Starting phenix.real_space_refine on Sun Aug 9 09:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sc0_54745/08_2026/9sc0_54745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sc0_54745/08_2026/9sc0_54745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sc0_54745/08_2026/9sc0_54745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sc0_54745/08_2026/9sc0_54745.map" model { file = "/net/cci-nas-00/data/ceres_data/9sc0_54745/08_2026/9sc0_54745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sc0_54745/08_2026/9sc0_54745.cif" } resolution = 3.31 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= 0.035 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 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 67 105.430 70.744 95.110 1.00107.80 S ATOM 479 SG CYS A 70 104.945 67.206 93.644 1.00100.71 S ATOM 532 SG CYS A 77 102.320 69.925 93.029 1.00102.36 S ATOM 762 SG CYS A 107 80.372 76.529 135.174 1.00145.43 S ATOM 786 SG CYS A 110 82.042 73.265 135.996 1.00141.17 S ATOM 1091 SG CYS A 148 78.559 74.013 137.378 1.00154.26 S ATOM 1105 SG CYS A 167 81.626 75.939 138.674 1.00156.45 S ATOM 19603 SG CYS B1163 97.220 58.315 105.024 1.00 99.45 S ATOM 19621 SG CYS B1166 95.688 61.594 105.928 1.00108.37 S ATOM 19746 SG CYS B1182 99.377 61.310 104.846 1.00108.13 S ATOM 19765 SG CYS B1185 98.190 60.155 108.328 1.00110.35 S ATOM 20753 SG CYS C 86 92.020 74.902 25.901 1.00153.17 S ATOM 20770 SG CYS C 88 94.085 77.275 27.957 1.00167.76 S ATOM 20803 SG CYS C 92 93.014 78.270 24.484 1.00136.03 S ATOM 20826 SG CYS C 95 90.424 78.143 27.254 1.00121.58 S ATOM 28411 SG CYS I 7 40.481 125.080 128.209 1.00221.68 S ATOM 28436 SG CYS I 10 44.200 124.446 128.128 1.00219.35 S ATOM 28602 SG CYS I 29 41.894 121.963 129.852 1.00227.97 S ATOM 28626 SG CYS I 32 42.442 125.273 131.483 1.00227.85 S ATOM 28953 SG CYS I 75 15.891 115.915 90.251 1.00208.33 S ATOM 28975 SG CYS I 78 15.625 119.431 89.029 1.00221.92 S ATOM 29191 SG CYS I 103 18.835 117.498 88.317 1.00196.15 S ATOM 29211 SG CYS I 106 17.988 118.543 91.896 1.00204.64 S ATOM 29313 SG CYS J 7 62.966 90.466 37.711 1.00 82.75 S ATOM 29336 SG CYS J 10 62.374 88.304 34.596 1.00 91.09 S ATOM 29616 SG CYS J 45 59.449 89.227 36.902 1.00 93.61 S ATOM 29622 SG CYS J 46 61.063 91.675 34.532 1.00 80.67 S ATOM 30745 SG CYS L 31 96.414 113.776 54.107 1.00177.62 S ATOM 30765 SG CYS L 34 97.179 115.399 50.816 1.00181.30 S ATOM 30869 SG CYS L 48 99.952 114.462 53.363 1.00191.56 S ATOM 30892 SG CYS L 51 97.781 117.445 54.013 1.00193.64 S Time building chain proxies: 6.86, per 1000 atoms: 0.21 Number of scatterers: 33083 At special positions: 0 Unit cell: (151.241, 154.505, 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 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 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " 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 B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " 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 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " 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 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 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 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " 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: 145 helices and 48 sheets defined 39.0% alpha, 20.2% beta 42 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 4.59 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 213 removed outlier: 3.610A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.509A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.734A 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: 3.947A 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: 3.745A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.885A 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 659 removed outlier: 3.534A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.633A 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 749 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: 3.694A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 removed outlier: 4.038A 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 removed outlier: 3.554A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.945A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.530A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.601A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.323A 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 1143 through 1147 removed outlier: 3.625A pdb=" N THR A1147 " --> pdb=" O LYS A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1173 Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.578A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.604A 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: 3.903A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.589A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1451 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.146A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.509A 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 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.861A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.739A 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 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.692A 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 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.821A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.717A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 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: 3.759A 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 748 Processing helix chain 'B' and resid 751 through 756 removed outlier: 3.814A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 756 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.558A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.887A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.336A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.803A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.608A 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 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.542A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.525A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.849A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.573A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.585A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 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 5 through 27 removed outlier: 3.596A 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: 3.765A 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: 3.578A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 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 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.581A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.854A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 131 through 135 removed outlier: 4.286A pdb=" N ASN H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.813A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (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: 3.773A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.565A 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 52 removed outlier: 4.243A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 10.053A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.331A 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: 4.799A 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 removed outlier: 3.502A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.664A 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: 3.679A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.978A 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: 6.502A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.555A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) 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: 7.015A 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 769 through 770 Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.705A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB6, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.592A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.386A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.161A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.161A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.620A pdb=" N ILE B 90 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.620A pdb=" N ILE B 90 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.139A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.910A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.592A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.323A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.264A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.264A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.178A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.590A pdb=" N THR B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.654A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 removed outlier: 3.511A pdb=" N GLU B1181 " --> pdb=" O ILE B1172 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.822A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.625A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.519A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.998A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.539A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER G 141 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.703A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.012A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 1362 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 10.64 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5409 1.31 - 1.43: 8965 1.43 - 1.56: 19011 1.56 - 1.69: 196 1.69 - 1.81: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.181 0.193 1.00e-02 1.00e+04 3.72e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.208 0.162 1.20e-02 6.94e+03 1.83e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.447 -0.110 1.10e-02 8.26e+03 9.94e+01 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 bond pdb=" C2' ATP A1801 " pdb=" C3' ATP A1801 " ideal model delta sigma weight residual 1.531 1.452 0.079 1.20e-02 6.94e+03 4.30e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 46064 4.37 - 8.74: 86 8.74 - 13.11: 0 13.11 - 17.49: 2 17.49 - 21.86: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 121.38 15.45 1.00e+00 1.00e+00 2.39e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.50 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.09 8.60 1.00e+00 1.00e+00 7.40e+01 angle pdb=" N3 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 127.04 133.23 -6.19 1.15e+00 7.59e-01 2.90e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 19849 32.77 - 65.54: 578 65.54 - 98.31: 36 98.31 - 131.08: 3 131.08 - 163.85: 1 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 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE A 22 " pdb=" C PHE A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+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 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3706 0.040 - 0.080: 1027 0.080 - 0.121: 401 0.121 - 0.161: 52 0.161 - 0.201: 4 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CB THR I 55 " pdb=" CA THR I 55 " pdb=" OG1 THR I 55 " pdb=" CG2 THR I 55 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 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 -2.44 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.29e-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 3.32e-02 1.10e+01 pdb=" C LEU A 710 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 1 " 0.025 2.00e-02 2.50e+03 1.12e-02 3.48e+00 pdb=" N9 A R 1 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A R 1 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A R 1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A R 1 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A R 1 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A R 1 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A R 1 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A R 1 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A R 1 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A R 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 245 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.026 5.00e-02 4.00e+02 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 78 2.37 - 3.00: 17322 3.00 - 3.63: 48782 3.63 - 4.27: 76766 4.27 - 4.90: 128931 Nonbonded interactions: 271879 Sorted by model distance: nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.732 2.170 nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.783 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.885 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1803 " model vdw 2.047 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1802 " model vdw 2.100 2.170 ... (remaining 271874 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 41.860 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 33905 Z= 0.314 Angle : 0.610 21.857 46198 Z= 0.412 Chirality : 0.043 0.201 5190 Planarity : 0.003 0.045 5630 Dihedral : 14.342 163.854 13127 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.35 (0.14), residues: 3854 helix: 1.46 (0.15), residues: 1317 sheet: -0.16 (0.21), residues: 644 loop : -0.46 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1366 TYR 0.029 0.001 TYR B 797 PHE 0.024 0.001 PHE I 4 TRP 0.020 0.001 TRP A1044 HIS 0.010 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.31 (33873) covalent geometry : angle 0.60576 / 0.41 (46153) hydrogen bonds : bond 0.18229 / 12.08 ( 1428) hydrogen bonds : angle 6.73908 / 4.90 ( 3981) metal coordination : bond 0.00375 / 0.23 ( 32) metal coordination : angle 2.47435 / 1.53 ( 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 648 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9065 (mtt) cc_final: 0.8602 (mtt) REVERT: A 175 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7744 (ptp-110) REVERT: A 277 GLU cc_start: 0.8651 (tt0) cc_final: 0.8147 (tp30) REVERT: A 317 LYS cc_start: 0.8849 (mmpt) cc_final: 0.8201 (ttpp) REVERT: A 676 MET cc_start: 0.8828 (mmm) cc_final: 0.8572 (mmt) REVERT: A 696 GLU cc_start: 0.8200 (tt0) cc_final: 0.7215 (tm-30) REVERT: A 708 MET cc_start: 0.7235 (mtt) cc_final: 0.7031 (ttm) REVERT: A 716 ASP cc_start: 0.8822 (t70) cc_final: 0.8610 (t0) REVERT: A 795 GLU cc_start: 0.8485 (pm20) cc_final: 0.8265 (pm20) REVERT: A 992 ASP cc_start: 0.8725 (m-30) cc_final: 0.8459 (t70) REVERT: A 1127 ASP cc_start: 0.8158 (t0) cc_final: 0.7727 (p0) REVERT: A 1325 THR cc_start: 0.9452 (p) cc_final: 0.9087 (t) REVERT: A 1444 MET cc_start: 0.8592 (mmm) cc_final: 0.8342 (mmm) REVERT: B 133 LYS cc_start: 0.8434 (mttt) cc_final: 0.8142 (mtmm) REVERT: B 216 GLU cc_start: 0.8955 (tt0) cc_final: 0.8624 (tt0) REVERT: B 344 LYS cc_start: 0.8577 (pttp) cc_final: 0.8332 (mmmt) REVERT: B 359 GLU cc_start: 0.8517 (mp0) cc_final: 0.8015 (mp0) REVERT: B 431 TYR cc_start: 0.8271 (t80) cc_final: 0.7358 (t80) REVERT: B 476 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7775 (ttp-170) REVERT: B 508 LEU cc_start: 0.7839 (mm) cc_final: 0.7417 (tp) REVERT: B 618 ASP cc_start: 0.8634 (t0) cc_final: 0.8264 (t0) REVERT: B 621 GLU cc_start: 0.8770 (tp30) cc_final: 0.8092 (tp30) REVERT: B 622 LYS cc_start: 0.8904 (mttt) cc_final: 0.8639 (mtpt) REVERT: B 641 GLU cc_start: 0.8513 (tt0) cc_final: 0.7933 (pp20) REVERT: B 730 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7700 (mtt90) REVERT: B 783 THR cc_start: 0.9467 (m) cc_final: 0.9209 (p) REVERT: B 862 GLN cc_start: 0.8029 (mt0) cc_final: 0.7648 (mt0) REVERT: B 1178 ASN cc_start: 0.8954 (m-40) cc_final: 0.8645 (t0) REVERT: C 75 MET cc_start: 0.8909 (mmm) cc_final: 0.8627 (tpt) REVERT: C 224 GLN cc_start: 0.8632 (mt0) cc_final: 0.8191 (mm-40) REVERT: D 28 GLN cc_start: 0.5941 (tt0) cc_final: 0.5131 (mm110) REVERT: D 35 LEU cc_start: 0.7458 (mt) cc_final: 0.6600 (mt) REVERT: D 211 LEU cc_start: 0.6974 (mt) cc_final: 0.6707 (tp) REVERT: D 214 LEU cc_start: 0.7806 (tt) cc_final: 0.7459 (mp) REVERT: D 220 LEU cc_start: 0.6952 (pp) cc_final: 0.6624 (mt) REVERT: E 8 ASN cc_start: 0.8872 (m-40) cc_final: 0.8403 (m-40) REVERT: E 48 ASP cc_start: 0.8636 (t70) cc_final: 0.8376 (t0) REVERT: E 50 MET cc_start: 0.9052 (ptp) cc_final: 0.8580 (ppp) REVERT: E 104 ASN cc_start: 0.8702 (t0) cc_final: 0.8471 (t0) REVERT: E 106 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8089 (tp40) REVERT: E 192 ARG cc_start: 0.9092 (ttt180) cc_final: 0.8878 (ttt-90) REVERT: F 87 LYS cc_start: 0.9160 (ptpt) cc_final: 0.8925 (ptpp) REVERT: F 129 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8465 (mmtt) REVERT: G 44 TYR cc_start: 0.8091 (m-80) cc_final: 0.7038 (m-80) REVERT: G 60 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8448 (ttt-90) REVERT: G 115 MET cc_start: 0.5498 (mtp) cc_final: 0.5132 (mtp) REVERT: G 140 LYS cc_start: 0.7286 (mttt) cc_final: 0.7025 (mmtt) REVERT: H 9 ILE cc_start: 0.8708 (mp) cc_final: 0.8412 (mt) REVERT: H 24 CYS cc_start: 0.9129 (m) cc_final: 0.8848 (m) REVERT: H 33 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8055 (mp10) REVERT: H 41 ASP cc_start: 0.8847 (m-30) cc_final: 0.8640 (m-30) REVERT: H 87 ARG cc_start: 0.8845 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: H 103 LYS cc_start: 0.8931 (tptt) cc_final: 0.8668 (tptp) REVERT: H 112 ILE cc_start: 0.8999 (tt) cc_final: 0.8662 (tp) REVERT: H 137 GLN cc_start: 0.8743 (tt0) cc_final: 0.8352 (tm-30) REVERT: I 8 ARG cc_start: 0.7863 (tmm160) cc_final: 0.7064 (ttp80) REVERT: I 45 ARG cc_start: 0.7068 (ttt90) cc_final: 0.6416 (ttt-90) REVERT: I 81 ARG cc_start: 0.7677 (mmt-90) cc_final: 0.7016 (mmt90) REVERT: J 23 ASN cc_start: 0.8551 (m-40) cc_final: 0.8321 (m-40) REVERT: J 29 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8680 (pt0) REVERT: K 36 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8872 (tp30) REVERT: K 38 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8538 (mm-30) REVERT: K 49 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8675 (mm-30) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.2642 time to fit residues: 260.7316 Evaluate side-chains 404 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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: 4.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN A 736 ASN A 975 HIS B 115 GLN B 433 GLN B 878 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN D 9 GLN D 37 GLN E 3 GLN E 101 GLN G 10 ASN I 12 ASN I 46 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086977 restraints weight = 51681.172| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.18 r_work: 0.2968 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 33905 Z= 0.269 Angle : 0.650 11.094 46198 Z= 0.343 Chirality : 0.048 0.261 5190 Planarity : 0.005 0.071 5630 Dihedral : 16.810 163.165 5346 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 0.90 % Allowed : 6.81 % Favored : 92.28 % 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: 0.18 (0.14), residues: 3854 helix: 1.27 (0.14), residues: 1352 sheet: -0.19 (0.21), residues: 634 loop : -0.57 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 241 TYR 0.022 0.002 TYR H 95 PHE 0.026 0.002 PHE A1225 TRP 0.010 0.001 TRP A1044 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 (33873) covalent geometry : angle 0.64209 / 0.34 (46153) hydrogen bonds : bond 0.04902 / 3.27 ( 1428) hydrogen bonds : angle 5.14368 / 3.72 ( 3981) metal coordination : bond 0.00745 / 0.49 ( 32) metal coordination : angle 3.38391 / 2.13 ( 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 439 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 408 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 74 MET cc_start: 0.8984 (mtt) cc_final: 0.8745 (mtt) REVERT: A 175 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7883 (ptp-110) REVERT: A 277 GLU cc_start: 0.8628 (tt0) cc_final: 0.8207 (tp30) REVERT: A 290 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 317 LYS cc_start: 0.8835 (mmpt) cc_final: 0.8263 (ttpp) REVERT: A 696 GLU cc_start: 0.8324 (tt0) cc_final: 0.7485 (tm-30) REVERT: A 1127 ASP cc_start: 0.8595 (t0) cc_final: 0.7910 (p0) REVERT: A 1444 MET cc_start: 0.8774 (mmm) cc_final: 0.8468 (mmm) REVERT: B 313 MET cc_start: 0.9360 (mmm) cc_final: 0.9144 (mmm) REVERT: B 359 GLU cc_start: 0.8678 (mp0) cc_final: 0.8308 (mp0) REVERT: B 431 TYR cc_start: 0.8484 (t80) cc_final: 0.7764 (t80) REVERT: B 476 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7835 (ttp-170) REVERT: B 508 LEU cc_start: 0.7820 (mm) cc_final: 0.7402 (tp) REVERT: B 618 ASP cc_start: 0.8466 (t0) cc_final: 0.8172 (t0) REVERT: B 620 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8336 (mtp-110) REVERT: B 621 GLU cc_start: 0.8632 (tp30) cc_final: 0.7989 (tp30) REVERT: B 622 LYS cc_start: 0.9039 (mttt) cc_final: 0.8833 (mtpt) REVERT: B 641 GLU cc_start: 0.8468 (tt0) cc_final: 0.7993 (pp20) REVERT: B 730 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7809 (mtt90) REVERT: C 75 MET cc_start: 0.9083 (mmm) cc_final: 0.8842 (tpt) REVERT: C 224 GLN cc_start: 0.8707 (mt0) cc_final: 0.8379 (mm-40) REVERT: D 22 GLU cc_start: 0.5008 (mt-10) cc_final: 0.4514 (pm20) REVERT: D 50 LEU cc_start: 0.7037 (mp) cc_final: 0.6772 (tp) REVERT: D 144 THR cc_start: 0.8321 (m) cc_final: 0.7998 (p) REVERT: D 211 LEU cc_start: 0.7038 (mt) cc_final: 0.6629 (tp) REVERT: D 214 LEU cc_start: 0.7824 (tt) cc_final: 0.7450 (mp) REVERT: D 220 LEU cc_start: 0.6906 (pp) cc_final: 0.6580 (mt) REVERT: E 50 MET cc_start: 0.9095 (ptp) cc_final: 0.8721 (ppp) REVERT: E 104 ASN cc_start: 0.8668 (t0) cc_final: 0.8438 (t0) REVERT: E 106 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8111 (tp40) REVERT: F 116 ASP cc_start: 0.8709 (t0) cc_final: 0.8392 (t0) REVERT: F 129 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8602 (mmtt) REVERT: G 25 TYR cc_start: 0.8147 (t80) cc_final: 0.7853 (t80) REVERT: G 44 TYR cc_start: 0.7999 (m-80) cc_final: 0.7106 (m-80) REVERT: G 60 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8694 (ttt-90) REVERT: G 140 LYS cc_start: 0.7296 (mttt) cc_final: 0.7076 (mmtt) REVERT: G 146 LYS cc_start: 0.6313 (ttmt) cc_final: 0.5868 (pttm) REVERT: G 153 GLN cc_start: 0.7001 (mp10) cc_final: 0.6576 (mp10) REVERT: H 9 ILE cc_start: 0.8896 (mp) cc_final: 0.8649 (mt) REVERT: H 24 CYS cc_start: 0.9090 (m) cc_final: 0.8763 (m) REVERT: H 33 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8182 (mp10) REVERT: H 41 ASP cc_start: 0.8800 (m-30) cc_final: 0.8527 (m-30) REVERT: H 52 GLN cc_start: 0.8704 (mp10) cc_final: 0.8112 (mp10) REVERT: H 87 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8574 (mmm-85) REVERT: H 103 LYS cc_start: 0.9022 (tptt) cc_final: 0.8784 (tptp) REVERT: H 137 GLN cc_start: 0.8636 (tt0) cc_final: 0.8338 (tm-30) REVERT: I 8 ARG cc_start: 0.7963 (tmm160) cc_final: 0.7050 (ttp80) REVERT: I 30 ARG cc_start: 0.5928 (mpp80) cc_final: 0.5655 (mpp80) REVERT: I 45 ARG cc_start: 0.7507 (ttt90) cc_final: 0.6857 (ttt-90) REVERT: I 81 ARG cc_start: 0.7654 (mmt-90) cc_final: 0.6993 (mmt90) outliers start: 31 outliers final: 23 residues processed: 425 average time/residue: 0.2536 time to fit residues: 167.3854 Evaluate side-chains 395 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 372 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain K residue 17 SER 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: 6.9990 chunk 191 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 239 optimal weight: 0.1980 chunk 7 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN B 878 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN E 101 GLN G 10 ASN G 57 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087197 restraints weight = 51408.741| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.12 r_work: 0.2940 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33905 Z= 0.223 Angle : 0.585 9.454 46198 Z= 0.311 Chirality : 0.046 0.275 5190 Planarity : 0.004 0.048 5630 Dihedral : 16.680 163.175 5346 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 1.40 % Allowed : 7.95 % Favored : 90.65 % 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: 0.16 (0.14), residues: 3854 helix: 1.31 (0.14), residues: 1350 sheet: -0.26 (0.20), residues: 632 loop : -0.61 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 119 TYR 0.019 0.001 TYR K 61 PHE 0.032 0.002 PHE A 219 TRP 0.009 0.001 TRP A1228 HIS 0.008 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (33873) covalent geometry : angle 0.57776 / 0.31 (46153) hydrogen bonds : bond 0.04286 / 2.86 ( 1428) hydrogen bonds : angle 4.79267 / 3.48 ( 3981) metal coordination : bond 0.00698 / 0.46 ( 32) metal coordination : angle 3.01403 / 1.91 ( 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 450 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8464 (mt-10) REVERT: A 74 MET cc_start: 0.9000 (mtt) cc_final: 0.8769 (mtt) REVERT: A 175 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7982 (ttm110) REVERT: A 277 GLU cc_start: 0.8625 (tt0) cc_final: 0.8253 (tp30) REVERT: A 290 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 317 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8218 (ttpp) REVERT: A 696 GLU cc_start: 0.8366 (tt0) cc_final: 0.7513 (tm-30) REVERT: A 708 MET cc_start: 0.7695 (ttm) cc_final: 0.7136 (ttm) REVERT: A 795 GLU cc_start: 0.8505 (pm20) cc_final: 0.8292 (pm20) REVERT: A 1127 ASP cc_start: 0.8579 (t0) cc_final: 0.7901 (p0) REVERT: A 1144 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8681 (ttmm) REVERT: A 1211 GLN cc_start: 0.7923 (mt0) cc_final: 0.7624 (mp10) REVERT: A 1444 MET cc_start: 0.8811 (mmm) cc_final: 0.8488 (mmm) REVERT: A 1453 TYR cc_start: 0.7817 (m-80) cc_final: 0.6775 (m-10) REVERT: B 313 MET cc_start: 0.9338 (mmm) cc_final: 0.9121 (mmm) REVERT: B 359 GLU cc_start: 0.8688 (mp0) cc_final: 0.8291 (mp0) REVERT: B 431 TYR cc_start: 0.8480 (t80) cc_final: 0.7802 (t80) REVERT: B 476 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7854 (ttp-170) REVERT: B 508 LEU cc_start: 0.7727 (mm) cc_final: 0.7310 (tp) REVERT: B 618 ASP cc_start: 0.8428 (t0) cc_final: 0.8141 (t0) REVERT: B 620 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8382 (mtp-110) REVERT: B 621 GLU cc_start: 0.8607 (tp30) cc_final: 0.7965 (tp30) REVERT: B 641 GLU cc_start: 0.8453 (tt0) cc_final: 0.8020 (pp20) REVERT: B 730 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7708 (mtt90) REVERT: C 19 ASP cc_start: 0.8077 (t0) cc_final: 0.7791 (t0) REVERT: C 75 MET cc_start: 0.9087 (mmm) cc_final: 0.8870 (tpt) REVERT: C 224 GLN cc_start: 0.8694 (mt0) cc_final: 0.8353 (mm-40) REVERT: D 22 GLU cc_start: 0.5073 (mt-10) cc_final: 0.4557 (pm20) REVERT: D 144 THR cc_start: 0.8360 (m) cc_final: 0.8063 (p) REVERT: D 211 LEU cc_start: 0.7048 (mt) cc_final: 0.6627 (tp) REVERT: D 214 LEU cc_start: 0.7850 (tt) cc_final: 0.7498 (mp) REVERT: D 220 LEU cc_start: 0.6923 (pp) cc_final: 0.6589 (mt) REVERT: E 50 MET cc_start: 0.9065 (ptp) cc_final: 0.8690 (ppp) REVERT: E 104 ASN cc_start: 0.8700 (t0) cc_final: 0.8461 (t0) REVERT: E 122 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8249 (mtmm) REVERT: F 129 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8642 (mmtt) REVERT: G 25 TYR cc_start: 0.8109 (t80) cc_final: 0.7837 (t80) REVERT: G 44 TYR cc_start: 0.8045 (m-80) cc_final: 0.7610 (m-80) REVERT: G 60 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8707 (ttt-90) REVERT: G 140 LYS cc_start: 0.7337 (mttt) cc_final: 0.7105 (mmtt) REVERT: G 144 ARG cc_start: 0.5869 (mtp-110) cc_final: 0.5403 (mtp-110) REVERT: G 146 LYS cc_start: 0.6269 (ttmt) cc_final: 0.5853 (pttm) REVERT: G 153 GLN cc_start: 0.6814 (mp10) cc_final: 0.6580 (mp10) REVERT: H 9 ILE cc_start: 0.8933 (mp) cc_final: 0.8713 (mt) REVERT: H 24 CYS cc_start: 0.9089 (m) cc_final: 0.8747 (m) REVERT: H 33 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8202 (mp10) REVERT: H 41 ASP cc_start: 0.8832 (m-30) cc_final: 0.8531 (m-30) REVERT: H 87 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8564 (mmm-85) REVERT: H 103 LYS cc_start: 0.9009 (tptt) cc_final: 0.8787 (tptp) REVERT: H 106 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8584 (mp0) REVERT: H 137 GLN cc_start: 0.8672 (tt0) cc_final: 0.8371 (tm-30) REVERT: I 8 ARG cc_start: 0.7846 (tmm160) cc_final: 0.6882 (ttp80) REVERT: I 30 ARG cc_start: 0.6053 (mpp80) cc_final: 0.5754 (mpp80) REVERT: I 45 ARG cc_start: 0.7430 (ttt90) cc_final: 0.6764 (ttt-90) REVERT: I 81 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7146 (mmt90) REVERT: K 16 GLU cc_start: 0.8648 (tt0) cc_final: 0.8215 (tt0) outliers start: 48 outliers final: 37 residues processed: 429 average time/residue: 0.2539 time to fit residues: 169.6260 Evaluate side-chains 413 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 352 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 37 GLN G 10 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085623 restraints weight = 51340.707| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.27 r_work: 0.2945 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 33905 Z= 0.246 Angle : 0.592 10.718 46198 Z= 0.312 Chirality : 0.046 0.276 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.670 163.890 5346 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 1.78 % Allowed : 9.06 % Favored : 89.17 % 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: 0.10 (0.13), residues: 3854 helix: 1.30 (0.14), residues: 1353 sheet: -0.36 (0.20), residues: 631 loop : -0.65 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 241 TYR 0.015 0.001 TYR K 61 PHE 0.029 0.002 PHE A 219 TRP 0.010 0.001 TRP A1228 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (33873) covalent geometry : angle 0.58354 / 0.31 (46153) hydrogen bonds : bond 0.04104 / 2.74 ( 1428) hydrogen bonds : angle 4.66366 / 3.38 ( 3981) metal coordination : bond 0.00774 / 0.51 ( 32) metal coordination : angle 3.19666 / 1.98 ( 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 448 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 387 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8515 (mt-10) REVERT: A 175 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7990 (ttm110) REVERT: A 277 GLU cc_start: 0.8667 (tt0) cc_final: 0.8286 (tp30) REVERT: A 290 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8445 (tm-30) REVERT: A 317 LYS cc_start: 0.8936 (mmpt) cc_final: 0.8417 (ttpp) REVERT: A 455 MET cc_start: 0.9150 (ttp) cc_final: 0.8935 (ttm) REVERT: A 708 MET cc_start: 0.7745 (ttm) cc_final: 0.7145 (ttm) REVERT: A 795 GLU cc_start: 0.8573 (pm20) cc_final: 0.8358 (pm20) REVERT: A 1127 ASP cc_start: 0.8628 (t0) cc_final: 0.7916 (p0) REVERT: A 1144 LYS cc_start: 0.9118 (ttmm) cc_final: 0.8908 (ttmm) REVERT: A 1262 LYS cc_start: 0.8424 (tmmt) cc_final: 0.8198 (mttt) REVERT: A 1269 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7934 (tm-30) REVERT: A 1444 MET cc_start: 0.8868 (mmm) cc_final: 0.8435 (mmm) REVERT: A 1453 TYR cc_start: 0.7811 (m-80) cc_final: 0.6784 (m-10) REVERT: B 164 LYS cc_start: 0.8389 (mttt) cc_final: 0.8138 (mtpt) REVERT: B 289 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8845 (mm) REVERT: B 313 MET cc_start: 0.9368 (mmm) cc_final: 0.9151 (mmm) REVERT: B 431 TYR cc_start: 0.8573 (t80) cc_final: 0.7924 (t80) REVERT: B 476 ARG cc_start: 0.8140 (ttp-170) cc_final: 0.7868 (ttp-170) REVERT: B 508 LEU cc_start: 0.7642 (mm) cc_final: 0.7294 (tp) REVERT: B 618 ASP cc_start: 0.8415 (t0) cc_final: 0.8132 (t0) REVERT: B 621 GLU cc_start: 0.8622 (tp30) cc_final: 0.7911 (tp30) REVERT: B 641 GLU cc_start: 0.8466 (tt0) cc_final: 0.8054 (pp20) REVERT: B 730 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7750 (mtt90) REVERT: C 224 GLN cc_start: 0.8739 (mt0) cc_final: 0.8374 (mm-40) REVERT: C 230 MET cc_start: 0.9134 (mtt) cc_final: 0.8909 (mtp) REVERT: D 22 GLU cc_start: 0.5068 (mt-10) cc_final: 0.4559 (pm20) REVERT: D 144 THR cc_start: 0.8253 (m) cc_final: 0.7966 (p) REVERT: D 211 LEU cc_start: 0.6950 (mt) cc_final: 0.6563 (tp) REVERT: D 214 LEU cc_start: 0.7868 (tt) cc_final: 0.7501 (mp) REVERT: E 4 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8342 (tm-30) REVERT: E 104 ASN cc_start: 0.8735 (t0) cc_final: 0.8469 (t0) REVERT: F 129 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8651 (mmtt) REVERT: G 25 TYR cc_start: 0.8146 (t80) cc_final: 0.7792 (t80) REVERT: G 44 TYR cc_start: 0.8061 (m-80) cc_final: 0.7655 (m-80) REVERT: G 146 LYS cc_start: 0.6276 (ttmt) cc_final: 0.5869 (pttm) REVERT: G 153 GLN cc_start: 0.6679 (mp10) cc_final: 0.6285 (mp10) REVERT: H 24 CYS cc_start: 0.9124 (m) cc_final: 0.8762 (m) REVERT: H 33 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8248 (mp10) REVERT: H 41 ASP cc_start: 0.8857 (m-30) cc_final: 0.8544 (m-30) REVERT: H 52 GLN cc_start: 0.8773 (mp10) cc_final: 0.7948 (mp10) REVERT: H 87 ARG cc_start: 0.8821 (mmm-85) cc_final: 0.8587 (mmm-85) REVERT: H 103 LYS cc_start: 0.8975 (tptt) cc_final: 0.8758 (tptp) REVERT: I 8 ARG cc_start: 0.7828 (tmm160) cc_final: 0.6831 (ttp80) REVERT: I 30 ARG cc_start: 0.6003 (mpp80) cc_final: 0.5642 (mpp80) REVERT: I 45 ARG cc_start: 0.7505 (ttt90) cc_final: 0.6815 (ttt-90) REVERT: I 81 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.7169 (mmt90) REVERT: K 16 GLU cc_start: 0.8673 (tt0) cc_final: 0.8346 (tt0) outliers start: 61 outliers final: 47 residues processed: 423 average time/residue: 0.2540 time to fit residues: 167.6104 Evaluate side-chains 422 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 0.1980 chunk 140 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 182 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 427 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN D 2 ASN G 10 ASN ** K 2 ASN ** 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 = 0.3763 r_free = 0.3763 target = 0.131128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087961 restraints weight = 51206.078| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.21 r_work: 0.2990 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33905 Z= 0.126 Angle : 0.526 9.360 46198 Z= 0.280 Chirality : 0.043 0.265 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.568 161.307 5346 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 1.49 % Allowed : 10.05 % Favored : 88.47 % 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: 1.48 (0.14), residues: 1351 sheet: -0.28 (0.20), residues: 629 loop : -0.54 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 241 TYR 0.012 0.001 TYR K 61 PHE 0.028 0.001 PHE A 219 TRP 0.008 0.001 TRP A1228 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (33873) covalent geometry : angle 0.51870 / 0.28 (46153) hydrogen bonds : bond 0.03542 / 2.35 ( 1428) hydrogen bonds : angle 4.43029 / 3.22 ( 3981) metal coordination : bond 0.00422 / 0.27 ( 32) metal coordination : angle 2.75323 / 1.73 ( 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 452 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.9111 (mtp) cc_final: 0.8905 (mtm) REVERT: A 277 GLU cc_start: 0.8642 (tt0) cc_final: 0.8259 (tp30) REVERT: A 290 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 317 LYS cc_start: 0.8919 (mmpt) cc_final: 0.8374 (ttpp) REVERT: A 455 MET cc_start: 0.9075 (ttp) cc_final: 0.8833 (ttm) REVERT: A 708 MET cc_start: 0.7625 (ttm) cc_final: 0.7133 (ttm) REVERT: A 795 GLU cc_start: 0.8625 (pm20) cc_final: 0.8393 (pm20) REVERT: A 830 LYS cc_start: 0.9307 (mmtm) cc_final: 0.8956 (mmtp) REVERT: A 1127 ASP cc_start: 0.8608 (t0) cc_final: 0.7932 (p0) REVERT: A 1144 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8726 (ttmm) REVERT: A 1211 GLN cc_start: 0.7818 (mt0) cc_final: 0.7473 (mp10) REVERT: A 1262 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8181 (mttt) REVERT: A 1444 MET cc_start: 0.8754 (mmm) cc_final: 0.8425 (mmm) REVERT: A 1453 TYR cc_start: 0.7784 (m-80) cc_final: 0.6764 (m-10) REVERT: B 164 LYS cc_start: 0.8300 (mttt) cc_final: 0.8022 (mtpt) REVERT: B 239 GLU cc_start: 0.8769 (pt0) cc_final: 0.8416 (pt0) REVERT: B 313 MET cc_start: 0.9346 (mmm) cc_final: 0.9109 (mmm) REVERT: B 431 TYR cc_start: 0.8498 (t80) cc_final: 0.7804 (t80) REVERT: B 476 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7754 (ttp-170) REVERT: B 508 LEU cc_start: 0.7709 (mm) cc_final: 0.7358 (tp) REVERT: B 641 GLU cc_start: 0.8445 (tt0) cc_final: 0.8029 (pp20) REVERT: B 730 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7741 (mtt90) REVERT: C 224 GLN cc_start: 0.8706 (mt0) cc_final: 0.8332 (mm-40) REVERT: D 22 GLU cc_start: 0.4959 (mt-10) cc_final: 0.4520 (pm20) REVERT: D 144 THR cc_start: 0.8365 (m) cc_final: 0.8047 (p) REVERT: D 211 LEU cc_start: 0.6846 (mt) cc_final: 0.6462 (tp) REVERT: D 214 LEU cc_start: 0.7856 (tt) cc_final: 0.7509 (mp) REVERT: E 4 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8238 (tm-30) REVERT: E 104 ASN cc_start: 0.8710 (t0) cc_final: 0.8441 (t0) REVERT: F 129 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8616 (mmtt) REVERT: G 25 TYR cc_start: 0.8073 (t80) cc_final: 0.7762 (t80) REVERT: G 44 TYR cc_start: 0.8061 (m-80) cc_final: 0.7259 (m-80) REVERT: G 115 MET cc_start: 0.4622 (mpp) cc_final: 0.4343 (mpp) REVERT: G 146 LYS cc_start: 0.5898 (ttmt) cc_final: 0.5608 (pttm) REVERT: G 153 GLN cc_start: 0.6614 (mp10) cc_final: 0.6264 (mp10) REVERT: H 24 CYS cc_start: 0.9114 (m) cc_final: 0.8771 (m) REVERT: H 41 ASP cc_start: 0.8872 (m-30) cc_final: 0.8581 (m-30) REVERT: H 87 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8616 (mmm-85) REVERT: H 103 LYS cc_start: 0.8971 (tptt) cc_final: 0.8741 (tptp) REVERT: H 137 GLN cc_start: 0.8594 (tt0) cc_final: 0.8314 (tm-30) REVERT: H 146 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8369 (ttm-80) REVERT: I 8 ARG cc_start: 0.7879 (tmm160) cc_final: 0.6974 (ttp80) REVERT: I 45 ARG cc_start: 0.7504 (ttt90) cc_final: 0.6528 (ttt-90) REVERT: I 81 ARG cc_start: 0.7737 (mmt-90) cc_final: 0.7144 (mmt90) REVERT: K 16 GLU cc_start: 0.8660 (tt0) cc_final: 0.8291 (tt0) REVERT: K 38 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8558 (mm-30) outliers start: 51 outliers final: 35 residues processed: 429 average time/residue: 0.2497 time to fit residues: 167.6304 Evaluate side-chains 405 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN 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 1051 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 293 optimal weight: 40.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086137 restraints weight = 51292.054| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.18 r_work: 0.2960 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33905 Z= 0.221 Angle : 0.571 9.270 46198 Z= 0.300 Chirality : 0.045 0.271 5190 Planarity : 0.004 0.051 5630 Dihedral : 16.559 163.200 5346 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.66 % Allowed : 10.86 % Favored : 87.48 % 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: 0.21 (0.14), residues: 3854 helix: 1.44 (0.15), residues: 1352 sheet: -0.39 (0.20), residues: 620 loop : -0.60 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 241 TYR 0.016 0.001 TYR H 95 PHE 0.027 0.002 PHE A 219 TRP 0.008 0.001 TRP A1228 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (33873) covalent geometry : angle 0.56418 / 0.30 (46153) hydrogen bonds : bond 0.03778 / 2.51 ( 1428) hydrogen bonds : angle 4.46694 / 3.25 ( 3981) metal coordination : bond 0.00662 / 0.43 ( 32) metal coordination : angle 2.87454 / 1.77 ( 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 435 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8681 (tt0) cc_final: 0.8281 (tp30) REVERT: A 290 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 311 GLN cc_start: 0.8426 (tp40) cc_final: 0.8092 (mm110) REVERT: A 317 LYS cc_start: 0.8950 (mmpt) cc_final: 0.8438 (ttpp) REVERT: A 455 MET cc_start: 0.9098 (ttp) cc_final: 0.8863 (ttm) REVERT: A 708 MET cc_start: 0.7697 (ttm) cc_final: 0.7186 (ttm) REVERT: A 1127 ASP cc_start: 0.8626 (t0) cc_final: 0.7937 (p0) REVERT: A 1262 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8185 (mttt) REVERT: A 1269 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7819 (tm-30) REVERT: A 1444 MET cc_start: 0.8795 (mmm) cc_final: 0.8408 (mmm) REVERT: A 1453 TYR cc_start: 0.7838 (m-80) cc_final: 0.6884 (m-10) REVERT: B 164 LYS cc_start: 0.8331 (mttt) cc_final: 0.8056 (mtpt) REVERT: B 313 MET cc_start: 0.9378 (mmm) cc_final: 0.9125 (mmm) REVERT: B 431 TYR cc_start: 0.8582 (t80) cc_final: 0.7810 (t80) REVERT: B 508 LEU cc_start: 0.7746 (mm) cc_final: 0.7379 (tp) REVERT: B 618 ASP cc_start: 0.8475 (t0) cc_final: 0.8171 (t0) REVERT: B 641 GLU cc_start: 0.8456 (tt0) cc_final: 0.8014 (pp20) REVERT: B 730 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7746 (mtt90) REVERT: C 19 ASP cc_start: 0.8230 (t0) cc_final: 0.7980 (t0) REVERT: C 224 GLN cc_start: 0.8666 (mt0) cc_final: 0.8313 (mm-40) REVERT: D 22 GLU cc_start: 0.5021 (mt-10) cc_final: 0.4538 (pm20) REVERT: D 144 THR cc_start: 0.8405 (m) cc_final: 0.8178 (p) REVERT: D 211 LEU cc_start: 0.6874 (mt) cc_final: 0.6476 (tp) REVERT: D 214 LEU cc_start: 0.7868 (tt) cc_final: 0.7505 (mp) REVERT: E 4 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8306 (tm-30) REVERT: E 104 ASN cc_start: 0.8742 (t0) cc_final: 0.8466 (t0) REVERT: F 129 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8626 (mmtt) REVERT: G 25 TYR cc_start: 0.8099 (t80) cc_final: 0.7762 (t80) REVERT: G 44 TYR cc_start: 0.8098 (m-80) cc_final: 0.7763 (m-80) REVERT: G 75 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.8163 (ttm-80) REVERT: G 115 MET cc_start: 0.4668 (OUTLIER) cc_final: 0.4363 (mpp) REVERT: G 146 LYS cc_start: 0.5838 (ttmt) cc_final: 0.5572 (pttm) REVERT: G 153 GLN cc_start: 0.6957 (mp10) cc_final: 0.6563 (mp10) REVERT: H 24 CYS cc_start: 0.9119 (m) cc_final: 0.8743 (m) REVERT: H 41 ASP cc_start: 0.8885 (m-30) cc_final: 0.8579 (m-30) REVERT: H 103 LYS cc_start: 0.8978 (tptt) cc_final: 0.8753 (tptp) REVERT: H 137 GLN cc_start: 0.8594 (tt0) cc_final: 0.8256 (tm-30) REVERT: I 8 ARG cc_start: 0.7907 (tmm160) cc_final: 0.6943 (ttp80) REVERT: I 45 ARG cc_start: 0.7347 (ttt90) cc_final: 0.6517 (ttt-90) REVERT: I 81 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7082 (mmt90) outliers start: 57 outliers final: 45 residues processed: 409 average time/residue: 0.2496 time to fit residues: 159.5349 Evaluate side-chains 411 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 365 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 354 optimal weight: 3.9990 chunk 270 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 357 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1211 GLN B 224 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088139 restraints weight = 51163.041| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.21 r_work: 0.3005 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2384 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= 0.110 Angle : 0.520 9.390 46198 Z= 0.276 Chirality : 0.042 0.262 5190 Planarity : 0.004 0.058 5630 Dihedral : 16.501 161.416 5346 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.51 % Allowed : 11.39 % Favored : 87.10 % 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: 0.35 (0.14), residues: 3854 helix: 1.58 (0.15), residues: 1350 sheet: -0.31 (0.20), residues: 626 loop : -0.52 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 241 TYR 0.012 0.001 TYR H 95 PHE 0.027 0.001 PHE A 219 TRP 0.007 0.001 TRP C 201 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (33873) covalent geometry : angle 0.51397 / 0.28 (46153) hydrogen bonds : bond 0.03384 / 2.24 ( 1428) hydrogen bonds : angle 4.30638 / 3.14 ( 3981) metal coordination : bond 0.00367 / 0.23 ( 32) metal coordination : angle 2.56783 / 1.61 ( 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 429 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 377 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8657 (tt0) cc_final: 0.8266 (tp30) REVERT: A 290 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8408 (tm-30) REVERT: A 311 GLN cc_start: 0.8402 (tp40) cc_final: 0.8073 (mm110) REVERT: A 317 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8388 (ttpp) REVERT: A 708 MET cc_start: 0.7558 (ttm) cc_final: 0.7074 (ttm) REVERT: A 830 LYS cc_start: 0.9317 (mmtm) cc_final: 0.8976 (mmtp) REVERT: A 1127 ASP cc_start: 0.8619 (t0) cc_final: 0.7996 (p0) REVERT: A 1211 GLN cc_start: 0.7812 (mt0) cc_final: 0.7446 (mp10) REVERT: A 1262 LYS cc_start: 0.8423 (tmmt) cc_final: 0.8184 (mttt) REVERT: A 1269 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7909 (tm-30) REVERT: A 1453 TYR cc_start: 0.7793 (m-80) cc_final: 0.6844 (m-10) REVERT: B 164 LYS cc_start: 0.8311 (mttt) cc_final: 0.7858 (mttt) REVERT: B 313 MET cc_start: 0.9363 (mmm) cc_final: 0.9119 (mmm) REVERT: B 431 TYR cc_start: 0.8508 (t80) cc_final: 0.7752 (t80) REVERT: B 508 LEU cc_start: 0.7648 (mm) cc_final: 0.7301 (tp) REVERT: B 641 GLU cc_start: 0.8432 (tt0) cc_final: 0.8099 (pp20) REVERT: B 730 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7730 (mtt90) REVERT: C 19 ASP cc_start: 0.8191 (t0) cc_final: 0.7923 (t0) REVERT: C 224 GLN cc_start: 0.8623 (mt0) cc_final: 0.8306 (mm-40) REVERT: D 67 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7511 (tpp-160) REVERT: D 144 THR cc_start: 0.8276 (m) cc_final: 0.8046 (p) REVERT: D 214 LEU cc_start: 0.7862 (tt) cc_final: 0.7487 (mp) REVERT: E 4 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 104 ASN cc_start: 0.8700 (t0) cc_final: 0.8419 (t0) REVERT: F 129 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8628 (mmtt) REVERT: G 25 TYR cc_start: 0.8071 (t80) cc_final: 0.7369 (t80) REVERT: G 42 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: G 44 TYR cc_start: 0.8055 (m-80) cc_final: 0.7722 (m-80) REVERT: G 75 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: G 115 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4465 (mpp) REVERT: G 144 ARG cc_start: 0.5999 (mtp-110) cc_final: 0.5662 (mtp-110) REVERT: G 153 GLN cc_start: 0.6671 (mp10) cc_final: 0.6459 (mp10) REVERT: H 24 CYS cc_start: 0.9145 (m) cc_final: 0.8797 (m) REVERT: H 41 ASP cc_start: 0.8885 (m-30) cc_final: 0.8592 (m-30) REVERT: H 103 LYS cc_start: 0.8957 (tptt) cc_final: 0.8738 (tptp) REVERT: H 137 GLN cc_start: 0.8588 (tt0) cc_final: 0.8287 (tm-30) REVERT: H 146 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (ttm-80) REVERT: I 8 ARG cc_start: 0.7867 (tmm160) cc_final: 0.6992 (ttp80) REVERT: I 45 ARG cc_start: 0.7334 (ttt90) cc_final: 0.6498 (ttt-90) REVERT: I 81 ARG cc_start: 0.7675 (mmt-90) cc_final: 0.7070 (mmt90) REVERT: K 38 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8572 (mm-30) outliers start: 52 outliers final: 37 residues processed: 408 average time/residue: 0.2501 time to fit residues: 159.2947 Evaluate side-chains 402 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 362 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 363 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 736 ASN B 224 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089055 restraints weight = 51178.184| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.27 r_work: 0.3002 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33905 Z= 0.120 Angle : 0.520 10.205 46198 Z= 0.275 Chirality : 0.042 0.262 5190 Planarity : 0.004 0.062 5630 Dihedral : 16.445 161.445 5346 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.54 % Allowed : 11.76 % Favored : 86.69 % 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: 0.41 (0.14), residues: 3854 helix: 1.62 (0.15), residues: 1351 sheet: -0.25 (0.21), residues: 624 loop : -0.50 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 241 TYR 0.010 0.001 TYR H 95 PHE 0.030 0.001 PHE A1225 TRP 0.007 0.001 TRP A1228 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33873) covalent geometry : angle 0.51469 / 0.27 (46153) hydrogen bonds : bond 0.03300 / 2.18 ( 1428) hydrogen bonds : angle 4.23174 / 3.09 ( 3981) metal coordination : bond 0.00382 / 0.25 ( 32) metal coordination : angle 2.40635 / 1.51 ( 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 420 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8654 (tt0) cc_final: 0.8279 (tp30) REVERT: A 290 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 311 GLN cc_start: 0.8410 (tp40) cc_final: 0.8095 (mm110) REVERT: A 317 LYS cc_start: 0.8924 (mmpt) cc_final: 0.8393 (ttpp) REVERT: A 708 MET cc_start: 0.7476 (ttm) cc_final: 0.7082 (ttm) REVERT: A 830 LYS cc_start: 0.9314 (mmtm) cc_final: 0.8995 (mmtp) REVERT: A 1127 ASP cc_start: 0.8619 (t0) cc_final: 0.7919 (p0) REVERT: A 1211 GLN cc_start: 0.7762 (mt0) cc_final: 0.7402 (mp10) REVERT: A 1218 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7914 (tt0) REVERT: A 1262 LYS cc_start: 0.8410 (tmmt) cc_final: 0.8194 (mttt) REVERT: A 1269 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7850 (tm-30) REVERT: A 1453 TYR cc_start: 0.7823 (m-80) cc_final: 0.6916 (m-10) REVERT: B 164 LYS cc_start: 0.8328 (mttt) cc_final: 0.8000 (mtpp) REVERT: B 241 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7471 (mtp85) REVERT: B 313 MET cc_start: 0.9363 (mmm) cc_final: 0.9131 (mmm) REVERT: B 431 TYR cc_start: 0.8616 (t80) cc_final: 0.7934 (t80) REVERT: B 508 LEU cc_start: 0.7668 (mm) cc_final: 0.7321 (tp) REVERT: B 618 ASP cc_start: 0.8446 (t0) cc_final: 0.8189 (t0) REVERT: B 641 GLU cc_start: 0.8443 (tt0) cc_final: 0.8116 (pp20) REVERT: B 730 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7823 (mtt90) REVERT: C 224 GLN cc_start: 0.8610 (mt0) cc_final: 0.8322 (mm-40) REVERT: D 4 SER cc_start: 0.7558 (t) cc_final: 0.7023 (p) REVERT: D 144 THR cc_start: 0.8204 (m) cc_final: 0.7979 (p) REVERT: D 214 LEU cc_start: 0.7873 (tt) cc_final: 0.7497 (mp) REVERT: E 4 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8249 (tm-30) REVERT: E 104 ASN cc_start: 0.8695 (t0) cc_final: 0.8419 (t0) REVERT: F 129 LYS cc_start: 0.9024 (mmtm) cc_final: 0.8652 (mmtt) REVERT: G 25 TYR cc_start: 0.8044 (t80) cc_final: 0.7452 (t80) REVERT: G 42 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: G 44 TYR cc_start: 0.8105 (m-80) cc_final: 0.7835 (m-80) REVERT: G 75 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8201 (ttm-80) REVERT: G 115 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4478 (mpp) REVERT: G 153 GLN cc_start: 0.6691 (mp10) cc_final: 0.6476 (mp10) REVERT: H 24 CYS cc_start: 0.9141 (m) cc_final: 0.8800 (m) REVERT: H 41 ASP cc_start: 0.8876 (m-30) cc_final: 0.8612 (m-30) REVERT: H 87 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8536 (mmm-85) REVERT: H 103 LYS cc_start: 0.8965 (tptt) cc_final: 0.8746 (tptp) REVERT: H 137 GLN cc_start: 0.8569 (tt0) cc_final: 0.8279 (tm-30) REVERT: H 146 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8337 (ttm-80) REVERT: I 8 ARG cc_start: 0.7896 (tmm160) cc_final: 0.7026 (ttp80) REVERT: I 45 ARG cc_start: 0.7423 (ttt90) cc_final: 0.6387 (ttt-90) REVERT: I 81 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7105 (mmt90) REVERT: K 38 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8578 (mm-30) outliers start: 53 outliers final: 40 residues processed: 399 average time/residue: 0.2354 time to fit residues: 147.8720 Evaluate side-chains 397 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 354 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 1.9990 chunk 377 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 862 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086906 restraints weight = 51266.929| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.17 r_work: 0.2970 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33905 Z= 0.205 Angle : 0.568 10.121 46198 Z= 0.297 Chirality : 0.044 0.268 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.478 163.726 5346 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 1.63 % Allowed : 12.11 % 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: 0.30 (0.14), residues: 3854 helix: 1.53 (0.15), residues: 1350 sheet: -0.31 (0.20), residues: 634 loop : -0.55 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 241 TYR 0.012 0.001 TYR H 95 PHE 0.028 0.001 PHE A1225 TRP 0.007 0.001 TRP A1228 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (33873) covalent geometry : angle 0.56222 / 0.30 (46153) hydrogen bonds : bond 0.03639 / 2.41 ( 1428) hydrogen bonds : angle 4.32478 / 3.15 ( 3981) metal coordination : bond 0.00601 / 0.40 ( 32) metal coordination : angle 2.70378 / 1.67 ( 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 411 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 355 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8678 (tt0) cc_final: 0.8287 (tp30) REVERT: A 290 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 311 GLN cc_start: 0.8424 (tp40) cc_final: 0.8084 (mm110) REVERT: A 317 LYS cc_start: 0.8914 (mmpt) cc_final: 0.8359 (ttpp) REVERT: A 708 MET cc_start: 0.7623 (ttm) cc_final: 0.7126 (ttm) REVERT: A 1127 ASP cc_start: 0.8644 (t0) cc_final: 0.7890 (p0) REVERT: A 1218 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7913 (tt0) REVERT: A 1262 LYS cc_start: 0.8414 (tmmt) cc_final: 0.8210 (mttt) REVERT: A 1269 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7955 (tm-30) REVERT: B 164 LYS cc_start: 0.8340 (mttt) cc_final: 0.8021 (mtpp) REVERT: B 241 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7576 (mtp85) REVERT: B 289 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8832 (mm) REVERT: B 313 MET cc_start: 0.9358 (mmm) cc_final: 0.9081 (mmm) REVERT: B 433 GLN cc_start: 0.8108 (mt0) cc_final: 0.7616 (mt0) REVERT: B 618 ASP cc_start: 0.8511 (t0) cc_final: 0.8234 (t0) REVERT: B 641 GLU cc_start: 0.8435 (tt0) cc_final: 0.8092 (pp20) REVERT: B 730 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7826 (mtt90) REVERT: C 224 GLN cc_start: 0.8661 (mt0) cc_final: 0.8332 (mm-40) REVERT: D 4 SER cc_start: 0.7571 (t) cc_final: 0.7028 (p) REVERT: D 61 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8032 (tm-30) REVERT: D 144 THR cc_start: 0.8086 (m) cc_final: 0.7859 (p) REVERT: D 198 LEU cc_start: 0.7786 (mp) cc_final: 0.7465 (pt) REVERT: D 214 LEU cc_start: 0.7894 (tt) cc_final: 0.7508 (mp) REVERT: E 104 ASN cc_start: 0.8715 (t0) cc_final: 0.8438 (t0) REVERT: F 129 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8698 (mmtt) REVERT: G 25 TYR cc_start: 0.8116 (t80) cc_final: 0.7721 (t80) REVERT: G 42 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: G 44 TYR cc_start: 0.8092 (m-80) cc_final: 0.7286 (m-80) REVERT: G 115 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4435 (mpp) REVERT: G 144 ARG cc_start: 0.5657 (mtp-110) cc_final: 0.5343 (mtp-110) REVERT: G 153 GLN cc_start: 0.7057 (mp10) cc_final: 0.6824 (mp10) REVERT: H 24 CYS cc_start: 0.9122 (m) cc_final: 0.8752 (m) REVERT: H 41 ASP cc_start: 0.8917 (m-30) cc_final: 0.8632 (m-30) REVERT: H 87 ARG cc_start: 0.8741 (mmm-85) cc_final: 0.8530 (mmm-85) REVERT: H 103 LYS cc_start: 0.8963 (tptt) cc_final: 0.8725 (tptp) REVERT: H 137 GLN cc_start: 0.8610 (tt0) cc_final: 0.8272 (tm-30) REVERT: I 8 ARG cc_start: 0.7838 (tmm160) cc_final: 0.6995 (ttp80) REVERT: I 45 ARG cc_start: 0.7213 (ttt90) cc_final: 0.6301 (ttt-90) REVERT: I 81 ARG cc_start: 0.7732 (mmt-90) cc_final: 0.7142 (mmt90) outliers start: 56 outliers final: 45 residues processed: 389 average time/residue: 0.2312 time to fit residues: 140.2122 Evaluate side-chains 396 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 164 optimal weight: 0.1980 chunk 321 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A1211 GLN B 862 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089029 restraints weight = 51422.779| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.21 r_work: 0.3009 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33905 Z= 0.109 Angle : 0.525 12.952 46198 Z= 0.276 Chirality : 0.042 0.261 5190 Planarity : 0.004 0.059 5630 Dihedral : 16.410 162.253 5346 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 1.34 % Allowed : 12.52 % Favored : 86.14 % 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: 0.43 (0.14), residues: 3854 helix: 1.61 (0.15), residues: 1357 sheet: -0.20 (0.21), residues: 629 loop : -0.49 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 241 TYR 0.010 0.001 TYR H 95 PHE 0.031 0.001 PHE A1225 TRP 0.008 0.001 TRP C 201 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (33873) covalent geometry : angle 0.51958 / 0.28 (46153) hydrogen bonds : bond 0.03249 / 2.14 ( 1428) hydrogen bonds : angle 4.19111 / 3.05 ( 3981) metal coordination : bond 0.00346 / 0.22 ( 32) metal coordination : angle 2.39611 / 1.50 ( 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 419 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 373 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8649 (tt0) cc_final: 0.8254 (tp30) REVERT: A 290 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 311 GLN cc_start: 0.8421 (tp40) cc_final: 0.8094 (mm110) REVERT: A 317 LYS cc_start: 0.8919 (mmpt) cc_final: 0.8380 (ttpp) REVERT: A 708 MET cc_start: 0.7407 (ttm) cc_final: 0.7011 (ttm) REVERT: A 830 LYS cc_start: 0.9323 (mmtm) cc_final: 0.8997 (mmtp) REVERT: A 1127 ASP cc_start: 0.8640 (t0) cc_final: 0.7958 (p0) REVERT: A 1211 GLN cc_start: 0.7711 (mt0) cc_final: 0.7364 (mp10) REVERT: A 1218 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7898 (tt0) REVERT: A 1269 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7977 (tm-30) REVERT: B 164 LYS cc_start: 0.8308 (mttt) cc_final: 0.7974 (mtpp) REVERT: B 241 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7439 (mtp85) REVERT: B 289 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8851 (mm) REVERT: B 313 MET cc_start: 0.9369 (mmm) cc_final: 0.9123 (mmm) REVERT: B 641 GLU cc_start: 0.8468 (tt0) cc_final: 0.8112 (pp20) REVERT: B 730 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7779 (mtt90) REVERT: C 224 GLN cc_start: 0.8614 (mt0) cc_final: 0.8299 (mm-40) REVERT: D 4 SER cc_start: 0.7492 (t) cc_final: 0.6942 (p) REVERT: D 61 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 144 THR cc_start: 0.8134 (m) cc_final: 0.7841 (p) REVERT: D 198 LEU cc_start: 0.7772 (mp) cc_final: 0.7473 (pt) REVERT: D 214 LEU cc_start: 0.7913 (tt) cc_final: 0.7516 (mp) REVERT: E 104 ASN cc_start: 0.8691 (t0) cc_final: 0.8415 (t0) REVERT: F 129 LYS cc_start: 0.9032 (mmtm) cc_final: 0.8626 (mmtt) REVERT: G 25 TYR cc_start: 0.8017 (t80) cc_final: 0.7410 (t80) REVERT: G 42 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: G 44 TYR cc_start: 0.8078 (m-80) cc_final: 0.7295 (m-80) REVERT: G 115 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.4500 (mpp) REVERT: G 144 ARG cc_start: 0.5843 (mtp-110) cc_final: 0.5481 (mtp-110) REVERT: G 153 GLN cc_start: 0.7023 (mp10) cc_final: 0.6793 (mp10) REVERT: H 24 CYS cc_start: 0.9134 (m) cc_final: 0.8798 (m) REVERT: H 41 ASP cc_start: 0.8904 (m-30) cc_final: 0.8628 (m-30) REVERT: H 52 GLN cc_start: 0.8936 (mp10) cc_final: 0.8559 (mm-40) REVERT: H 87 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8520 (mmm-85) REVERT: H 103 LYS cc_start: 0.8966 (tptt) cc_final: 0.8744 (tptp) REVERT: H 137 GLN cc_start: 0.8594 (tt0) cc_final: 0.8266 (tm-30) REVERT: H 146 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8313 (ttm-80) REVERT: I 8 ARG cc_start: 0.7886 (tmm160) cc_final: 0.7022 (ttp80) REVERT: I 45 ARG cc_start: 0.7199 (ttt90) cc_final: 0.6299 (ttt-90) REVERT: I 81 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.7164 (mmt90) REVERT: K 38 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8625 (mm-30) outliers start: 46 outliers final: 39 residues processed: 402 average time/residue: 0.2390 time to fit residues: 150.2763 Evaluate side-chains 401 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 358 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 53 HIS 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: 5.9990 chunk 354 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 374 optimal weight: 0.0030 chunk 155 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 343 optimal weight: 0.2980 chunk 296 optimal weight: 6.9990 chunk 250 optimal weight: 0.0020 chunk 10 optimal weight: 7.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 822 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091315 restraints weight = 51256.536| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.17 r_work: 0.3059 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33905 Z= 0.110 Angle : 0.523 12.072 46198 Z= 0.273 Chirality : 0.042 0.260 5190 Planarity : 0.004 0.058 5630 Dihedral : 16.345 162.577 5346 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 1.25 % Allowed : 12.81 % Favored : 85.93 % 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: 0.50 (0.14), residues: 3854 helix: 1.67 (0.15), residues: 1362 sheet: -0.17 (0.21), residues: 620 loop : -0.45 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 241 TYR 0.015 0.001 TYR H 95 PHE 0.026 0.001 PHE A 219 TRP 0.008 0.001 TRP B 31 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (33873) covalent geometry : angle 0.51912 / 0.27 (46153) hydrogen bonds : bond 0.03168 / 2.09 ( 1428) hydrogen bonds : angle 4.14296 / 3.02 ( 3981) metal coordination : bond 0.00326 / 0.20 ( 32) metal coordination : angle 2.20808 / 1.39 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9828.76 seconds wall clock time: 168 minutes 41.04 seconds (10121.04 seconds total)