Starting phenix.real_space_refine on Sun Aug 9 04:01:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sb1_54709/08_2026/9sb1_54709.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sb1_54709/08_2026/9sb1_54709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sb1_54709/08_2026/9sb1_54709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sb1_54709/08_2026/9sb1_54709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sb1_54709/08_2026/9sb1_54709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sb1_54709/08_2026/9sb1_54709.map" } resolution = 2.98 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= 0.049 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 171 5.16 5 C 19706 2.51 5 N 5482 2.21 5 O 6080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31502 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 11053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1403, 11053 Classifications: {'peptide': 1403} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1338} Chain breaks: 7 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MG': 1, ' ZN': 2, 'PPV': 1} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 457 SG CYS A 67 56.522 71.507 85.712 1.00 84.80 S ATOM 479 SG CYS A 70 56.130 74.698 83.668 1.00 78.47 S ATOM 532 SG CYS A 77 59.588 73.048 84.118 1.00 60.70 S ATOM 762 SG CYS A 107 75.117 80.759 129.014 1.00117.97 S ATOM 786 SG CYS A 110 72.681 83.528 128.353 1.00111.47 S ATOM 1091 SG CYS A 148 75.651 83.858 130.929 1.00149.61 S ATOM 1190 SG CYS A 167 72.513 81.774 131.659 1.00125.28 S ATOM 19827 SG CYS B1163 58.620 87.288 93.822 1.00 67.40 S ATOM 19845 SG CYS B1166 61.011 84.883 95.411 1.00 59.88 S ATOM 19970 SG CYS B1182 57.557 83.787 94.062 1.00 71.15 S ATOM 19989 SG CYS B1185 57.884 85.793 97.330 1.00 75.11 S ATOM 20977 SG CYS C 86 82.731 61.183 21.425 1.00132.37 S ATOM 20994 SG CYS C 88 81.355 58.894 24.020 1.00136.89 S ATOM 21027 SG CYS C 92 83.092 57.402 21.027 1.00 90.73 S ATOM 21050 SG CYS C 95 85.158 59.216 23.661 1.00 93.82 S ATOM 28628 SG CYS J 7 113.165 58.945 39.089 1.00 28.30 S ATOM 28651 SG CYS J 10 113.423 60.830 35.746 1.00 40.46 S ATOM 28931 SG CYS J 45 116.159 61.171 38.339 1.00 40.78 S ATOM 28937 SG CYS J 46 115.654 58.016 36.270 1.00 48.89 S ATOM 30060 SG CYS L 31 87.784 27.748 56.337 1.00188.74 S ATOM 30080 SG CYS L 34 88.009 25.008 53.677 1.00201.76 S ATOM 30184 SG CYS L 48 84.933 25.352 55.983 1.00191.56 S ATOM 30207 SG CYS L 51 88.336 24.114 57.300 1.00203.06 S Time building chain proxies: 5.34, per 1000 atoms: 0.17 Number of scatterers: 31502 At special positions: 0 Unit cell: (164.587, 154.842, 159.173, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 171 16.00 P 56 15.00 Mg 1 11.99 O 6080 8.00 N 5482 7.00 C 19706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 70 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 33 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7180 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 45 sheets defined 39.8% alpha, 19.9% beta 27 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.541A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.632A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.717A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.586A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.686A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 700 removed outlier: 3.757A pdb=" N ASN A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.526A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.949A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.527A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.521A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.546A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.580A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1082 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 4.079A pdb=" N LEU A1101 " --> pdb=" O GLY A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.504A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.889A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.691A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.977A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.507A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.812A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.504A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.585A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.786A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 4.597A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.535A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.611A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.633A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.601A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.542A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.670A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.808A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.562A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.550A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.518A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.884A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.062A pdb=" N GLN D 132 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.041A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.546A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.504A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.510A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 103 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.672A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.894A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.615A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.539A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.954A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.422A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.800A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.656A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.648A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.778A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.889A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.822A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1147 through 1153 removed outlier: 6.359A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.737A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.737A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.949A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 134 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.949A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.079A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.642A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 280 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.739A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.424A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.772A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 861 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.772A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 861 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.954A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.775A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.653A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.356A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.940A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.419A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.709A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 86 through 95 removed outlier: 5.598A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 143 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY G 89 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL G 87 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.582A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.699A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.551A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 13550 1.44 - 1.67: 18336 1.67 - 1.90: 281 1.90 - 2.13: 1 2.13 - 2.35: 4 Bond restraints: 32172 Sorted by residual: bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.528 2.090 -0.561 1.59e-02 3.96e+03 1.25e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.354 -0.972 3.00e-02 1.11e+03 1.05e+03 bond pdb=" CE2 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.344 -0.962 3.00e-02 1.11e+03 1.03e+03 bond pdb=" CE1 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.342 -0.960 3.00e-02 1.11e+03 1.02e+03 bond pdb=" CD1 PHE D 70 " pdb=" CE1 PHE D 70 " ideal model delta sigma weight residual 1.382 2.318 -0.936 3.00e-02 1.11e+03 9.73e+02 ... (remaining 32167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 43636 4.96 - 9.91: 29 9.91 - 14.87: 3 14.87 - 19.82: 2 19.82 - 24.78: 1 Bond angle restraints: 43671 Sorted by residual: angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 110.50 135.28 -24.78 1.70e+00 3.46e-01 2.12e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 128.20 -18.60 1.50e+00 4.44e-01 1.54e+02 angle pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" C THR D 133 " ideal model delta sigma weight residual 111.36 101.91 9.45 1.09e+00 8.42e-01 7.52e+01 angle pdb=" OG1 THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 109.30 92.45 16.85 2.00e+00 2.50e-01 7.10e+01 angle pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 110.85 124.07 -13.22 1.70e+00 3.46e-01 6.05e+01 ... (remaining 43666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.78: 18971 25.78 - 51.55: 505 51.55 - 77.33: 92 77.33 - 103.11: 4 103.11 - 128.88: 1 Dihedral angle restraints: 19573 sinusoidal: 8484 harmonic: 11089 Sorted by residual: dihedral pdb=" C THR D 133 " pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual -122.00 -141.41 19.41 0 2.50e+00 1.60e-01 6.03e+01 dihedral pdb=" N THR D 133 " pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual 123.40 139.25 -15.85 0 2.50e+00 1.60e-01 4.02e+01 dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 19570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4919 0.206 - 0.412: 0 0.412 - 0.618: 0 0.618 - 0.823: 0 0.823 - 1.029: 1 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CB THR D 133 " pdb=" CA THR D 133 " pdb=" OG1 THR D 133 " pdb=" CG2 THR D 133 " both_signs ideal model delta sigma weight residual False 2.55 1.52 1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CB VAL B 482 " pdb=" CA VAL B 482 " pdb=" CG1 VAL B 482 " pdb=" CG2 VAL B 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 4917 not shown) Planarity restraints: 5462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " -0.003 2.00e-02 2.50e+03 5.15e-02 4.65e+01 pdb=" CG PHE D 70 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.082 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.083 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 133 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C THR D 133 " 0.043 2.00e-02 2.50e+03 pdb=" O THR D 133 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 134 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 245 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.029 5.00e-02 4.00e+02 ... (remaining 5459 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 218 2.56 - 3.14: 24455 3.14 - 3.73: 48510 3.73 - 4.31: 69469 4.31 - 4.90: 116458 Nonbonded interactions: 259110 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1802 " model vdw 1.972 2.170 nonbonded pdb=" O3' A R 18 " pdb="MG MG A1802 " model vdw 2.031 2.170 nonbonded pdb=" CE2 PHE D 70 " pdb=" OG1 THR D 133 " model vdw 2.055 3.340 nonbonded pdb=" O LYS B 801 " pdb=" OG1 THR J 52 " model vdw 2.105 3.040 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1802 " model vdw 2.109 2.170 ... (remaining 259105 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 35.190 Find NCS groups from input model: 0.150 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:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.012 0.972 32196 Z= 0.479 Angle : 0.571 24.781 43704 Z= 0.342 Chirality : 0.045 1.029 4920 Planarity : 0.004 0.052 5462 Dihedral : 11.845 128.883 12393 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3773 helix: 1.57 (0.15), residues: 1320 sheet: 0.37 (0.22), residues: 587 loop : -0.19 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.032 0.001 TYR B 797 PHE 0.083 0.002 PHE D 70 TRP 0.018 0.001 TRP A1044 HIS 0.010 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01223 / 0.48 (32172) covalent geometry : angle 0.56660 / 0.34 (43671) hydrogen bonds : bond 0.17971 / 11.89 ( 1360) hydrogen bonds : angle 6.50380 / 4.59 ( 3817) metal coordination : bond 0.00463 / 0.29 ( 24) metal coordination : angle 2.73965 / 1.69 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 714 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.6200 (mmtt) cc_final: 0.5274 (tptm) REVERT: A 716 ASP cc_start: 0.7223 (t70) cc_final: 0.6971 (t0) REVERT: A 830 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7106 (tttt) REVERT: A 969 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8189 (mm-40) REVERT: A 1124 HIS cc_start: 0.6980 (p90) cc_final: 0.6745 (p90) REVERT: A 1138 ILE cc_start: 0.8723 (mt) cc_final: 0.8442 (mm) REVERT: A 1284 MET cc_start: 0.7458 (ttm) cc_final: 0.7071 (mtp) REVERT: A 1285 MET cc_start: 0.8126 (mmt) cc_final: 0.7885 (mmt) REVERT: A 1411 GLU cc_start: 0.8405 (tp30) cc_final: 0.8035 (tp30) REVERT: A 1448 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 1453 TYR cc_start: 0.6951 (m-80) cc_final: 0.6639 (m-80) REVERT: B 173 MET cc_start: 0.9217 (ttm) cc_final: 0.8719 (ttp) REVERT: B 273 LEU cc_start: 0.7769 (mt) cc_final: 0.7552 (mt) REVERT: B 358 LYS cc_start: 0.8430 (mmtm) cc_final: 0.7780 (mmtt) REVERT: B 396 ASP cc_start: 0.8270 (m-30) cc_final: 0.7992 (m-30) REVERT: B 422 LYS cc_start: 0.7925 (mmtm) cc_final: 0.7656 (mttt) REVERT: B 531 GLN cc_start: 0.7977 (pm20) cc_final: 0.7578 (pt0) REVERT: B 570 VAL cc_start: 0.7907 (t) cc_final: 0.7689 (t) REVERT: B 615 MET cc_start: 0.8282 (mtm) cc_final: 0.7896 (ptp) REVERT: B 618 ASP cc_start: 0.8327 (t0) cc_final: 0.7842 (t0) REVERT: B 857 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7650 (tpt90) REVERT: B 885 MET cc_start: 0.2422 (mmm) cc_final: 0.2211 (mmm) REVERT: B 1125 ASP cc_start: 0.8628 (t0) cc_final: 0.8337 (t0) REVERT: C 85 ASP cc_start: 0.6558 (m-30) cc_final: 0.5781 (t0) REVERT: C 94 LYS cc_start: 0.7261 (mtmt) cc_final: 0.7051 (mmtm) REVERT: C 152 GLU cc_start: 0.8569 (tt0) cc_final: 0.8182 (tp30) REVERT: D 8 PHE cc_start: 0.5009 (m-80) cc_final: 0.4146 (m-10) REVERT: E 8 ASN cc_start: 0.8070 (m110) cc_final: 0.7826 (t0) REVERT: E 103 LYS cc_start: 0.6751 (mtpp) cc_final: 0.5501 (tppt) REVERT: E 115 ASN cc_start: 0.7663 (t0) cc_final: 0.7371 (p0) REVERT: E 137 GLU cc_start: 0.7890 (tt0) cc_final: 0.7660 (pt0) REVERT: F 85 MET cc_start: 0.9126 (ttm) cc_final: 0.8849 (ttp) REVERT: H 16 ASP cc_start: 0.8967 (t0) cc_final: 0.8715 (t0) REVERT: H 24 CYS cc_start: 0.8870 (m) cc_final: 0.8657 (m) REVERT: H 27 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7793 (mp0) REVERT: H 129 TYR cc_start: 0.7809 (p90) cc_final: 0.7443 (p90) REVERT: K 102 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8373 (tttm) outliers start: 0 outliers final: 0 residues processed: 714 average time/residue: 0.7136 time to fit residues: 597.1480 Evaluate side-chains 368 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 5 GLN A 124 GLN A 281 HIS A 299 HIS A 394 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN A1312 ASN C 17 ASN C 123 ASN C 252 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 99 HIS H 134 ASN J 23 ASN L 66 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105315 restraints weight = 42847.859| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.22 r_work: 0.3173 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.027 32196 Z= 0.499 Angle : 0.655 24.646 43704 Z= 0.350 Chirality : 0.048 0.801 4920 Planarity : 0.005 0.054 5462 Dihedral : 12.012 132.049 4767 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 2.89 % Allowed : 9.83 % Favored : 87.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3773 helix: 1.31 (0.14), residues: 1345 sheet: 0.23 (0.22), residues: 596 loop : -0.30 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 591 TYR 0.026 0.002 TYR G 74 PHE 0.086 0.002 PHE D 70 TRP 0.012 0.002 TRP A1044 HIS 0.012 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01304 / 0.50 (32172) covalent geometry : angle 0.64779 / 0.35 (43671) hydrogen bonds : bond 0.05076 / 3.34 ( 1360) hydrogen bonds : angle 5.11404 / 3.59 ( 3817) metal coordination : bond 0.00726 / 0.45 ( 24) metal coordination : angle 3.64783 / 2.25 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 403 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7437 (mmm) cc_final: 0.7160 (mmm) REVERT: A 609 ASP cc_start: 0.8370 (t0) cc_final: 0.8134 (t0) REVERT: A 830 LYS cc_start: 0.7718 (mmtt) cc_final: 0.6807 (ttpt) REVERT: A 1109 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8373 (mppt) REVERT: A 1121 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7048 (mm-30) REVERT: A 1284 MET cc_start: 0.7716 (ttm) cc_final: 0.7255 (mtp) REVERT: A 1285 MET cc_start: 0.8139 (mmt) cc_final: 0.7652 (mmm) REVERT: A 1336 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7799 (ttp) REVERT: A 1411 GLU cc_start: 0.8354 (tp30) cc_final: 0.7704 (tp30) REVERT: B 173 MET cc_start: 0.9279 (ttm) cc_final: 0.8874 (ttp) REVERT: B 257 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6802 (mtpp) REVERT: B 273 LEU cc_start: 0.7813 (mt) cc_final: 0.7480 (mt) REVERT: B 358 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7747 (mmtt) REVERT: B 422 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7489 (mttt) REVERT: B 531 GLN cc_start: 0.7895 (pm20) cc_final: 0.7548 (pt0) REVERT: B 595 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7277 (ttp80) REVERT: B 615 MET cc_start: 0.8449 (mtm) cc_final: 0.7835 (ptp) REVERT: B 616 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 618 ASP cc_start: 0.8245 (t0) cc_final: 0.7675 (t0) REVERT: B 658 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 885 MET cc_start: 0.2323 (mmm) cc_final: 0.2107 (mmm) REVERT: B 1050 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9225 (mp) REVERT: B 1125 ASP cc_start: 0.8685 (t0) cc_final: 0.8276 (t0) REVERT: C 85 ASP cc_start: 0.6417 (m-30) cc_final: 0.5914 (t0) REVERT: C 94 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6964 (mppt) REVERT: C 136 ASP cc_start: 0.7633 (t0) cc_final: 0.7096 (t70) REVERT: C 137 LYS cc_start: 0.8076 (tppp) cc_final: 0.7432 (tttm) REVERT: C 152 GLU cc_start: 0.8708 (tt0) cc_final: 0.8151 (tp30) REVERT: E 8 ASN cc_start: 0.7914 (m110) cc_final: 0.7679 (t0) REVERT: E 36 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: E 115 ASN cc_start: 0.7986 (t0) cc_final: 0.7580 (p0) REVERT: E 137 GLU cc_start: 0.8213 (tt0) cc_final: 0.7551 (pt0) REVERT: E 187 TYR cc_start: 0.8712 (t80) cc_final: 0.8376 (t80) REVERT: F 129 LYS cc_start: 0.8330 (mmtp) cc_final: 0.8079 (mmtt) REVERT: G 47 CYS cc_start: 0.8332 (p) cc_final: 0.8077 (p) REVERT: G 53 ASN cc_start: 0.6450 (t0) cc_final: 0.6115 (t0) REVERT: G 143 ILE cc_start: 0.3343 (tt) cc_final: 0.3016 (pp) REVERT: H 24 CYS cc_start: 0.8975 (m) cc_final: 0.8732 (m) REVERT: H 27 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7844 (tt0) REVERT: H 87 ARG cc_start: 0.7661 (mmp80) cc_final: 0.7291 (mmp80) REVERT: H 129 TYR cc_start: 0.7835 (p90) cc_final: 0.7236 (p90) REVERT: K 12 LEU cc_start: 0.8172 (mt) cc_final: 0.7946 (mm) REVERT: K 20 LYS cc_start: 0.8285 (tmtm) cc_final: 0.7980 (tmmm) REVERT: K 84 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7455 (mtpm) REVERT: K 102 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7968 (tttm) outliers start: 97 outliers final: 35 residues processed: 452 average time/residue: 0.6651 time to fit residues: 357.5871 Evaluate side-chains 384 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 19 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 299 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 190 optimal weight: 0.1980 chunk 267 optimal weight: 3.9990 chunk 342 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 348 optimal weight: 0.0270 chunk 331 optimal weight: 0.7980 chunk 286 optimal weight: 20.0000 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 281 HIS A 394 ASN A 969 GLN A 975 HIS A1173 HIS B 433 GLN B 469 GLN C 17 ASN C 252 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN K 96 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107610 restraints weight = 42824.323| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.15 r_work: 0.3221 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.055 32196 Z= 0.460 Angle : 0.563 24.430 43704 Z= 0.303 Chirality : 0.044 0.719 4920 Planarity : 0.004 0.066 5462 Dihedral : 11.996 132.238 4767 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 2.68 % Allowed : 12.12 % Favored : 85.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3773 helix: 1.41 (0.14), residues: 1349 sheet: 0.30 (0.22), residues: 593 loop : -0.24 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 857 TYR 0.021 0.001 TYR G 51 PHE 0.074 0.002 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.46 (32172) covalent geometry : angle 0.55676 / 0.30 (43671) hydrogen bonds : bond 0.04175 / 2.74 ( 1360) hydrogen bonds : angle 4.70266 / 3.29 ( 3817) metal coordination : bond 0.00412 / 0.27 ( 24) metal coordination : angle 3.11014 / 1.95 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 387 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7458 (mmm) cc_final: 0.7185 (mmm) REVERT: A 146 MET cc_start: 0.6414 (mmp) cc_final: 0.6154 (mmm) REVERT: A 609 ASP cc_start: 0.8292 (t0) cc_final: 0.7976 (t0) REVERT: A 830 LYS cc_start: 0.7707 (mmtt) cc_final: 0.6678 (ttpt) REVERT: A 1004 ASN cc_start: 0.8458 (p0) cc_final: 0.8182 (p0) REVERT: A 1259 MET cc_start: 0.0068 (mmp) cc_final: -0.0223 (tpp) REVERT: A 1284 MET cc_start: 0.7635 (ttm) cc_final: 0.7193 (mtp) REVERT: A 1285 MET cc_start: 0.8134 (mmt) cc_final: 0.7562 (mmm) REVERT: A 1287 TYR cc_start: 0.8425 (m-10) cc_final: 0.8174 (m-10) REVERT: A 1319 VAL cc_start: 0.8285 (p) cc_final: 0.7905 (m) REVERT: A 1411 GLU cc_start: 0.8286 (tp30) cc_final: 0.7588 (tp30) REVERT: A 1454 MET cc_start: 0.7231 (ttm) cc_final: 0.6690 (ptm) REVERT: B 133 LYS cc_start: 0.5997 (mmtt) cc_final: 0.5751 (tptt) REVERT: B 173 MET cc_start: 0.9239 (ttm) cc_final: 0.8740 (ttp) REVERT: B 358 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7804 (mmtt) REVERT: B 387 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 396 ASP cc_start: 0.8276 (m-30) cc_final: 0.7879 (m-30) REVERT: B 422 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7422 (mttt) REVERT: B 531 GLN cc_start: 0.7898 (pm20) cc_final: 0.7542 (pt0) REVERT: B 615 MET cc_start: 0.8377 (mtm) cc_final: 0.7742 (ptp) REVERT: B 616 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 618 ASP cc_start: 0.8209 (t0) cc_final: 0.7659 (t0) REVERT: B 667 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5855 (tm-30) REVERT: B 953 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7018 (tm) REVERT: B 1041 GLU cc_start: 0.8055 (tp30) cc_final: 0.7832 (tp30) REVERT: B 1050 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9208 (mp) REVERT: B 1125 ASP cc_start: 0.8687 (t0) cc_final: 0.8283 (t0) REVERT: C 85 ASP cc_start: 0.6476 (m-30) cc_final: 0.5947 (t0) REVERT: C 94 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6961 (mppt) REVERT: C 110 THR cc_start: 0.9250 (m) cc_final: 0.9044 (p) REVERT: C 137 LYS cc_start: 0.7935 (tppp) cc_final: 0.7637 (tttm) REVERT: C 152 GLU cc_start: 0.8652 (tt0) cc_final: 0.7886 (tp30) REVERT: D 1 MET cc_start: 0.2430 (pmm) cc_final: 0.1076 (ppp) REVERT: E 8 ASN cc_start: 0.7817 (m110) cc_final: 0.7603 (t0) REVERT: E 115 ASN cc_start: 0.7900 (t0) cc_final: 0.7567 (p0) REVERT: E 137 GLU cc_start: 0.8184 (tt0) cc_final: 0.7360 (pt0) REVERT: F 129 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7713 (tptt) REVERT: G 2 PHE cc_start: 0.4816 (m-80) cc_final: 0.4594 (m-10) REVERT: G 47 CYS cc_start: 0.8397 (p) cc_final: 0.8160 (p) REVERT: G 106 MET cc_start: 0.1990 (ttp) cc_final: 0.1771 (ttp) REVERT: G 143 ILE cc_start: 0.3209 (tt) cc_final: 0.2871 (pp) REVERT: H 24 CYS cc_start: 0.8954 (m) cc_final: 0.8707 (m) REVERT: H 27 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7814 (tt0) REVERT: H 52 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7669 (mm-40) REVERT: H 87 ARG cc_start: 0.7731 (mmp80) cc_final: 0.7384 (mmp80) REVERT: H 129 TYR cc_start: 0.7686 (p90) cc_final: 0.7142 (p90) REVERT: J 19 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7736 (pm20) outliers start: 90 outliers final: 24 residues processed: 433 average time/residue: 0.6304 time to fit residues: 323.3042 Evaluate side-chains 378 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 348 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 234 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 155 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 335 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 281 HIS A 589 GLN A 659 HIS ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN A1278 ASN B 433 GLN C 17 ASN C 252 GLN C 264 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106542 restraints weight = 42882.487| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.31 r_work: 0.3173 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.982 32196 Z= 0.467 Angle : 0.568 28.883 43704 Z= 0.305 Chirality : 0.044 0.652 4920 Planarity : 0.004 0.053 5462 Dihedral : 11.985 133.127 4767 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 2.74 % Allowed : 13.14 % Favored : 84.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3773 helix: 1.42 (0.14), residues: 1355 sheet: 0.24 (0.22), residues: 596 loop : -0.27 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 54 TYR 0.020 0.001 TYR G 51 PHE 0.076 0.002 PHE D 70 TRP 0.009 0.001 TRP A1044 HIS 0.012 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01232 / 0.47 (32172) covalent geometry : angle 0.56231 / 0.30 (43671) hydrogen bonds : bond 0.04019 / 2.65 ( 1360) hydrogen bonds : angle 4.56726 / 3.20 ( 3817) metal coordination : bond 0.00453 / 0.30 ( 24) metal coordination : angle 3.08201 / 1.93 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 361 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7388 (mmm) cc_final: 0.7131 (mmm) REVERT: A 146 MET cc_start: 0.6592 (mmp) cc_final: 0.6367 (mmm) REVERT: A 609 ASP cc_start: 0.8460 (t0) cc_final: 0.8084 (OUTLIER) REVERT: A 789 LYS cc_start: 0.7737 (mptt) cc_final: 0.7458 (mmmm) REVERT: A 830 LYS cc_start: 0.7622 (mmtt) cc_final: 0.6651 (ttpt) REVERT: A 973 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6913 (mp) REVERT: A 1148 ILE cc_start: 0.4134 (OUTLIER) cc_final: 0.3838 (tp) REVERT: A 1284 MET cc_start: 0.7691 (ttm) cc_final: 0.7199 (mtp) REVERT: A 1285 MET cc_start: 0.8055 (mmt) cc_final: 0.7565 (mmm) REVERT: A 1287 TYR cc_start: 0.8457 (m-10) cc_final: 0.8254 (m-10) REVERT: A 1301 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7329 (pp20) REVERT: A 1319 VAL cc_start: 0.8396 (p) cc_final: 0.8034 (m) REVERT: A 1336 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7987 (ttp) REVERT: A 1406 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8841 (m) REVERT: A 1411 GLU cc_start: 0.8324 (tp30) cc_final: 0.7683 (tp30) REVERT: A 1454 MET cc_start: 0.7488 (ttm) cc_final: 0.7015 (ptm) REVERT: B 133 LYS cc_start: 0.6036 (mmtt) cc_final: 0.5804 (tptt) REVERT: B 310 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.5163 (mtm) REVERT: B 311 LEU cc_start: 0.6618 (mp) cc_final: 0.6322 (mp) REVERT: B 358 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7842 (mmtt) REVERT: B 387 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8422 (mm) REVERT: B 422 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7523 (mttt) REVERT: B 531 GLN cc_start: 0.7977 (pm20) cc_final: 0.7654 (pt0) REVERT: B 595 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7322 (ttp80) REVERT: B 615 MET cc_start: 0.8376 (mtm) cc_final: 0.7751 (ptp) REVERT: B 616 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 618 ASP cc_start: 0.8227 (t0) cc_final: 0.7793 (t0) REVERT: B 620 ARG cc_start: 0.8853 (ptm160) cc_final: 0.8596 (ppp80) REVERT: B 658 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 667 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5937 (tm-30) REVERT: B 885 MET cc_start: 0.1647 (mmm) cc_final: 0.1226 (mmm) REVERT: B 953 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7029 (tm) REVERT: B 1041 GLU cc_start: 0.8026 (tp30) cc_final: 0.7800 (tp30) REVERT: B 1125 ASP cc_start: 0.8723 (t0) cc_final: 0.8317 (t0) REVERT: C 85 ASP cc_start: 0.6526 (m-30) cc_final: 0.5970 (t0) REVERT: C 94 LYS cc_start: 0.7363 (mtmt) cc_final: 0.7098 (mppt) REVERT: C 137 LYS cc_start: 0.8197 (tppp) cc_final: 0.7701 (tttm) REVERT: C 152 GLU cc_start: 0.8677 (tt0) cc_final: 0.8215 (tp30) REVERT: D 1 MET cc_start: 0.2228 (pmm) cc_final: 0.1280 (ppp) REVERT: D 32 GLU cc_start: 0.6360 (mm-30) cc_final: 0.6134 (tp30) REVERT: D 218 GLU cc_start: 0.4239 (OUTLIER) cc_final: 0.3297 (tm-30) REVERT: E 8 ASN cc_start: 0.7844 (m110) cc_final: 0.7641 (t0) REVERT: E 33 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: E 115 ASN cc_start: 0.7976 (t0) cc_final: 0.7721 (p0) REVERT: E 137 GLU cc_start: 0.8205 (tt0) cc_final: 0.7980 (tt0) REVERT: F 129 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7801 (mmtm) REVERT: G 47 CYS cc_start: 0.8378 (p) cc_final: 0.8175 (p) REVERT: G 106 MET cc_start: 0.2603 (ttp) cc_final: 0.2390 (ttp) REVERT: G 143 ILE cc_start: 0.3222 (tt) cc_final: 0.2887 (pp) REVERT: H 24 CYS cc_start: 0.8953 (m) cc_final: 0.8731 (m) REVERT: H 27 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7720 (tt0) REVERT: H 52 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7797 (mm-40) REVERT: H 86 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: H 87 ARG cc_start: 0.7736 (mmp80) cc_final: 0.7369 (mmp80) REVERT: H 129 TYR cc_start: 0.7677 (p90) cc_final: 0.7156 (p90) REVERT: J 19 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7798 (pm20) outliers start: 92 outliers final: 32 residues processed: 412 average time/residue: 0.6700 time to fit residues: 329.0935 Evaluate side-chains 384 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 137 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 318 optimal weight: 6.9990 chunk 367 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 281 HIS A 363 GLN ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 GLN C 79 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN J 23 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100096 restraints weight = 43498.063| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.15 r_work: 0.3111 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.980 32196 Z= 0.572 Angle : 0.756 28.802 43704 Z= 0.396 Chirality : 0.052 0.650 4920 Planarity : 0.005 0.056 5462 Dihedral : 12.211 134.021 4767 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 3.78 % Allowed : 13.46 % Favored : 82.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 3773 helix: 0.87 (0.14), residues: 1348 sheet: -0.07 (0.21), residues: 602 loop : -0.63 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 857 TYR 0.023 0.002 TYR G 51 PHE 0.076 0.003 PHE D 70 TRP 0.015 0.002 TRP B 308 HIS 0.014 0.002 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01475 / 0.57 (32172) covalent geometry : angle 0.74679 / 0.40 (43671) hydrogen bonds : bond 0.05260 / 3.48 ( 1360) hydrogen bonds : angle 4.94636 / 3.48 ( 3817) metal coordination : bond 0.01077 / 0.69 ( 24) metal coordination : angle 4.45296 / 2.73 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 337 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7479 (mmm) cc_final: 0.7176 (mmm) REVERT: A 146 MET cc_start: 0.6606 (mmp) cc_final: 0.6379 (mmm) REVERT: A 268 ASP cc_start: 0.8475 (t70) cc_final: 0.8223 (t0) REVERT: A 609 ASP cc_start: 0.8656 (t0) cc_final: 0.8230 (OUTLIER) REVERT: A 708 MET cc_start: 0.2563 (ttp) cc_final: 0.2086 (ptm) REVERT: A 714 PHE cc_start: 0.6619 (t80) cc_final: 0.6238 (t80) REVERT: A 789 LYS cc_start: 0.7966 (mptt) cc_final: 0.7664 (mmmm) REVERT: A 790 ASP cc_start: 0.6878 (m-30) cc_final: 0.6406 (t0) REVERT: A 795 GLU cc_start: 0.8699 (pp20) cc_final: 0.8313 (pt0) REVERT: A 830 LYS cc_start: 0.7769 (mmtt) cc_final: 0.6717 (ttpt) REVERT: A 1112 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7796 (pttm) REVERT: A 1191 TRP cc_start: 0.4135 (OUTLIER) cc_final: 0.3211 (t-100) REVERT: A 1285 MET cc_start: 0.8032 (mmt) cc_final: 0.7628 (mmm) REVERT: A 1287 TYR cc_start: 0.8559 (m-10) cc_final: 0.8020 (m-10) REVERT: A 1307 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: A 1411 GLU cc_start: 0.8498 (tp30) cc_final: 0.7869 (tp30) REVERT: B 88 TYR cc_start: 0.7192 (m-10) cc_final: 0.6406 (m-80) REVERT: B 358 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7870 (mmtt) REVERT: B 387 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 422 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7553 (mttt) REVERT: B 531 GLN cc_start: 0.7818 (pm20) cc_final: 0.7563 (pt0) REVERT: B 595 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7341 (ttp80) REVERT: B 616 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 618 ASP cc_start: 0.8179 (t0) cc_final: 0.7690 (t0) REVERT: B 658 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 953 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7171 (tm) REVERT: B 1041 GLU cc_start: 0.8231 (tp30) cc_final: 0.7990 (tp30) REVERT: B 1125 ASP cc_start: 0.8714 (t0) cc_final: 0.8273 (t0) REVERT: C 94 LYS cc_start: 0.7495 (mtmt) cc_final: 0.7093 (mmtm) REVERT: C 137 LYS cc_start: 0.8182 (tppp) cc_final: 0.7676 (tttm) REVERT: C 152 GLU cc_start: 0.8750 (tt0) cc_final: 0.8183 (tp30) REVERT: D 1 MET cc_start: 0.2070 (pmm) cc_final: 0.1160 (ppp) REVERT: D 32 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6174 (tp30) REVERT: E 8 ASN cc_start: 0.7973 (m110) cc_final: 0.7719 (t0) REVERT: E 40 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8379 (mm-30) REVERT: E 115 ASN cc_start: 0.8148 (t0) cc_final: 0.7824 (p0) REVERT: E 137 GLU cc_start: 0.8308 (tt0) cc_final: 0.8042 (tt0) REVERT: F 81 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8490 (p) REVERT: F 129 LYS cc_start: 0.8401 (mmtp) cc_final: 0.8101 (mmtt) REVERT: G 11 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8122 (mt) REVERT: G 106 MET cc_start: 0.2835 (ttp) cc_final: 0.2618 (ttp) REVERT: G 143 ILE cc_start: 0.3229 (OUTLIER) cc_final: 0.2573 (mp) REVERT: H 24 CYS cc_start: 0.8983 (m) cc_final: 0.8782 (m) REVERT: H 27 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7912 (tt0) REVERT: H 52 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7732 (mm-40) REVERT: H 86 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: H 87 ARG cc_start: 0.7657 (mmp80) cc_final: 0.7147 (mmp80) REVERT: H 129 TYR cc_start: 0.7879 (p90) cc_final: 0.7127 (p90) REVERT: J 6 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8041 (mtm-85) REVERT: K 12 LEU cc_start: 0.8218 (mt) cc_final: 0.8015 (mm) outliers start: 127 outliers final: 50 residues processed: 413 average time/residue: 0.7210 time to fit residues: 352.7362 Evaluate side-chains 379 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 112 optimal weight: 10.0000 chunk 365 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 320 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 281 HIS A 394 ASN A 975 HIS B 433 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN G 53 ASN H 133 ASN J 23 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104694 restraints weight = 42845.064| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.15 r_work: 0.3174 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.978 32196 Z= 0.460 Angle : 0.584 28.775 43704 Z= 0.313 Chirality : 0.045 0.714 4920 Planarity : 0.004 0.053 5462 Dihedral : 12.087 133.404 4767 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 3.01 % Allowed : 15.31 % Favored : 81.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3773 helix: 1.24 (0.14), residues: 1347 sheet: 0.08 (0.22), residues: 574 loop : -0.50 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 961 TYR 0.022 0.001 TYR B 275 PHE 0.077 0.002 PHE D 70 TRP 0.016 0.001 TRP B 308 HIS 0.009 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.46 (32172) covalent geometry : angle 0.57512 / 0.31 (43671) hydrogen bonds : bond 0.03980 / 2.63 ( 1360) hydrogen bonds : angle 4.54795 / 3.19 ( 3817) metal coordination : bond 0.00489 / 0.32 ( 24) metal coordination : angle 3.64686 / 2.25 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 359 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.5920 (mmtt) cc_final: 0.5707 (mmtt) REVERT: A 108 MET cc_start: 0.7473 (mmm) cc_final: 0.7141 (mmm) REVERT: A 609 ASP cc_start: 0.8499 (t0) cc_final: 0.8114 (t0) REVERT: A 708 MET cc_start: 0.2687 (ttp) cc_final: 0.2303 (ptm) REVERT: A 739 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8002 (t0) REVERT: A 789 LYS cc_start: 0.7845 (mptt) cc_final: 0.7587 (mmmm) REVERT: A 790 ASP cc_start: 0.7032 (m-30) cc_final: 0.6533 (t0) REVERT: A 795 GLU cc_start: 0.8701 (pp20) cc_final: 0.8299 (pt0) REVERT: A 830 LYS cc_start: 0.7645 (mmtt) cc_final: 0.6605 (ttpt) REVERT: A 961 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7535 (ttp-110) REVERT: A 973 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6904 (mp) REVERT: A 1112 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7698 (pttm) REVERT: A 1191 TRP cc_start: 0.4071 (OUTLIER) cc_final: 0.3831 (t-100) REVERT: A 1285 MET cc_start: 0.8088 (mmt) cc_final: 0.7666 (mmt) REVERT: A 1287 TYR cc_start: 0.8484 (m-10) cc_final: 0.7939 (m-10) REVERT: A 1307 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: A 1319 VAL cc_start: 0.8334 (p) cc_final: 0.7968 (m) REVERT: A 1377 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8726 (m) REVERT: A 1406 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8848 (m) REVERT: A 1411 GLU cc_start: 0.8369 (tp30) cc_final: 0.7666 (tp30) REVERT: B 65 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: B 68 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 358 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7867 (mmtt) REVERT: B 387 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 396 ASP cc_start: 0.8392 (m-30) cc_final: 0.7934 (m-30) REVERT: B 422 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7538 (mttt) REVERT: B 531 GLN cc_start: 0.7832 (pm20) cc_final: 0.7597 (pt0) REVERT: B 595 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: B 615 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7718 (ptp) REVERT: B 616 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7949 (tt) REVERT: B 618 ASP cc_start: 0.8194 (t0) cc_final: 0.7727 (t0) REVERT: B 667 GLN cc_start: 0.6070 (OUTLIER) cc_final: 0.5840 (tm-30) REVERT: B 953 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7063 (tm) REVERT: B 1041 GLU cc_start: 0.8198 (tp30) cc_final: 0.7931 (tp30) REVERT: B 1125 ASP cc_start: 0.8655 (t0) cc_final: 0.8239 (t0) REVERT: C 85 ASP cc_start: 0.6433 (m-30) cc_final: 0.5836 (t0) REVERT: C 94 LYS cc_start: 0.7418 (mtmt) cc_final: 0.7016 (mmtm) REVERT: C 137 LYS cc_start: 0.8148 (tppp) cc_final: 0.7688 (tttm) REVERT: C 152 GLU cc_start: 0.8734 (tt0) cc_final: 0.8237 (tp30) REVERT: D 1 MET cc_start: 0.2176 (pmm) cc_final: 0.1198 (ppp) REVERT: D 32 GLU cc_start: 0.6403 (mm-30) cc_final: 0.5905 (tp30) REVERT: E 54 GLN cc_start: 0.7513 (mt0) cc_final: 0.6877 (mt0) REVERT: E 57 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7586 (ptp) REVERT: E 115 ASN cc_start: 0.8078 (t0) cc_final: 0.7820 (p0) REVERT: E 137 GLU cc_start: 0.8233 (tt0) cc_final: 0.7964 (tt0) REVERT: F 81 THR cc_start: 0.8747 (m) cc_final: 0.8418 (p) REVERT: F 129 LYS cc_start: 0.8358 (mmtp) cc_final: 0.8036 (mmtt) REVERT: G 22 MET cc_start: 0.7539 (ttp) cc_final: 0.7253 (ttp) REVERT: G 41 LYS cc_start: 0.6728 (mmtt) cc_final: 0.6469 (mppt) REVERT: G 42 PHE cc_start: 0.6044 (m-80) cc_final: 0.5647 (m-80) REVERT: G 106 MET cc_start: 0.2834 (ttp) cc_final: 0.2503 (ttp) REVERT: G 143 ILE cc_start: 0.3231 (OUTLIER) cc_final: 0.2889 (mp) REVERT: H 27 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7855 (tt0) REVERT: H 86 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: H 87 ARG cc_start: 0.7768 (mmp80) cc_final: 0.7450 (mmp80) REVERT: H 129 TYR cc_start: 0.7833 (p90) cc_final: 0.7012 (p90) outliers start: 101 outliers final: 27 residues processed: 417 average time/residue: 0.6360 time to fit residues: 316.8400 Evaluate side-chains 383 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain K residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 363 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 309 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN B 433 GLN B 794 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 61 GLN G 53 ASN H 64 ASN J 23 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100968 restraints weight = 43420.243| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.13 r_work: 0.3122 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.980 32196 Z= 0.532 Angle : 0.682 28.781 43704 Z= 0.360 Chirality : 0.049 0.673 4920 Planarity : 0.005 0.055 5462 Dihedral : 12.163 134.108 4767 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 3.16 % Allowed : 15.70 % Favored : 81.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 3773 helix: 1.02 (0.14), residues: 1342 sheet: -0.17 (0.21), residues: 617 loop : -0.64 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.024 0.002 TYR E 187 PHE 0.077 0.002 PHE D 70 TRP 0.013 0.002 TRP B 308 HIS 0.012 0.002 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01381 / 0.53 (32172) covalent geometry : angle 0.67295 / 0.36 (43671) hydrogen bonds : bond 0.04774 / 3.17 ( 1360) hydrogen bonds : angle 4.75650 / 3.34 ( 3817) metal coordination : bond 0.00879 / 0.56 ( 24) metal coordination : angle 4.07427 / 2.48 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 324 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7442 (mmm) cc_final: 0.7123 (mmm) REVERT: A 609 ASP cc_start: 0.8582 (t0) cc_final: 0.8224 (t0) REVERT: A 789 LYS cc_start: 0.7901 (mptt) cc_final: 0.7659 (mmmm) REVERT: A 790 ASP cc_start: 0.6996 (m-30) cc_final: 0.6520 (t0) REVERT: A 795 GLU cc_start: 0.8728 (pp20) cc_final: 0.8404 (pp20) REVERT: A 830 LYS cc_start: 0.7712 (mmtt) cc_final: 0.6603 (ttpt) REVERT: A 1112 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7801 (pttm) REVERT: A 1191 TRP cc_start: 0.3981 (OUTLIER) cc_final: 0.3055 (t-100) REVERT: A 1259 MET cc_start: 0.0398 (OUTLIER) cc_final: -0.0085 (mpp) REVERT: A 1285 MET cc_start: 0.8060 (mmt) cc_final: 0.7662 (mmt) REVERT: A 1287 TYR cc_start: 0.8514 (m-10) cc_final: 0.8001 (m-10) REVERT: A 1307 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: A 1319 VAL cc_start: 0.8399 (p) cc_final: 0.8015 (m) REVERT: A 1377 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8744 (m) REVERT: A 1411 GLU cc_start: 0.8481 (tp30) cc_final: 0.7809 (tp30) REVERT: B 68 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8308 (p) REVERT: B 88 TYR cc_start: 0.7148 (m-10) cc_final: 0.6384 (m-80) REVERT: B 358 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7969 (mmtt) REVERT: B 387 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8376 (mm) REVERT: B 422 LYS cc_start: 0.7905 (mmtm) cc_final: 0.7489 (mttt) REVERT: B 531 GLN cc_start: 0.7842 (pm20) cc_final: 0.7573 (pt0) REVERT: B 595 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7352 (ttp80) REVERT: B 616 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 618 ASP cc_start: 0.8195 (t0) cc_final: 0.7703 (t0) REVERT: B 904 ARG cc_start: 0.5820 (ttt180) cc_final: 0.5150 (mtp85) REVERT: B 953 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7174 (tm) REVERT: B 1041 GLU cc_start: 0.8257 (tp30) cc_final: 0.8001 (tp30) REVERT: B 1125 ASP cc_start: 0.8712 (t0) cc_final: 0.8272 (t0) REVERT: C 19 ASP cc_start: 0.8436 (t0) cc_final: 0.8212 (t0) REVERT: C 94 LYS cc_start: 0.7535 (mtmt) cc_final: 0.7117 (mmtm) REVERT: C 137 LYS cc_start: 0.8349 (tppp) cc_final: 0.7802 (tttm) REVERT: C 152 GLU cc_start: 0.8765 (tt0) cc_final: 0.8198 (tp30) REVERT: D 1 MET cc_start: 0.2014 (pmm) cc_final: 0.1205 (ppp) REVERT: D 32 GLU cc_start: 0.6455 (mm-30) cc_final: 0.5857 (tp30) REVERT: D 132 GLN cc_start: 0.2696 (mm-40) cc_final: 0.2344 (mp10) REVERT: D 218 GLU cc_start: 0.4078 (OUTLIER) cc_final: 0.3073 (tm-30) REVERT: E 54 GLN cc_start: 0.7459 (mt0) cc_final: 0.7130 (mt0) REVERT: E 57 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7623 (ptp) REVERT: E 115 ASN cc_start: 0.8152 (t0) cc_final: 0.7856 (p0) REVERT: E 137 GLU cc_start: 0.8371 (tt0) cc_final: 0.8046 (tt0) REVERT: F 129 LYS cc_start: 0.8478 (mmtp) cc_final: 0.8106 (mmtm) REVERT: G 22 MET cc_start: 0.7696 (ttp) cc_final: 0.7436 (ttp) REVERT: G 41 LYS cc_start: 0.6915 (mmtt) cc_final: 0.6335 (mppt) REVERT: G 42 PHE cc_start: 0.6323 (m-80) cc_final: 0.5938 (m-80) REVERT: G 106 MET cc_start: 0.2871 (ttp) cc_final: 0.2588 (ttp) REVERT: G 143 ILE cc_start: 0.3239 (OUTLIER) cc_final: 0.2809 (mp) REVERT: H 27 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7881 (tt0) REVERT: H 86 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: H 87 ARG cc_start: 0.7688 (mmp80) cc_final: 0.7183 (mmp80) REVERT: K 12 LEU cc_start: 0.8222 (mt) cc_final: 0.7965 (mm) outliers start: 106 outliers final: 39 residues processed: 393 average time/residue: 0.6538 time to fit residues: 304.7831 Evaluate side-chains 376 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain K residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 379 optimal weight: 20.0000 chunk 174 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 254 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS A 706 HIS ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN G 53 ASN H 64 ASN J 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104521 restraints weight = 43155.566| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.15 r_work: 0.3172 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.979 32196 Z= 0.460 Angle : 0.582 28.752 43704 Z= 0.312 Chirality : 0.044 0.716 4920 Planarity : 0.004 0.053 5462 Dihedral : 12.072 134.131 4767 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 2.17 % Allowed : 16.65 % Favored : 81.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3773 helix: 1.30 (0.14), residues: 1341 sheet: -0.02 (0.21), residues: 580 loop : -0.51 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 961 TYR 0.022 0.001 TYR E 187 PHE 0.078 0.001 PHE D 70 TRP 0.015 0.001 TRP B 308 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01216 / 0.46 (32172) covalent geometry : angle 0.57475 / 0.31 (43671) hydrogen bonds : bond 0.03876 / 2.57 ( 1360) hydrogen bonds : angle 4.46504 / 3.13 ( 3817) metal coordination : bond 0.00470 / 0.31 ( 24) metal coordination : angle 3.44624 / 2.13 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 352 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7492 (mmm) cc_final: 0.7123 (mmm) REVERT: A 609 ASP cc_start: 0.8495 (t0) cc_final: 0.8183 (t0) REVERT: A 789 LYS cc_start: 0.7880 (mptt) cc_final: 0.7637 (mtpm) REVERT: A 790 ASP cc_start: 0.7052 (m-30) cc_final: 0.6625 (t0) REVERT: A 795 GLU cc_start: 0.8708 (pp20) cc_final: 0.8234 (pt0) REVERT: A 830 LYS cc_start: 0.7641 (mmtt) cc_final: 0.6534 (ttpt) REVERT: A 973 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6889 (mp) REVERT: A 1112 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7792 (pttm) REVERT: A 1191 TRP cc_start: 0.3999 (OUTLIER) cc_final: 0.3752 (t-100) REVERT: A 1283 VAL cc_start: 0.8647 (p) cc_final: 0.8428 (t) REVERT: A 1285 MET cc_start: 0.8018 (mmt) cc_final: 0.7522 (mmt) REVERT: A 1287 TYR cc_start: 0.8500 (m-10) cc_final: 0.8201 (m-10) REVERT: A 1319 VAL cc_start: 0.8331 (p) cc_final: 0.7963 (m) REVERT: A 1406 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8840 (m) REVERT: A 1411 GLU cc_start: 0.8371 (tp30) cc_final: 0.7657 (tp30) REVERT: B 68 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8275 (p) REVERT: B 71 LEU cc_start: 0.7485 (tt) cc_final: 0.7268 (tp) REVERT: B 88 TYR cc_start: 0.7231 (m-10) cc_final: 0.6391 (m-80) REVERT: B 358 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7842 (mmtt) REVERT: B 387 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8349 (mm) REVERT: B 396 ASP cc_start: 0.8406 (m-30) cc_final: 0.7947 (m-30) REVERT: B 422 LYS cc_start: 0.7945 (mmtm) cc_final: 0.7550 (mttt) REVERT: B 433 GLN cc_start: 0.6891 (mt0) cc_final: 0.6544 (mt0) REVERT: B 531 GLN cc_start: 0.7828 (pm20) cc_final: 0.7596 (pt0) REVERT: B 616 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7981 (tt) REVERT: B 618 ASP cc_start: 0.8138 (t0) cc_final: 0.7679 (t0) REVERT: B 953 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7006 (tm) REVERT: B 1041 GLU cc_start: 0.8255 (tp30) cc_final: 0.7989 (tp30) REVERT: B 1049 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: B 1125 ASP cc_start: 0.8669 (t0) cc_final: 0.8247 (t0) REVERT: C 19 ASP cc_start: 0.8336 (t0) cc_final: 0.8080 (t0) REVERT: C 94 LYS cc_start: 0.7430 (mtmt) cc_final: 0.7039 (mmtm) REVERT: C 137 LYS cc_start: 0.8312 (tppp) cc_final: 0.7766 (tttm) REVERT: C 152 GLU cc_start: 0.8734 (tt0) cc_final: 0.8204 (tp30) REVERT: D 1 MET cc_start: 0.2039 (pmm) cc_final: 0.1126 (ppp) REVERT: D 32 GLU cc_start: 0.6386 (mm-30) cc_final: 0.5841 (tp30) REVERT: E 54 GLN cc_start: 0.7331 (mt0) cc_final: 0.7101 (mt0) REVERT: E 57 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7555 (ptp) REVERT: E 115 ASN cc_start: 0.8117 (t0) cc_final: 0.7853 (p0) REVERT: E 137 GLU cc_start: 0.8291 (tt0) cc_final: 0.8047 (tt0) REVERT: F 81 THR cc_start: 0.8731 (m) cc_final: 0.8403 (p) REVERT: F 129 LYS cc_start: 0.8419 (mmtp) cc_final: 0.8086 (mmtt) REVERT: G 22 MET cc_start: 0.7459 (ttp) cc_final: 0.7186 (ttp) REVERT: G 41 LYS cc_start: 0.6911 (mmtt) cc_final: 0.6597 (mppt) REVERT: G 42 PHE cc_start: 0.6411 (m-80) cc_final: 0.6054 (m-80) REVERT: G 106 MET cc_start: 0.3288 (ttp) cc_final: 0.3018 (ttp) REVERT: G 143 ILE cc_start: 0.3342 (OUTLIER) cc_final: 0.2924 (mp) REVERT: H 27 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7831 (tt0) REVERT: H 52 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7765 (mm-40) REVERT: H 86 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7756 (m-30) outliers start: 73 outliers final: 31 residues processed: 400 average time/residue: 0.6557 time to fit residues: 312.8010 Evaluate side-chains 376 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 223 optimal weight: 0.0470 chunk 261 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 254 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS A 903 ASN ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN G 53 ASN H 64 ASN J 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103783 restraints weight = 42987.001| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.14 r_work: 0.3161 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.979 32196 Z= 0.471 Angle : 0.600 28.738 43704 Z= 0.319 Chirality : 0.045 0.707 4920 Planarity : 0.004 0.053 5462 Dihedral : 12.046 134.436 4767 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.85 % Allowed : 17.40 % Favored : 80.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3773 helix: 1.35 (0.14), residues: 1341 sheet: 0.02 (0.21), residues: 570 loop : -0.51 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 19 TYR 0.025 0.001 TYR E 46 PHE 0.079 0.002 PHE D 70 TRP 0.015 0.001 TRP B 308 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01241 / 0.47 (32172) covalent geometry : angle 0.59301 / 0.32 (43671) hydrogen bonds : bond 0.03954 / 2.63 ( 1360) hydrogen bonds : angle 4.44616 / 3.12 ( 3817) metal coordination : bond 0.00534 / 0.35 ( 24) metal coordination : angle 3.32131 / 2.03 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7535 (mmm) cc_final: 0.7119 (mmm) REVERT: A 609 ASP cc_start: 0.8509 (t0) cc_final: 0.8202 (t0) REVERT: A 708 MET cc_start: 0.0016 (ptm) cc_final: -0.0276 (ttp) REVERT: A 789 LYS cc_start: 0.7885 (mptt) cc_final: 0.7641 (mtpm) REVERT: A 790 ASP cc_start: 0.7057 (m-30) cc_final: 0.6619 (OUTLIER) REVERT: A 795 GLU cc_start: 0.8706 (pp20) cc_final: 0.8229 (pt0) REVERT: A 830 LYS cc_start: 0.7647 (mmtt) cc_final: 0.6551 (ttpt) REVERT: A 1112 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7798 (pttm) REVERT: A 1191 TRP cc_start: 0.4022 (OUTLIER) cc_final: 0.3755 (t-100) REVERT: A 1285 MET cc_start: 0.8048 (mmt) cc_final: 0.7609 (mmt) REVERT: A 1287 TYR cc_start: 0.8471 (m-10) cc_final: 0.7812 (m-10) REVERT: A 1319 VAL cc_start: 0.8292 (p) cc_final: 0.7935 (m) REVERT: A 1406 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8881 (m) REVERT: A 1411 GLU cc_start: 0.8396 (tp30) cc_final: 0.7683 (tp30) REVERT: B 68 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 71 LEU cc_start: 0.7459 (tt) cc_final: 0.7243 (tp) REVERT: B 88 TYR cc_start: 0.7175 (m-10) cc_final: 0.6368 (m-80) REVERT: B 150 GLU cc_start: 0.6569 (tp30) cc_final: 0.6016 (pm20) REVERT: B 358 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7659 (mmtt) REVERT: B 387 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8357 (mm) REVERT: B 396 ASP cc_start: 0.8405 (m-30) cc_final: 0.7949 (m-30) REVERT: B 422 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7585 (mttt) REVERT: B 433 GLN cc_start: 0.6946 (mt0) cc_final: 0.6621 (mt0) REVERT: B 531 GLN cc_start: 0.7887 (pm20) cc_final: 0.7621 (pt0) REVERT: B 616 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7982 (tt) REVERT: B 618 ASP cc_start: 0.8148 (t0) cc_final: 0.7692 (t0) REVERT: B 953 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7104 (tm) REVERT: B 1041 GLU cc_start: 0.8307 (tp30) cc_final: 0.8019 (tp30) REVERT: B 1125 ASP cc_start: 0.8688 (t0) cc_final: 0.8256 (t0) REVERT: C 19 ASP cc_start: 0.8313 (t0) cc_final: 0.8050 (t0) REVERT: C 61 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: C 94 LYS cc_start: 0.7454 (mtmt) cc_final: 0.7043 (mmtm) REVERT: C 137 LYS cc_start: 0.8325 (tppp) cc_final: 0.7791 (tttm) REVERT: C 152 GLU cc_start: 0.8752 (tt0) cc_final: 0.8237 (tp30) REVERT: D 1 MET cc_start: 0.2045 (pmm) cc_final: 0.1157 (ppp) REVERT: D 32 GLU cc_start: 0.6390 (mm-30) cc_final: 0.5840 (tp30) REVERT: D 157 GLN cc_start: 0.5998 (pm20) cc_final: 0.5393 (pt0) REVERT: E 115 ASN cc_start: 0.8080 (t0) cc_final: 0.7843 (p0) REVERT: E 137 GLU cc_start: 0.8323 (tt0) cc_final: 0.8079 (tt0) REVERT: F 129 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8075 (mmtt) REVERT: G 22 MET cc_start: 0.7497 (ttp) cc_final: 0.7272 (ttp) REVERT: G 41 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6610 (mptt) REVERT: G 42 PHE cc_start: 0.6469 (m-80) cc_final: 0.6111 (m-80) REVERT: G 106 MET cc_start: 0.3303 (ttp) cc_final: 0.3007 (ttp) REVERT: G 143 ILE cc_start: 0.3414 (OUTLIER) cc_final: 0.3015 (pp) REVERT: H 27 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7857 (tt0) outliers start: 62 outliers final: 33 residues processed: 370 average time/residue: 0.6440 time to fit residues: 282.0409 Evaluate side-chains 368 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 137 optimal weight: 0.6980 chunk 374 optimal weight: 0.0570 chunk 230 optimal weight: 7.9990 chunk 220 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS A 903 ASN ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN G 53 ASN H 64 ASN J 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106770 restraints weight = 42964.058| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.08 r_work: 0.3197 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.978 32196 Z= 0.458 Angle : 0.575 28.730 43704 Z= 0.307 Chirality : 0.044 0.722 4920 Planarity : 0.004 0.053 5462 Dihedral : 12.000 134.593 4767 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 1.37 % Allowed : 17.90 % Favored : 80.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3773 helix: 1.52 (0.14), residues: 1335 sheet: 0.16 (0.22), residues: 569 loop : -0.45 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 19 TYR 0.025 0.001 TYR E 46 PHE 0.079 0.001 PHE D 70 TRP 0.014 0.001 TRP B 308 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.46 (32172) covalent geometry : angle 0.56620 / 0.31 (43671) hydrogen bonds : bond 0.03606 / 2.40 ( 1360) hydrogen bonds : angle 4.29500 / 3.01 ( 3817) metal coordination : bond 0.00485 / 0.33 ( 24) metal coordination : angle 3.64410 / 2.34 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7546 Ramachandran restraints generated. 3773 Oldfield, 0 Emsley, 3773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7016 (mmm) cc_final: 0.6596 (mmm) REVERT: A 609 ASP cc_start: 0.8504 (t0) cc_final: 0.8201 (t0) REVERT: A 695 LYS cc_start: 0.6628 (mptt) cc_final: 0.5740 (mttt) REVERT: A 789 LYS cc_start: 0.7939 (mptt) cc_final: 0.7671 (mtpm) REVERT: A 790 ASP cc_start: 0.7079 (m-30) cc_final: 0.6661 (t0) REVERT: A 795 GLU cc_start: 0.8704 (pp20) cc_final: 0.8249 (pt0) REVERT: A 830 LYS cc_start: 0.7558 (mmtt) cc_final: 0.6477 (ttpt) REVERT: A 1112 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7747 (pttm) REVERT: A 1191 TRP cc_start: 0.3940 (OUTLIER) cc_final: 0.3624 (t-100) REVERT: A 1285 MET cc_start: 0.8065 (mmt) cc_final: 0.7587 (mmm) REVERT: A 1319 VAL cc_start: 0.8188 (p) cc_final: 0.7847 (m) REVERT: A 1411 GLU cc_start: 0.8272 (tp30) cc_final: 0.7514 (tp30) REVERT: B 68 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8227 (p) REVERT: B 88 TYR cc_start: 0.7193 (m-10) cc_final: 0.6375 (m-80) REVERT: B 150 GLU cc_start: 0.6617 (tp30) cc_final: 0.6047 (pm20) REVERT: B 294 ASP cc_start: 0.5069 (m-30) cc_final: 0.4003 (t0) REVERT: B 358 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7660 (mmtt) REVERT: B 387 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 396 ASP cc_start: 0.8377 (m-30) cc_final: 0.7937 (m-30) REVERT: B 422 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7538 (mttt) REVERT: B 433 GLN cc_start: 0.7158 (mt0) cc_final: 0.6851 (mt0) REVERT: B 531 GLN cc_start: 0.7870 (pm20) cc_final: 0.7592 (pt0) REVERT: B 616 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7984 (tt) REVERT: B 618 ASP cc_start: 0.8118 (t0) cc_final: 0.7700 (t0) REVERT: B 953 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7040 (tm) REVERT: B 1041 GLU cc_start: 0.8295 (tp30) cc_final: 0.8006 (tp30) REVERT: B 1125 ASP cc_start: 0.8691 (t0) cc_final: 0.8263 (t0) REVERT: C 19 ASP cc_start: 0.8215 (t0) cc_final: 0.7945 (t0) REVERT: C 61 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: C 94 LYS cc_start: 0.7426 (mtmt) cc_final: 0.7042 (mmtm) REVERT: C 136 ASP cc_start: 0.7901 (t70) cc_final: 0.7633 (t70) REVERT: C 137 LYS cc_start: 0.8410 (tppp) cc_final: 0.7821 (tttm) REVERT: C 152 GLU cc_start: 0.8725 (tt0) cc_final: 0.8171 (tp30) REVERT: D 1 MET cc_start: 0.2198 (pmm) cc_final: 0.1121 (ppp) REVERT: D 32 GLU cc_start: 0.6406 (mm-30) cc_final: 0.5888 (tp30) REVERT: D 157 GLN cc_start: 0.5964 (pm20) cc_final: 0.5242 (pt0) REVERT: E 115 ASN cc_start: 0.8063 (t0) cc_final: 0.7835 (p0) REVERT: E 137 GLU cc_start: 0.8277 (tt0) cc_final: 0.8062 (tt0) REVERT: F 129 LYS cc_start: 0.8374 (mmtp) cc_final: 0.7954 (mmtt) REVERT: G 42 PHE cc_start: 0.6507 (m-80) cc_final: 0.5764 (m-80) REVERT: G 106 MET cc_start: 0.3403 (ttp) cc_final: 0.3178 (ttp) REVERT: G 143 ILE cc_start: 0.3336 (OUTLIER) cc_final: 0.2936 (pp) REVERT: H 27 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7774 (tt0) REVERT: K 11 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8245 (mm) outliers start: 46 outliers final: 25 residues processed: 375 average time/residue: 0.6421 time to fit residues: 286.4983 Evaluate side-chains 358 residues out of total 3357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 1191 TRP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.3980 chunk 350 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 282 optimal weight: 0.3980 chunk 361 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN H 64 ASN J 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104476 restraints weight = 43274.523| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.13 r_work: 0.3167 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.068 32196 Z= 0.475 Angle : 0.615 25.720 43704 Z= 0.323 Chirality : 0.044 0.316 4920 Planarity : 0.004 0.058 5462 Dihedral : 12.005 134.694 4767 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.31 % Allowed : 18.50 % Favored : 80.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3773 helix: 1.46 (0.14), residues: 1342 sheet: 0.06 (0.22), residues: 578 loop : -0.48 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 19 TYR 0.029 0.001 TYR E 46 PHE 0.023 0.002 PHE A 444 TRP 0.013 0.001 TRP B 308 HIS 0.012 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01252 / 0.48 (32172) covalent geometry : angle 0.60788 / 0.32 (43671) hydrogen bonds : bond 0.03869 / 2.58 ( 1360) hydrogen bonds : angle 4.35790 / 3.05 ( 3817) metal coordination : bond 0.00551 / 0.37 ( 24) metal coordination : angle 3.46829 / 2.13 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12217.15 seconds wall clock time: 208 minutes 20.63 seconds (12500.63 seconds total)