirality : 0.046 0.242 5585 Planarity : 0.004 0.048 6361 Dihedral : 5.770 84.317 4905 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.87 % Favored : 93.79 % Rotamer: Outliers : 2.43 % Allowed : 24.07 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.04 (0.13), residues: 4443 helix: 1.00 (0.12), residues: 1749 sheet: -0.51 (0.22), residues: 574 loop : -0.58 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 694 TYR 0.026 0.001 TYR D 16 PHE 0.023 0.001 PHE A 918 TRP 0.051 0.002 TRP B 701 HIS 0.008 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00319 (36497) covalent geometry : angle 0.60325 (49404) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.37723 ( 2) hydrogen bonds : bond 0.03842 ( 1544) hydrogen bonds : angle 4.91184 ( 4323) metal coordination : bond 0.00543 ( 23) metal coordination : angle 3.30693 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11842.30 seconds wall clock time: 202 minutes 31.01 seconds (12151.01 seconds total)