Starting phenix.real_space_refine on Sun Aug 9 10:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sby_54743/08_2026/9sby_54743.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sby_54743/08_2026/9sby_54743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sby_54743/08_2026/9sby_54743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sby_54743/08_2026/9sby_54743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sby_54743/08_2026/9sby_54743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sby_54743/08_2026/9sby_54743.map" } resolution = 3.41 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= 0.031 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 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s 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: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 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: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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 67 106.637 70.357 94.996 1.00149.09 S ATOM 479 SG CYS A 70 106.170 66.819 93.719 1.00150.38 S ATOM 532 SG CYS A 77 103.424 69.483 93.241 1.00141.39 S ATOM 762 SG CYS A 107 81.296 76.298 135.255 1.00185.47 S ATOM 786 SG CYS A 110 82.907 72.981 136.008 1.00181.46 S ATOM 1091 SG CYS A 148 79.441 73.698 137.356 1.00194.02 S ATOM 1105 SG CYS A 167 82.474 75.670 138.706 1.00191.97 S ATOM 19603 SG CYS B1163 98.691 57.960 104.837 1.00151.15 S ATOM 19621 SG CYS B1166 96.966 61.207 105.643 1.00151.88 S ATOM 19746 SG CYS B1182 100.713 61.064 104.898 1.00154.62 S ATOM 19765 SG CYS B1185 99.292 59.838 108.226 1.00152.60 S ATOM 20753 SG CYS C 86 93.190 75.029 25.935 1.00201.23 S ATOM 20770 SG CYS C 88 95.393 77.194 27.887 1.00199.38 S ATOM 20803 SG CYS C 92 94.302 78.408 24.503 1.00179.12 S ATOM 20826 SG CYS C 95 91.767 78.310 27.362 1.00173.50 S ATOM 28411 SG CYS I 7 40.951 125.146 127.891 1.00271.04 S ATOM 28436 SG CYS I 10 44.692 124.459 127.584 1.00263.09 S ATOM 28602 SG CYS I 29 42.488 122.023 129.512 1.00269.11 S ATOM 28626 SG CYS I 32 43.281 125.316 130.985 1.00272.17 S ATOM 28953 SG CYS I 75 16.719 116.081 89.564 1.00273.55 S ATOM 28975 SG CYS I 78 16.503 119.556 88.140 1.00279.82 S ATOM 29191 SG CYS I 103 19.844 117.707 88.171 1.00268.11 S ATOM 29211 SG CYS I 106 18.414 118.941 91.417 1.00267.13 S ATOM 29313 SG CYS J 7 64.036 90.642 37.730 1.00123.05 S ATOM 29336 SG CYS J 10 63.739 88.529 34.502 1.00129.54 S ATOM 29616 SG CYS J 45 60.677 89.209 36.796 1.00136.60 S ATOM 29622 SG CYS J 46 62.154 91.673 34.418 1.00132.87 S ATOM 30745 SG CYS L 31 97.434 113.789 54.224 1.00226.26 S ATOM 30765 SG CYS L 34 98.284 115.402 50.888 1.00220.46 S ATOM 30869 SG CYS L 48 100.946 114.387 53.466 1.00232.89 S ATOM 30892 SG CYS L 51 98.792 117.413 54.105 1.00234.45 S Time building chain proxies: 6.84, per 1000 atoms: 0.21 Number of scatterers: 33083 At special positions: 0 Unit cell: (152.329, 155.593, 183.883, 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 8 29.99 S 182 16.00 P 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " 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 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " 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 " Number of angles added : 45 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 47 sheets defined 38.9% alpha, 20.0% beta 41 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' 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 212 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.644A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.719A 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: 3.736A 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 525 through 536 removed outlier: 3.755A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 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 removed outlier: 3.572A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.558A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.790A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 845 removed outlier: 4.066A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.693A 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 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 1056 removed outlier: 3.535A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1083 removed outlier: 3.518A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1087 removed outlier: 3.569A pdb=" N ALA A1087 " --> pdb=" O PHE A1084 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1087' Processing helix chain 'A' and resid 1091 through 1106 removed outlier: 4.627A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix 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 1174 removed outlier: 4.359A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.556A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.500A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) 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 1376 removed outlier: 3.912A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 removed outlier: 3.621A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.666A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.064A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.658A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 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: 3.798A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.957A 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 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.534A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) 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: 3.535A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.762A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.767A 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 Processing helix chain 'B' and resid 751 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.686A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.110A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.618A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.899A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.259A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.777A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.579A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) 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: 3.540A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.523A 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 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.641A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.520A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.552A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.621A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 4.110A 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 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.761A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.517A 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 54 through 59 removed outlier: 3.928A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.688A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.516A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.542A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.119A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (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 removed outlier: 3.846A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) 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 53 removed outlier: 4.171A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (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 90 removed outlier: 10.130A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.892A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.646A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.706A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.520A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.943A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.852A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.251A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.666A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.666A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.000A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.000A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.016A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.997A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.947A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.486A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.629A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.629A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.204A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.841A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 10 through 13 removed outlier: 5.995A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.827A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.404A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.003A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.618A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.798A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.292A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 1364 hydrogen bonds defined for protein. 3747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 9.67 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.38: 12767 1.38 - 1.57: 20618 1.57 - 1.77: 195 1.77 - 1.96: 292 1.96 - 2.16: 1 Bond restraints: 33873 Sorted by residual: bond pdb=" O3' DC N 44 " pdb=" P DC N 45 " ideal model delta sigma weight residual 1.607 2.160 -0.553 1.20e-02 6.94e+03 2.12e+03 bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.184 0.190 1.00e-02 1.00e+04 3.60e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.210 0.160 1.20e-02 6.94e+03 1.77e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.448 -0.111 1.10e-02 8.26e+03 1.02e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.332 0.077 1.00e-02 1.00e+04 5.90e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.55: 46099 5.55 - 11.10: 47 11.10 - 16.65: 4 16.65 - 22.19: 2 22.19 - 27.74: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" C3' DC N 44 " pdb=" O3' DC N 44 " pdb=" P DC N 45 " ideal model delta sigma weight residual 119.70 91.96 27.74 1.20e+00 6.94e-01 5.34e+02 angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 121.42 18.45 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 122.43 14.40 1.00e+00 1.00e+00 2.07e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.38 -13.66 1.00e+00 1.00e+00 1.87e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.38 8.31 1.00e+00 1.00e+00 6.91e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.63: 19700 30.63 - 61.26: 703 61.26 - 91.88: 59 91.88 - 122.51: 2 122.51 - 153.14: 3 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: 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 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual 180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA VAL E 90 " pdb=" C VAL E 90 " pdb=" N LYS E 91 " pdb=" CA LYS E 91 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3404 0.037 - 0.074: 1246 0.074 - 0.110: 399 0.110 - 0.147: 131 0.147 - 0.184: 10 Chirality restraints: 5190 Sorted by residual: 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 8.48e-01 chirality pdb=" C3' DT T 46 " pdb=" C4' DT T 46 " pdb=" O3' DT T 46 " pdb=" C2' DT T 46 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" C3' DC N 38 " pdb=" C4' DC N 38 " pdb=" O3' DC N 38 " pdb=" C2' DC N 38 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU A 710 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A1099 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.019 2.00e-02 2.50e+03 1.40e-02 3.92e+00 pdb=" CG TYR B 797 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.002 2.00e-02 2.50e+03 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 49 2.32 - 2.96: 15777 2.96 - 3.61: 48043 3.61 - 4.25: 77354 4.25 - 4.90: 129782 Nonbonded interactions: 271005 Sorted by model distance: nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.674 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.975 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1802 " model vdw 2.012 2.170 nonbonded pdb=" O LEU D 148 " pdb=" OG SER D 152 " model vdw 2.134 3.040 nonbonded pdb=" NH1 ARG B 996 " pdb=" O CYS J 10 " model vdw 2.153 3.120 ... (remaining 271000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 38.190 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.007 0.553 33905 Z= 0.435 Angle : 0.676 27.742 46198 Z= 0.444 Chirality : 0.045 0.184 5190 Planarity : 0.004 0.053 5630 Dihedral : 14.632 153.142 13127 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 3854 helix: 1.44 (0.15), residues: 1323 sheet: -0.28 (0.20), residues: 669 loop : -0.29 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1366 TYR 0.034 0.001 TYR B 797 PHE 0.018 0.002 PHE A 219 TRP 0.023 0.001 TRP A1044 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.44 (33873) covalent geometry : angle 0.66892 / 0.44 (46153) hydrogen bonds : bond 0.18452 / 12.25 ( 1427) hydrogen bonds : angle 6.83425 / 4.91 ( 3959) metal coordination : bond 0.00724 / 0.45 ( 32) metal coordination : angle 3.09123 / 1.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 1.069 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 143 LYS cc_start: 0.8972 (pttt) cc_final: 0.8725 (ptpp) REVERT: A 175 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7762 (ptm-80) REVERT: A 250 ILE cc_start: 0.8563 (mm) cc_final: 0.8268 (tp) REVERT: A 268 ASP cc_start: 0.8641 (t0) cc_final: 0.8384 (t70) REVERT: A 317 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7634 (ptmm) REVERT: A 494 SER cc_start: 0.8201 (m) cc_final: 0.7957 (p) REVERT: A 542 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7802 (mp0) REVERT: A 602 ASP cc_start: 0.8918 (t0) cc_final: 0.8366 (t0) REVERT: A 605 MET cc_start: 0.9364 (tpt) cc_final: 0.9110 (tpp) REVERT: A 708 MET cc_start: 0.7795 (mtt) cc_final: 0.7427 (mtp) REVERT: A 748 MET cc_start: 0.8938 (mtm) cc_final: 0.8667 (mtp) REVERT: A 780 VAL cc_start: 0.8945 (t) cc_final: 0.8715 (m) REVERT: A 789 LYS cc_start: 0.8151 (mttt) cc_final: 0.7758 (mttp) REVERT: A 847 ASP cc_start: 0.8857 (p0) cc_final: 0.8613 (p0) REVERT: A 931 GLU cc_start: 0.8724 (tt0) cc_final: 0.8122 (tm-30) REVERT: A 1005 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7788 (tp30) REVERT: A 1071 SER cc_start: 0.9207 (m) cc_final: 0.8989 (m) REVERT: A 1112 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8714 (tppt) REVERT: A 1148 ILE cc_start: 0.8709 (mt) cc_final: 0.8048 (mt) REVERT: A 1285 MET cc_start: 0.7694 (mmt) cc_final: 0.7492 (mmt) REVERT: B 86 ARG cc_start: 0.8135 (mpt-90) cc_final: 0.7862 (mmt-90) REVERT: B 183 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7955 (pm20) REVERT: B 322 PHE cc_start: 0.8263 (t80) cc_final: 0.8019 (t80) REVERT: B 347 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7851 (tptt) REVERT: B 394 ASP cc_start: 0.9000 (t0) cc_final: 0.8497 (p0) REVERT: B 470 LYS cc_start: 0.9186 (mppt) cc_final: 0.8933 (mmtt) REVERT: B 498 THR cc_start: 0.8176 (m) cc_final: 0.7590 (p) REVERT: B 620 ARG cc_start: 0.8880 (ptp-170) cc_final: 0.8244 (ttt-90) REVERT: B 730 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8117 (ptp-110) REVERT: C 78 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8536 (mm-30) REVERT: C 136 ASP cc_start: 0.7823 (t70) cc_final: 0.7491 (t0) REVERT: C 207 CYS cc_start: 0.9019 (m) cc_final: 0.8739 (m) REVERT: C 209 TYR cc_start: 0.8898 (m-80) cc_final: 0.8297 (m-80) REVERT: D 23 ASN cc_start: 0.6244 (t0) cc_final: 0.6023 (t0) REVERT: D 39 ASN cc_start: 0.7286 (p0) cc_final: 0.6785 (p0) REVERT: D 65 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8243 (mt-10) REVERT: D 148 LEU cc_start: 0.7875 (mt) cc_final: 0.7652 (mt) REVERT: D 166 LEU cc_start: 0.8631 (tp) cc_final: 0.8320 (pp) REVERT: E 7 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8546 (ttm110) REVERT: E 32 GLN cc_start: 0.8560 (tt0) cc_final: 0.7543 (tp40) REVERT: E 36 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8438 (mp0) REVERT: E 41 ASP cc_start: 0.9259 (m-30) cc_final: 0.9014 (m-30) REVERT: E 52 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7607 (ttp80) REVERT: E 54 GLN cc_start: 0.7839 (mt0) cc_final: 0.7326 (mt0) REVERT: E 106 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8076 (mm-40) REVERT: E 179 GLN cc_start: 0.8584 (mt0) cc_final: 0.8350 (mt0) REVERT: E 192 ARG cc_start: 0.9115 (ttt180) cc_final: 0.8870 (ttm-80) REVERT: F 81 THR cc_start: 0.9233 (m) cc_final: 0.8575 (p) REVERT: F 84 TYR cc_start: 0.8605 (m-80) cc_final: 0.8368 (m-10) REVERT: F 87 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8452 (ptpp) REVERT: F 104 ASN cc_start: 0.9064 (m-40) cc_final: 0.8750 (t0) REVERT: F 112 GLU cc_start: 0.7716 (mp0) cc_final: 0.7435 (mp0) REVERT: F 116 ASP cc_start: 0.8751 (t0) cc_final: 0.8465 (t0) REVERT: G 8 SER cc_start: 0.8714 (p) cc_final: 0.8502 (m) REVERT: G 21 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8164 (tpp80) REVERT: G 24 GLN cc_start: 0.8163 (mt0) cc_final: 0.7947 (tt0) REVERT: G 28 THR cc_start: 0.8255 (m) cc_final: 0.7989 (p) REVERT: G 60 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7670 (ttp80) REVERT: G 99 PHE cc_start: 0.4832 (p90) cc_final: 0.4286 (p90) REVERT: G 115 MET cc_start: 0.5669 (mtp) cc_final: 0.4476 (ttm) REVERT: H 14 GLU cc_start: 0.8518 (tt0) cc_final: 0.8305 (tt0) REVERT: H 19 ARG cc_start: 0.8657 (mmt180) cc_final: 0.8386 (mmm160) REVERT: H 78 SER cc_start: 0.9317 (p) cc_final: 0.8821 (t) REVERT: H 137 GLN cc_start: 0.8797 (tt0) cc_final: 0.8192 (tm-30) REVERT: H 138 GLU cc_start: 0.8684 (pt0) cc_final: 0.8360 (pt0) REVERT: I 92 ARG cc_start: 0.6361 (mmt90) cc_final: 0.5996 (mtm110) REVERT: J 23 ASN cc_start: 0.7582 (m-40) cc_final: 0.7297 (t0) REVERT: J 42 LYS cc_start: 0.9063 (pttt) cc_final: 0.8853 (ptmm) REVERT: K 17 SER cc_start: 0.9017 (m) cc_final: 0.8636 (t) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.2241 time to fit residues: 216.3167 Evaluate side-chains 395 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 HIS A 706 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 469 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 64 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.128004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.086159 restraints weight = 57268.634| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.50 r_work: 0.2987 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 33905 Z= 0.265 Angle : 0.666 16.944 46198 Z= 0.349 Chirality : 0.048 0.246 5190 Planarity : 0.005 0.060 5630 Dihedral : 16.922 150.557 5346 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 1.37 % Allowed : 6.81 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.12 (0.14), residues: 3854 helix: 1.17 (0.14), residues: 1342 sheet: -0.42 (0.20), residues: 625 loop : -0.47 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1199 TYR 0.022 0.002 TYR H 129 PHE 0.022 0.002 PHE A 219 TRP 0.015 0.001 TRP B 308 HIS 0.012 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (33873) covalent geometry : angle 0.65315 / 0.35 (46153) hydrogen bonds : bond 0.04870 / 3.29 ( 1427) hydrogen bonds : angle 5.27479 / 3.79 ( 3959) metal coordination : bond 0.01040 / 0.63 ( 32) metal coordination : angle 4.29195 / 2.54 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 402 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8200 (ptm-80) REVERT: A 250 ILE cc_start: 0.8985 (mm) cc_final: 0.8755 (tp) REVERT: A 602 ASP cc_start: 0.9045 (t0) cc_final: 0.8432 (t0) REVERT: A 780 VAL cc_start: 0.9470 (t) cc_final: 0.9249 (m) REVERT: A 822 GLU cc_start: 0.8277 (tt0) cc_final: 0.7998 (mt-10) REVERT: A 931 GLU cc_start: 0.8859 (tt0) cc_final: 0.8414 (tm-30) REVERT: A 1228 TRP cc_start: 0.7597 (p90) cc_final: 0.7113 (p90) REVERT: B 73 GLN cc_start: 0.7315 (tt0) cc_final: 0.6828 (pt0) REVERT: B 86 ARG cc_start: 0.8190 (mpt-90) cc_final: 0.7787 (mmt90) REVERT: B 183 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8050 (pm20) REVERT: B 394 ASP cc_start: 0.8994 (t0) cc_final: 0.8531 (p0) REVERT: B 398 ARG cc_start: 0.8678 (mpt-90) cc_final: 0.8328 (mpp-170) REVERT: B 498 THR cc_start: 0.9086 (m) cc_final: 0.8660 (p) REVERT: B 620 ARG cc_start: 0.8733 (ptp-170) cc_final: 0.8422 (ttt-90) REVERT: B 885 MET cc_start: 0.5679 (mmt) cc_final: 0.5461 (ttt) REVERT: B 1189 ILE cc_start: 0.8962 (pt) cc_final: 0.8731 (mp) REVERT: C 75 MET cc_start: 0.9048 (mmm) cc_final: 0.8842 (tpp) REVERT: D 23 ASN cc_start: 0.6393 (t0) cc_final: 0.6152 (t0) REVERT: D 65 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8398 (mt-10) REVERT: D 142 LYS cc_start: 0.8376 (pttp) cc_final: 0.7991 (pttp) REVERT: D 143 ASN cc_start: 0.8438 (m-40) cc_final: 0.8053 (m-40) REVERT: D 166 LEU cc_start: 0.8795 (tp) cc_final: 0.8441 (pp) REVERT: E 36 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8700 (mt-10) REVERT: E 54 GLN cc_start: 0.8752 (mt0) cc_final: 0.8435 (mt0) REVERT: F 81 THR cc_start: 0.9186 (m) cc_final: 0.8830 (p) REVERT: F 87 LYS cc_start: 0.9377 (ptpt) cc_final: 0.9162 (ptpp) REVERT: F 116 ASP cc_start: 0.8974 (t0) cc_final: 0.8674 (t0) REVERT: G 6 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7517 (p0) REVERT: G 21 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8505 (mmm-85) REVERT: G 53 ASN cc_start: 0.8635 (t0) cc_final: 0.8353 (t0) REVERT: G 60 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8478 (ttp80) REVERT: G 99 PHE cc_start: 0.5063 (p90) cc_final: 0.4435 (p90) REVERT: G 115 MET cc_start: 0.5584 (mtp) cc_final: 0.4185 (ttm) REVERT: H 19 ARG cc_start: 0.8810 (mmt180) cc_final: 0.8505 (mmm160) REVERT: H 137 GLN cc_start: 0.8826 (tt0) cc_final: 0.8383 (tm-30) REVERT: I 13 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6335 (pmm) REVERT: I 92 ARG cc_start: 0.6848 (mmt90) cc_final: 0.6527 (mtm110) REVERT: J 23 ASN cc_start: 0.8363 (m-40) cc_final: 0.8137 (t0) outliers start: 47 outliers final: 33 residues processed: 429 average time/residue: 0.2191 time to fit residues: 149.0764 Evaluate side-chains 391 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1270 ASN Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 373 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 333 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 249 optimal weight: 6.9990 chunk 222 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 HIS A 479 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 538 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS E 32 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.131190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089968 restraints weight = 57006.147| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.50 r_work: 0.3055 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33905 Z= 0.119 Angle : 0.559 11.878 46198 Z= 0.294 Chirality : 0.043 0.216 5190 Planarity : 0.004 0.043 5630 Dihedral : 16.702 150.710 5346 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 1.25 % Allowed : 8.74 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.25 (0.14), residues: 3854 helix: 1.28 (0.14), residues: 1345 sheet: -0.37 (0.20), residues: 618 loop : -0.39 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 30 TYR 0.018 0.001 TYR B 137 PHE 0.023 0.001 PHE B 322 TRP 0.011 0.001 TRP A1044 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (33873) covalent geometry : angle 0.54790 / 0.29 (46153) hydrogen bonds : bond 0.03936 / 2.65 ( 1427) hydrogen bonds : angle 4.78205 / 3.43 ( 3959) metal coordination : bond 0.00586 / 0.34 ( 32) metal coordination : angle 3.65807 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9036 (mtm180) cc_final: 0.8514 (mtm110) REVERT: A 250 ILE cc_start: 0.8945 (mm) cc_final: 0.8706 (tp) REVERT: A 320 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8446 (mtm180) REVERT: A 602 ASP cc_start: 0.8958 (t0) cc_final: 0.8306 (t0) REVERT: A 847 ASP cc_start: 0.8999 (p0) cc_final: 0.8784 (p0) REVERT: A 931 GLU cc_start: 0.8888 (tt0) cc_final: 0.8426 (tm-30) REVERT: A 1284 MET cc_start: 0.8752 (ttm) cc_final: 0.8489 (mtm) REVERT: A 1285 MET cc_start: 0.8685 (mmm) cc_final: 0.8473 (mmm) REVERT: B 73 GLN cc_start: 0.7162 (tt0) cc_final: 0.6785 (pt0) REVERT: B 86 ARG cc_start: 0.8190 (mpt-90) cc_final: 0.7617 (mmt-90) REVERT: B 183 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7903 (pm20) REVERT: B 394 ASP cc_start: 0.9041 (t0) cc_final: 0.8458 (p0) REVERT: B 498 THR cc_start: 0.9055 (m) cc_final: 0.8708 (p) REVERT: B 531 GLN cc_start: 0.8684 (pm20) cc_final: 0.8441 (tp40) REVERT: B 620 ARG cc_start: 0.8789 (ptp-170) cc_final: 0.8494 (ttt-90) REVERT: B 860 MET cc_start: 0.8504 (tmm) cc_final: 0.8222 (tmm) REVERT: C 75 MET cc_start: 0.9049 (mmm) cc_final: 0.8841 (mmm) REVERT: C 221 TYR cc_start: 0.9509 (p90) cc_final: 0.9211 (p90) REVERT: D 23 ASN cc_start: 0.6395 (t0) cc_final: 0.6164 (t0) REVERT: D 65 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8385 (mt-10) REVERT: D 142 LYS cc_start: 0.8295 (pttp) cc_final: 0.7822 (mttp) REVERT: D 146 GLN cc_start: 0.7934 (pp30) cc_final: 0.7359 (mm-40) REVERT: D 166 LEU cc_start: 0.8804 (tp) cc_final: 0.8444 (pp) REVERT: E 48 ASP cc_start: 0.8428 (t0) cc_final: 0.8056 (t70) REVERT: E 54 GLN cc_start: 0.8528 (mt0) cc_final: 0.8071 (mt0) REVERT: F 87 LYS cc_start: 0.9360 (ptpt) cc_final: 0.9093 (ptpp) REVERT: F 116 ASP cc_start: 0.8900 (t0) cc_final: 0.8515 (t0) REVERT: G 6 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7450 (p0) REVERT: G 21 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8499 (mmm-85) REVERT: G 53 ASN cc_start: 0.8620 (t0) cc_final: 0.8324 (t0) REVERT: G 60 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8362 (ttp80) REVERT: G 115 MET cc_start: 0.5462 (mtp) cc_final: 0.5250 (mtm) REVERT: H 137 GLN cc_start: 0.8788 (tt0) cc_final: 0.8389 (tm-30) REVERT: I 92 ARG cc_start: 0.6763 (mmt90) cc_final: 0.6454 (mtm110) REVERT: J 23 ASN cc_start: 0.8448 (m-40) cc_final: 0.8156 (t0) REVERT: K 54 ARG cc_start: 0.9099 (mmm-85) cc_final: 0.8844 (mtp180) outliers start: 43 outliers final: 28 residues processed: 422 average time/residue: 0.2222 time to fit residues: 149.9484 Evaluate side-chains 382 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 169 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 286 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN E 101 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085292 restraints weight = 56600.199| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.42 r_work: 0.2998 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33905 Z= 0.228 Angle : 0.601 11.578 46198 Z= 0.312 Chirality : 0.045 0.236 5190 Planarity : 0.004 0.048 5630 Dihedral : 16.722 151.557 5346 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 1.75 % Allowed : 9.64 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.19 (0.14), residues: 3854 helix: 1.25 (0.14), residues: 1330 sheet: -0.45 (0.20), residues: 620 loop : -0.41 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 77 TYR 0.023 0.001 TYR H 129 PHE 0.021 0.002 PHE A 219 TRP 0.008 0.001 TRP A1044 HIS 0.010 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (33873) covalent geometry : angle 0.59046 / 0.31 (46153) hydrogen bonds : bond 0.04029 / 2.70 ( 1427) hydrogen bonds : angle 4.70888 / 3.39 ( 3959) metal coordination : bond 0.00802 / 0.48 ( 32) metal coordination : angle 3.68220 / 2.28 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 357 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ILE cc_start: 0.8949 (mm) cc_final: 0.8705 (tp) REVERT: A 602 ASP cc_start: 0.9064 (t0) cc_final: 0.8468 (t0) REVERT: A 708 MET cc_start: 0.8081 (mtp) cc_final: 0.7791 (mtp) REVERT: A 931 GLU cc_start: 0.8895 (tt0) cc_final: 0.8412 (tm-30) REVERT: A 1284 MET cc_start: 0.8748 (ttm) cc_final: 0.8450 (mtm) REVERT: A 1285 MET cc_start: 0.8721 (mmm) cc_final: 0.8485 (mmm) REVERT: B 73 GLN cc_start: 0.7130 (tt0) cc_final: 0.6790 (pt0) REVERT: B 86 ARG cc_start: 0.8192 (mpt-90) cc_final: 0.7654 (mmt-90) REVERT: B 183 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7980 (pm20) REVERT: B 394 ASP cc_start: 0.9088 (t0) cc_final: 0.8440 (p0) REVERT: B 498 THR cc_start: 0.9075 (m) cc_final: 0.8649 (p) REVERT: B 531 GLN cc_start: 0.8797 (pm20) cc_final: 0.8568 (tp40) REVERT: B 620 ARG cc_start: 0.8876 (ptp-170) cc_final: 0.8546 (ttt-90) REVERT: B 860 MET cc_start: 0.8578 (tmm) cc_final: 0.8147 (tmm) REVERT: B 1189 ILE cc_start: 0.8986 (pt) cc_final: 0.8724 (mp) REVERT: C 75 MET cc_start: 0.9117 (mmm) cc_final: 0.8875 (tpp) REVERT: C 209 TYR cc_start: 0.9054 (m-80) cc_final: 0.8759 (m-80) REVERT: D 23 ASN cc_start: 0.6464 (t0) cc_final: 0.6256 (t0) REVERT: D 65 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8332 (mt-10) REVERT: D 146 GLN cc_start: 0.7974 (pp30) cc_final: 0.7273 (mm-40) REVERT: D 166 LEU cc_start: 0.8791 (tp) cc_final: 0.8437 (pp) REVERT: E 48 ASP cc_start: 0.8517 (t0) cc_final: 0.8150 (t70) REVERT: E 54 GLN cc_start: 0.8590 (mt0) cc_final: 0.8245 (mt0) REVERT: F 87 LYS cc_start: 0.9396 (ptpt) cc_final: 0.9184 (ptpp) REVERT: F 116 ASP cc_start: 0.8970 (t0) cc_final: 0.8760 (t0) REVERT: G 53 ASN cc_start: 0.8709 (t0) cc_final: 0.8422 (t0) REVERT: G 60 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8392 (ttp80) REVERT: G 171 ILE cc_start: 0.4335 (OUTLIER) cc_final: 0.4083 (mm) REVERT: H 137 GLN cc_start: 0.8648 (tt0) cc_final: 0.8348 (tm-30) REVERT: I 92 ARG cc_start: 0.6756 (mmt90) cc_final: 0.6514 (mtm110) REVERT: J 23 ASN cc_start: 0.8395 (m-40) cc_final: 0.8118 (t0) REVERT: K 16 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8006 (mt-10) REVERT: K 54 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8833 (mtp180) outliers start: 60 outliers final: 42 residues processed: 399 average time/residue: 0.2217 time to fit residues: 141.7954 Evaluate side-chains 381 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 338 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 408 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 138 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089748 restraints weight = 57009.353| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.48 r_work: 0.3049 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 33905 Z= 0.111 Angle : 0.530 11.573 46198 Z= 0.278 Chirality : 0.042 0.222 5190 Planarity : 0.003 0.044 5630 Dihedral : 16.621 151.808 5346 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 1.37 % Allowed : 10.86 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 3854 helix: 1.34 (0.15), residues: 1342 sheet: -0.41 (0.20), residues: 620 loop : -0.37 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1100 TYR 0.012 0.001 TYR A1153 PHE 0.018 0.001 PHE A 219 TRP 0.009 0.001 TRP A1044 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (33873) covalent geometry : angle 0.52023 / 0.28 (46153) hydrogen bonds : bond 0.03489 / 2.34 ( 1427) hydrogen bonds : angle 4.48001 / 3.23 ( 3959) metal coordination : bond 0.00842 / 0.56 ( 32) metal coordination : angle 3.33434 / 2.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9069 (mtm180) cc_final: 0.8587 (mtm110) REVERT: A 250 ILE cc_start: 0.8953 (mm) cc_final: 0.8694 (tp) REVERT: A 602 ASP cc_start: 0.9015 (t0) cc_final: 0.8321 (t0) REVERT: A 708 MET cc_start: 0.7820 (mtp) cc_final: 0.7522 (mtp) REVERT: A 931 GLU cc_start: 0.8877 (tt0) cc_final: 0.8395 (tm-30) REVERT: A 1284 MET cc_start: 0.8719 (ttm) cc_final: 0.8405 (mtm) REVERT: A 1285 MET cc_start: 0.8699 (mmm) cc_final: 0.8472 (mmm) REVERT: A 1454 MET cc_start: 0.7040 (mtt) cc_final: 0.6703 (mmm) REVERT: B 73 GLN cc_start: 0.7102 (tt0) cc_final: 0.6628 (pt0) REVERT: B 86 ARG cc_start: 0.8184 (mpt-90) cc_final: 0.7491 (mpt-90) REVERT: B 183 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7903 (pm20) REVERT: B 394 ASP cc_start: 0.9094 (t0) cc_final: 0.8439 (p0) REVERT: B 498 THR cc_start: 0.9056 (m) cc_final: 0.8698 (p) REVERT: B 531 GLN cc_start: 0.8703 (pm20) cc_final: 0.8464 (tp40) REVERT: B 620 ARG cc_start: 0.8817 (ptp-170) cc_final: 0.8493 (ttt-90) REVERT: B 860 MET cc_start: 0.8482 (tmm) cc_final: 0.8195 (tmm) REVERT: C 75 MET cc_start: 0.9112 (mmm) cc_final: 0.8863 (tpp) REVERT: C 221 TYR cc_start: 0.9498 (p90) cc_final: 0.9228 (p90) REVERT: D 65 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8327 (mt-10) REVERT: D 142 LYS cc_start: 0.8326 (pttp) cc_final: 0.8049 (mttt) REVERT: D 166 LEU cc_start: 0.8806 (tp) cc_final: 0.8447 (pp) REVERT: E 32 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7456 (tp40) REVERT: E 54 GLN cc_start: 0.8528 (mt0) cc_final: 0.8238 (mt0) REVERT: E 121 MET cc_start: 0.8761 (mmm) cc_final: 0.8376 (mtm) REVERT: F 87 LYS cc_start: 0.9365 (ptpt) cc_final: 0.9089 (ptpp) REVERT: F 116 ASP cc_start: 0.8948 (t0) cc_final: 0.8528 (t0) REVERT: G 53 ASN cc_start: 0.8683 (t0) cc_final: 0.8421 (t0) REVERT: G 60 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8347 (ttp80) REVERT: H 137 GLN cc_start: 0.8617 (tt0) cc_final: 0.8285 (tm-30) REVERT: I 97 MET cc_start: 0.7666 (mtp) cc_final: 0.7461 (mmm) REVERT: J 23 ASN cc_start: 0.8518 (m-40) cc_final: 0.8208 (t0) REVERT: K 36 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8547 (mm-30) REVERT: K 54 ARG cc_start: 0.9091 (mmm-85) cc_final: 0.8795 (mtp180) outliers start: 47 outliers final: 31 residues processed: 388 average time/residue: 0.2233 time to fit residues: 138.7295 Evaluate side-chains 371 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 340 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 408 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 395 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086092 restraints weight = 56650.092| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.43 r_work: 0.3025 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 33905 Z= 0.198 Angle : 0.572 13.443 46198 Z= 0.295 Chirality : 0.044 0.239 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.636 153.061 5346 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % Rotamer: Outliers : 1.51 % Allowed : 11.24 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.26 (0.14), residues: 3854 helix: 1.33 (0.15), residues: 1337 sheet: -0.44 (0.20), residues: 621 loop : -0.38 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 857 TYR 0.015 0.001 TYR H 129 PHE 0.023 0.001 PHE A1225 TRP 0.008 0.001 TRP A1044 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (33873) covalent geometry : angle 0.56175 / 0.29 (46153) hydrogen bonds : bond 0.03644 / 2.43 ( 1427) hydrogen bonds : angle 4.50591 / 3.25 ( 3959) metal coordination : bond 0.00673 / 0.39 ( 32) metal coordination : angle 3.41597 / 2.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ILE cc_start: 0.8950 (mm) cc_final: 0.8720 (tp) REVERT: A 602 ASP cc_start: 0.9094 (t0) cc_final: 0.8440 (t0) REVERT: A 708 MET cc_start: 0.7890 (mtp) cc_final: 0.7579 (mtp) REVERT: A 931 GLU cc_start: 0.8923 (tt0) cc_final: 0.8429 (tm-30) REVERT: A 1284 MET cc_start: 0.8721 (ttm) cc_final: 0.8411 (mtm) REVERT: A 1285 MET cc_start: 0.8639 (mmm) cc_final: 0.8395 (mmm) REVERT: A 1454 MET cc_start: 0.7161 (mtt) cc_final: 0.6832 (mmm) REVERT: B 73 GLN cc_start: 0.7129 (tt0) cc_final: 0.6629 (pt0) REVERT: B 86 ARG cc_start: 0.8177 (mpt-90) cc_final: 0.7422 (mpt-90) REVERT: B 183 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8018 (pm20) REVERT: B 394 ASP cc_start: 0.9091 (t0) cc_final: 0.8430 (p0) REVERT: B 498 THR cc_start: 0.9086 (m) cc_final: 0.8686 (p) REVERT: B 531 GLN cc_start: 0.8770 (pm20) cc_final: 0.8528 (tp40) REVERT: B 620 ARG cc_start: 0.8793 (ptp-170) cc_final: 0.8517 (ttt-90) REVERT: B 1189 ILE cc_start: 0.9005 (pt) cc_final: 0.8732 (mp) REVERT: C 75 MET cc_start: 0.9147 (mmm) cc_final: 0.8894 (tpp) REVERT: C 209 TYR cc_start: 0.9045 (m-80) cc_final: 0.8771 (m-80) REVERT: C 221 TYR cc_start: 0.9525 (p90) cc_final: 0.9194 (p90) REVERT: D 65 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8330 (mt-10) REVERT: D 142 LYS cc_start: 0.8275 (pttp) cc_final: 0.8046 (pttp) REVERT: D 166 LEU cc_start: 0.8828 (tp) cc_final: 0.8471 (pp) REVERT: E 54 GLN cc_start: 0.8653 (mt0) cc_final: 0.8319 (mt0) REVERT: E 121 MET cc_start: 0.8821 (mmm) cc_final: 0.8438 (mtm) REVERT: F 87 LYS cc_start: 0.9394 (ptpt) cc_final: 0.9123 (ptpp) REVERT: F 116 ASP cc_start: 0.8978 (t0) cc_final: 0.8754 (t0) REVERT: G 53 ASN cc_start: 0.8642 (t0) cc_final: 0.8356 (t0) REVERT: G 60 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8343 (ttp80) REVERT: G 106 MET cc_start: 0.6125 (ptm) cc_final: 0.5892 (ptp) REVERT: G 115 MET cc_start: 0.5044 (mtp) cc_final: 0.4448 (mtp) REVERT: H 137 GLN cc_start: 0.8591 (tt0) cc_final: 0.8247 (tm-30) REVERT: J 23 ASN cc_start: 0.8430 (m-40) cc_final: 0.8166 (t0) REVERT: J 49 MET cc_start: 0.9165 (tpp) cc_final: 0.8891 (tpp) REVERT: K 54 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8801 (mtp180) outliers start: 52 outliers final: 41 residues processed: 385 average time/residue: 0.2139 time to fit residues: 132.7910 Evaluate side-chains 376 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 408 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 0.6980 chunk 306 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 357 optimal weight: 7.9990 chunk 254 optimal weight: 0.7980 chunk 351 optimal weight: 4.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.130704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.089357 restraints weight = 56874.662| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.51 r_work: 0.3055 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33905 Z= 0.108 Angle : 0.527 14.734 46198 Z= 0.274 Chirality : 0.042 0.233 5190 Planarity : 0.003 0.045 5630 Dihedral : 16.559 154.379 5346 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 1.43 % Allowed : 11.91 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.37 (0.14), residues: 3854 helix: 1.42 (0.15), residues: 1340 sheet: -0.36 (0.20), residues: 622 loop : -0.32 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 77 TYR 0.010 0.001 TYR B 830 PHE 0.024 0.001 PHE A1225 TRP 0.009 0.001 TRP A1044 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (33873) covalent geometry : angle 0.51716 / 0.27 (46153) hydrogen bonds : bond 0.03284 / 2.20 ( 1427) hydrogen bonds : angle 4.31975 / 3.11 ( 3959) metal coordination : bond 0.00460 / 0.26 ( 32) metal coordination : angle 3.24393 / 2.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9110 (mtm180) cc_final: 0.8651 (mtm110) REVERT: A 182 VAL cc_start: 0.8782 (t) cc_final: 0.8576 (m) REVERT: A 250 ILE cc_start: 0.8946 (mm) cc_final: 0.8692 (tp) REVERT: A 602 ASP cc_start: 0.9087 (t0) cc_final: 0.8054 (t0) REVERT: A 708 MET cc_start: 0.7632 (mtp) cc_final: 0.7309 (mtp) REVERT: A 919 ILE cc_start: 0.8870 (mm) cc_final: 0.8418 (mm) REVERT: A 931 GLU cc_start: 0.8903 (tt0) cc_final: 0.8403 (tm-30) REVERT: A 1284 MET cc_start: 0.8664 (ttm) cc_final: 0.8380 (mtm) REVERT: A 1285 MET cc_start: 0.8650 (mmm) cc_final: 0.8437 (mmm) REVERT: A 1454 MET cc_start: 0.7298 (mtt) cc_final: 0.7083 (mmm) REVERT: B 73 GLN cc_start: 0.7008 (tt0) cc_final: 0.6608 (pt0) REVERT: B 86 ARG cc_start: 0.8151 (mpt-90) cc_final: 0.7435 (mpt-90) REVERT: B 151 LEU cc_start: 0.8218 (tp) cc_final: 0.7656 (tt) REVERT: B 183 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7901 (pm20) REVERT: B 308 TRP cc_start: 0.8861 (p-90) cc_final: 0.8518 (p-90) REVERT: B 394 ASP cc_start: 0.9107 (t0) cc_final: 0.8435 (p0) REVERT: B 432 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: B 498 THR cc_start: 0.9064 (m) cc_final: 0.8707 (p) REVERT: B 531 GLN cc_start: 0.8724 (pm20) cc_final: 0.8481 (tp40) REVERT: B 620 ARG cc_start: 0.8759 (ptp-170) cc_final: 0.8455 (ttt-90) REVERT: C 75 MET cc_start: 0.9103 (mmm) cc_final: 0.8849 (tpp) REVERT: C 221 TYR cc_start: 0.9486 (p90) cc_final: 0.9245 (p90) REVERT: D 65 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8325 (mt-10) REVERT: D 166 LEU cc_start: 0.8836 (tp) cc_final: 0.8484 (pp) REVERT: E 54 GLN cc_start: 0.8673 (mt0) cc_final: 0.8146 (mt0) REVERT: E 121 MET cc_start: 0.8798 (mmm) cc_final: 0.8412 (mtm) REVERT: F 87 LYS cc_start: 0.9361 (ptpt) cc_final: 0.9089 (ptpp) REVERT: F 116 ASP cc_start: 0.8964 (t0) cc_final: 0.8548 (t0) REVERT: G 1 MET cc_start: 0.8664 (tpp) cc_final: 0.8403 (tpp) REVERT: G 42 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: G 53 ASN cc_start: 0.8659 (t0) cc_final: 0.8378 (t0) REVERT: G 60 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8323 (ttp80) REVERT: H 97 MET cc_start: 0.9056 (mtt) cc_final: 0.8804 (mtt) REVERT: H 137 GLN cc_start: 0.8564 (tt0) cc_final: 0.8130 (tm-30) REVERT: J 23 ASN cc_start: 0.8529 (m-40) cc_final: 0.8224 (t0) REVERT: J 49 MET cc_start: 0.9146 (tpp) cc_final: 0.8907 (tpp) outliers start: 49 outliers final: 40 residues processed: 390 average time/residue: 0.2286 time to fit residues: 143.3333 Evaluate side-chains 379 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 408 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 22 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 331 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.127750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087191 restraints weight = 56680.783| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.42 r_work: 0.3039 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33905 Z= 0.155 Angle : 0.545 16.385 46198 Z= 0.282 Chirality : 0.043 0.246 5190 Planarity : 0.004 0.051 5630 Dihedral : 16.566 155.986 5346 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.34 % Allowed : 12.00 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.37 (0.14), residues: 3854 helix: 1.43 (0.15), residues: 1340 sheet: -0.37 (0.20), residues: 622 loop : -0.33 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 54 TYR 0.015 0.001 TYR H 129 PHE 0.025 0.001 PHE A1225 TRP 0.007 0.001 TRP C 192 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (33873) covalent geometry : angle 0.53676 / 0.28 (46153) hydrogen bonds : bond 0.03394 / 2.27 ( 1427) hydrogen bonds : angle 4.29986 / 3.10 ( 3959) metal coordination : bond 0.00560 / 0.33 ( 32) metal coordination : angle 3.14935 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ILE cc_start: 0.8946 (mm) cc_final: 0.8686 (tp) REVERT: A 602 ASP cc_start: 0.9126 (t0) cc_final: 0.8098 (t0) REVERT: A 708 MET cc_start: 0.7672 (mtp) cc_final: 0.7363 (mtp) REVERT: A 847 ASP cc_start: 0.8806 (p0) cc_final: 0.8591 (p0) REVERT: A 919 ILE cc_start: 0.8902 (mm) cc_final: 0.8525 (tt) REVERT: A 931 GLU cc_start: 0.8882 (tt0) cc_final: 0.8307 (tm-30) REVERT: A 1196 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: A 1237 ILE cc_start: 0.7749 (mt) cc_final: 0.7339 (mp) REVERT: A 1269 GLU cc_start: 0.7363 (pm20) cc_final: 0.7117 (pm20) REVERT: A 1284 MET cc_start: 0.8662 (ttm) cc_final: 0.8401 (mtm) REVERT: A 1454 MET cc_start: 0.7237 (mtt) cc_final: 0.7007 (mmm) REVERT: B 73 GLN cc_start: 0.7036 (tt0) cc_final: 0.6676 (pt0) REVERT: B 86 ARG cc_start: 0.8208 (mpt-90) cc_final: 0.7425 (mpt-90) REVERT: B 151 LEU cc_start: 0.8294 (tp) cc_final: 0.7636 (tt) REVERT: B 183 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7966 (pm20) REVERT: B 308 TRP cc_start: 0.8805 (p-90) cc_final: 0.8444 (p-90) REVERT: B 394 ASP cc_start: 0.9099 (t0) cc_final: 0.8444 (p0) REVERT: B 398 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8154 (mmt-90) REVERT: B 498 THR cc_start: 0.9073 (m) cc_final: 0.8679 (p) REVERT: B 531 GLN cc_start: 0.8765 (pm20) cc_final: 0.8527 (tp40) REVERT: B 620 ARG cc_start: 0.8726 (ptp-170) cc_final: 0.8454 (ttt-90) REVERT: B 860 MET cc_start: 0.8565 (tmm) cc_final: 0.8275 (tmm) REVERT: C 75 MET cc_start: 0.9132 (mmm) cc_final: 0.8869 (tpp) REVERT: C 209 TYR cc_start: 0.9014 (m-80) cc_final: 0.8695 (m-80) REVERT: C 221 TYR cc_start: 0.9501 (p90) cc_final: 0.9194 (p90) REVERT: C 230 MET cc_start: 0.9033 (mtp) cc_final: 0.8766 (mmm) REVERT: D 65 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8325 (mt-10) REVERT: D 130 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5568 (tt) REVERT: D 166 LEU cc_start: 0.8835 (tp) cc_final: 0.8484 (pp) REVERT: E 121 MET cc_start: 0.8807 (mmm) cc_final: 0.8418 (mtm) REVERT: F 87 LYS cc_start: 0.9378 (ptpt) cc_final: 0.9115 (ptpp) REVERT: F 116 ASP cc_start: 0.8968 (t0) cc_final: 0.8739 (t0) REVERT: G 42 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: G 53 ASN cc_start: 0.8632 (t0) cc_final: 0.8325 (t0) REVERT: G 60 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8306 (ttp80) REVERT: G 115 MET cc_start: 0.5205 (mtm) cc_final: 0.4626 (mtp) REVERT: H 137 GLN cc_start: 0.8573 (tt0) cc_final: 0.8140 (tm-30) REVERT: J 23 ASN cc_start: 0.8553 (m-40) cc_final: 0.8198 (t0) REVERT: J 49 MET cc_start: 0.9169 (tpp) cc_final: 0.8886 (tpp) outliers start: 46 outliers final: 41 residues processed: 368 average time/residue: 0.2267 time to fit residues: 134.1646 Evaluate side-chains 377 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 331 optimal weight: 0.4980 chunk 134 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088787 restraints weight = 57098.028| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.46 r_work: 0.3040 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33905 Z= 0.156 Angle : 0.549 17.851 46198 Z= 0.283 Chirality : 0.043 0.251 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.568 157.975 5346 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 1.49 % Allowed : 12.17 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.36 (0.14), residues: 3854 helix: 1.44 (0.15), residues: 1341 sheet: -0.39 (0.20), residues: 622 loop : -0.35 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 54 TYR 0.028 0.001 TYR E 168 PHE 0.028 0.001 PHE A1225 TRP 0.008 0.001 TRP A1044 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (33873) covalent geometry : angle 0.54016 / 0.28 (46153) hydrogen bonds : bond 0.03410 / 2.28 ( 1427) hydrogen bonds : angle 4.29370 / 3.08 ( 3959) metal coordination : bond 0.00573 / 0.33 ( 32) metal coordination : angle 3.17879 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ILE cc_start: 0.8971 (mm) cc_final: 0.8699 (tp) REVERT: A 602 ASP cc_start: 0.9143 (t0) cc_final: 0.8663 (t0) REVERT: A 708 MET cc_start: 0.7752 (mtp) cc_final: 0.7473 (mtp) REVERT: A 847 ASP cc_start: 0.8808 (p0) cc_final: 0.8580 (p0) REVERT: A 919 ILE cc_start: 0.8908 (mm) cc_final: 0.8527 (tt) REVERT: A 931 GLU cc_start: 0.8899 (tt0) cc_final: 0.8325 (tm-30) REVERT: A 1196 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: A 1237 ILE cc_start: 0.7764 (mt) cc_final: 0.7373 (mp) REVERT: A 1284 MET cc_start: 0.8661 (ttm) cc_final: 0.8399 (mtm) REVERT: A 1285 MET cc_start: 0.8367 (mmt) cc_final: 0.8139 (mmm) REVERT: A 1454 MET cc_start: 0.7242 (mtt) cc_final: 0.7037 (mmm) REVERT: B 73 GLN cc_start: 0.7160 (tt0) cc_final: 0.6785 (pt0) REVERT: B 86 ARG cc_start: 0.8157 (mpt-90) cc_final: 0.7396 (mpt-90) REVERT: B 183 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7898 (pm20) REVERT: B 308 TRP cc_start: 0.8784 (p-90) cc_final: 0.8431 (p-90) REVERT: B 394 ASP cc_start: 0.9101 (t0) cc_final: 0.8454 (p0) REVERT: B 498 THR cc_start: 0.9085 (m) cc_final: 0.8698 (p) REVERT: B 531 GLN cc_start: 0.8764 (pm20) cc_final: 0.8535 (tp40) REVERT: B 620 ARG cc_start: 0.8737 (ptp-170) cc_final: 0.8452 (ttt-90) REVERT: C 75 MET cc_start: 0.9125 (mmm) cc_final: 0.8874 (tpp) REVERT: C 209 TYR cc_start: 0.9018 (m-80) cc_final: 0.8703 (m-80) REVERT: C 221 TYR cc_start: 0.9499 (p90) cc_final: 0.9194 (p90) REVERT: C 230 MET cc_start: 0.9089 (mtp) cc_final: 0.8758 (mmm) REVERT: D 65 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8325 (mt-10) REVERT: D 139 LYS cc_start: 0.6904 (ptpp) cc_final: 0.6579 (ptpt) REVERT: D 166 LEU cc_start: 0.8849 (tp) cc_final: 0.8489 (pp) REVERT: E 121 MET cc_start: 0.8834 (mmm) cc_final: 0.8415 (mtm) REVERT: F 87 LYS cc_start: 0.9380 (ptpt) cc_final: 0.9119 (ptpp) REVERT: F 116 ASP cc_start: 0.8981 (t0) cc_final: 0.8575 (t0) REVERT: G 1 MET cc_start: 0.8668 (tpp) cc_final: 0.8464 (tpp) REVERT: G 42 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: G 53 ASN cc_start: 0.8641 (t0) cc_final: 0.8326 (t0) REVERT: G 60 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8336 (ttp80) REVERT: G 115 MET cc_start: 0.5389 (mtm) cc_final: 0.4940 (mtp) REVERT: H 137 GLN cc_start: 0.8592 (tt0) cc_final: 0.8171 (tm-30) REVERT: J 23 ASN cc_start: 0.8561 (m-40) cc_final: 0.8219 (t0) REVERT: J 49 MET cc_start: 0.9159 (tpp) cc_final: 0.8906 (tpp) outliers start: 51 outliers final: 41 residues processed: 371 average time/residue: 0.2208 time to fit residues: 132.2379 Evaluate side-chains 379 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 336 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 314 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088966 restraints weight = 57476.268| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.47 r_work: 0.3037 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33905 Z= 0.147 Angle : 0.539 9.723 46198 Z= 0.280 Chirality : 0.042 0.255 5190 Planarity : 0.003 0.045 5630 Dihedral : 16.551 159.653 5346 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 1.34 % Allowed : 12.29 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.38 (0.14), residues: 3854 helix: 1.46 (0.15), residues: 1341 sheet: -0.38 (0.20), residues: 622 loop : -0.34 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 77 TYR 0.026 0.001 TYR H 129 PHE 0.030 0.001 PHE A1225 TRP 0.008 0.001 TRP A1044 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (33873) covalent geometry : angle 0.53031 / 0.28 (46153) hydrogen bonds : bond 0.03372 / 2.25 ( 1427) hydrogen bonds : angle 4.26667 / 3.06 ( 3959) metal coordination : bond 0.00553 / 0.33 ( 32) metal coordination : angle 3.17174 / 2.00 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ILE cc_start: 0.8983 (mm) cc_final: 0.8712 (tp) REVERT: A 602 ASP cc_start: 0.9147 (t0) cc_final: 0.8689 (t0) REVERT: A 708 MET cc_start: 0.7783 (mtp) cc_final: 0.7495 (mtp) REVERT: A 847 ASP cc_start: 0.8807 (p0) cc_final: 0.8569 (p0) REVERT: A 919 ILE cc_start: 0.8912 (mm) cc_final: 0.8531 (tt) REVERT: A 931 GLU cc_start: 0.8917 (tt0) cc_final: 0.8342 (tm-30) REVERT: A 1196 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: A 1237 ILE cc_start: 0.7745 (mt) cc_final: 0.7349 (mp) REVERT: A 1284 MET cc_start: 0.8661 (ttm) cc_final: 0.8410 (mtm) REVERT: A 1285 MET cc_start: 0.8390 (mmt) cc_final: 0.8167 (mmm) REVERT: B 73 GLN cc_start: 0.7115 (tt0) cc_final: 0.6763 (pt0) REVERT: B 86 ARG cc_start: 0.8153 (mpt-90) cc_final: 0.7384 (mpt-90) REVERT: B 151 LEU cc_start: 0.8203 (tp) cc_final: 0.7579 (tt) REVERT: B 183 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7912 (pm20) REVERT: B 308 TRP cc_start: 0.8766 (p-90) cc_final: 0.8416 (p-90) REVERT: B 394 ASP cc_start: 0.9101 (t0) cc_final: 0.8511 (p0) REVERT: B 498 THR cc_start: 0.9082 (m) cc_final: 0.8693 (p) REVERT: B 531 GLN cc_start: 0.8791 (pm20) cc_final: 0.8535 (tp40) REVERT: B 620 ARG cc_start: 0.8747 (ptp-170) cc_final: 0.8466 (ttt-90) REVERT: C 75 MET cc_start: 0.9133 (mmm) cc_final: 0.8882 (tpp) REVERT: C 221 TYR cc_start: 0.9494 (p90) cc_final: 0.9254 (p90) REVERT: D 65 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8324 (mt-10) REVERT: E 121 MET cc_start: 0.8828 (mmm) cc_final: 0.8402 (mtm) REVERT: E 192 ARG cc_start: 0.8960 (ttm-80) cc_final: 0.8728 (ttm110) REVERT: F 87 LYS cc_start: 0.9376 (ptpt) cc_final: 0.9120 (ptpp) REVERT: F 116 ASP cc_start: 0.8980 (t0) cc_final: 0.8572 (t0) REVERT: G 1 MET cc_start: 0.8638 (tpp) cc_final: 0.8427 (tpp) REVERT: G 42 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: G 53 ASN cc_start: 0.8636 (t0) cc_final: 0.8319 (t0) REVERT: G 60 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8328 (ttp80) REVERT: G 115 MET cc_start: 0.5626 (mtm) cc_final: 0.5096 (mtp) REVERT: H 137 GLN cc_start: 0.8613 (tt0) cc_final: 0.8174 (tm-30) REVERT: J 23 ASN cc_start: 0.8559 (m-40) cc_final: 0.8211 (t0) REVERT: J 49 MET cc_start: 0.9236 (tpp) cc_final: 0.8902 (tpp) REVERT: K 81 TYR cc_start: 0.8724 (t80) cc_final: 0.8395 (t80) outliers start: 46 outliers final: 40 residues processed: 373 average time/residue: 0.2255 time to fit residues: 135.2346 Evaluate side-chains 379 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 296 optimal weight: 0.9990 chunk 250 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.129987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089218 restraints weight = 57051.197| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.46 r_work: 0.3037 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33905 Z= 0.140 Angle : 0.536 9.778 46198 Z= 0.278 Chirality : 0.042 0.257 5190 Planarity : 0.003 0.045 5630 Dihedral : 16.524 161.361 5346 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.46 % Allowed : 12.29 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.40 (0.14), residues: 3854 helix: 1.48 (0.15), residues: 1342 sheet: -0.37 (0.20), residues: 622 loop : -0.33 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 54 TYR 0.031 0.001 TYR H 95 PHE 0.029 0.001 PHE A1225 TRP 0.009 0.001 TRP A1044 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (33873) covalent geometry : angle 0.52672 / 0.28 (46153) hydrogen bonds : bond 0.03347 / 2.23 ( 1427) hydrogen bonds : angle 4.24677 / 3.04 ( 3959) metal coordination : bond 0.00538 / 0.31 ( 32) metal coordination : angle 3.14224 / 1.98 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8716.41 seconds wall clock time: 150 minutes 10.43 seconds (9010.43 seconds total)