Starting phenix.real_space_refine on Sun Aug 9 10:29:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbx_54742/08_2026/9sbx_54742.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbx_54742/08_2026/9sbx_54742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbx_54742/08_2026/9sbx_54742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbx_54742/08_2026/9sbx_54742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbx_54742/08_2026/9sbx_54742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbx_54742/08_2026/9sbx_54742.map" } resolution = 3.53 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= 0.028 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 106.720 70.280 94.935 1.00171.99 S ATOM 479 SG CYS A 70 106.042 66.721 93.766 1.00173.30 S ATOM 532 SG CYS A 77 103.581 69.573 93.003 1.00173.28 S ATOM 762 SG CYS A 107 81.450 76.195 135.260 1.00208.35 S ATOM 786 SG CYS A 110 82.986 72.860 136.038 1.00209.37 S ATOM 1091 SG CYS A 148 79.608 73.855 137.604 1.00218.53 S ATOM 1105 SG CYS A 167 82.893 75.602 138.656 1.00215.58 S ATOM 19603 SG CYS B1163 98.388 57.812 104.958 1.00172.39 S ATOM 19621 SG CYS B1166 96.945 61.204 105.380 1.00178.41 S ATOM 19746 SG CYS B1182 100.728 60.650 104.817 1.00167.72 S ATOM 19765 SG CYS B1185 98.944 59.866 108.215 1.00174.33 S ATOM 20753 SG CYS C 86 93.263 74.887 26.286 1.00209.91 S ATOM 20770 SG CYS C 88 95.098 77.147 28.582 1.00223.87 S ATOM 20803 SG CYS C 92 94.430 78.223 25.011 1.00193.29 S ATOM 20826 SG CYS C 95 91.596 78.161 27.579 1.00185.98 S ATOM 28411 SG CYS I 7 40.194 125.696 127.787 1.00302.21 S ATOM 28436 SG CYS I 10 43.834 124.750 127.589 1.00293.18 S ATOM 28602 SG CYS I 29 41.435 122.532 129.559 1.00309.42 S ATOM 28626 SG CYS I 32 42.398 125.837 130.956 1.00304.47 S ATOM 28953 SG CYS I 75 16.712 116.111 89.873 1.00298.89 S ATOM 28975 SG CYS I 78 16.271 119.622 88.714 1.00309.41 S ATOM 29191 SG CYS I 103 19.708 117.999 88.363 1.00298.91 S ATOM 29211 SG CYS I 106 18.378 118.926 91.803 1.00302.31 S ATOM 29313 SG CYS J 7 64.056 90.649 37.814 1.00138.32 S ATOM 29336 SG CYS J 10 63.646 88.344 34.807 1.00149.52 S ATOM 29616 SG CYS J 45 60.658 89.147 36.867 1.00149.79 S ATOM 29622 SG CYS J 46 62.261 91.598 34.428 1.00152.17 S ATOM 30745 SG CYS L 31 97.468 113.949 53.949 1.00250.79 S ATOM 30765 SG CYS L 34 98.807 115.440 50.757 1.00258.55 S ATOM 30869 SG CYS L 48 101.179 114.612 53.655 1.00257.46 S ATOM 30892 SG CYS L 51 98.848 117.571 53.855 1.00265.40 S Time building chain proxies: 5.53, per 1000 atoms: 0.17 Number of scatterers: 33083 At special positions: 0 Unit cell: (152.329, 154.505, 184.971, 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: 2.93 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 67 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " 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 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " 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 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " 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 46 sheets defined 39.4% alpha, 19.3% beta 41 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 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: 3.595A 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 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.715A 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: 3.824A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.714A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.624A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 665 through 670 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: 4.194A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 845 removed outlier: 4.124A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.644A 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 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 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 996 removed outlier: 3.696A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (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: 3.738A 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 1106 removed outlier: 5.341A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.536A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.695A 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: 3.642A 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: 3.860A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.608A 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 1447 through 1452 removed outlier: 3.553A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1447 through 1452' Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.198A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 4.659A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.588A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.610A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.946A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.717A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.750A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.585A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.858A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.945A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.258A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.849A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.558A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.554A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.526A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.512A 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 135 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.577A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.695A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.722A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.571A 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 104 removed outlier: 3.712A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.599A 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 removed outlier: 3.615A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.735A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.591A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.848A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.736A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.514A pdb=" N LEU A 86 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.605A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.799A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.369A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.565A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.992A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.747A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.421A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.540A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.540A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.796A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.796A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.084A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.959A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.683A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.269A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 793 removed outlier: 6.239A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 793 removed outlier: 6.239A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.110A 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: 6.663A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.799A pdb=" N THR B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 915 " --> pdb=" O THR B 873 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.700A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.836A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.585A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.550A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.450A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.774A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.407A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.702A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.554A pdb=" N ASP I 19 " --> pdb=" O ARG I 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.774A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 21 through 23 1356 hydrogen bonds defined for protein. 3726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 9.44 Time building geometry restraints manager: 3.70 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: 5402 1.31 - 1.43: 8947 1.43 - 1.56: 19036 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 1.180 0.194 1.00e-02 1.00e+04 3.77e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.211 0.159 1.20e-02 6.94e+03 1.75e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.446 -0.109 1.10e-02 8.26e+03 9.84e+01 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.333 0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.452 -0.065 1.00e-02 1.00e+04 4.24e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 46033 4.23 - 8.47: 117 8.47 - 12.70: 0 12.70 - 16.93: 2 16.93 - 21.16: 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 139.87 118.71 21.16 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 122.76 14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.48 -13.76 1.00e+00 1.00e+00 1.89e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.30 8.39 1.00e+00 1.00e+00 7.05e+01 angle pdb=" C GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 116.63 110.12 6.51 1.16e+00 7.43e-01 3.15e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 19784 32.42 - 64.85: 640 64.85 - 97.27: 39 97.27 - 129.69: 1 129.69 - 162.11: 3 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+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 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DC N 38 " pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " pdb=" P DC N 39 " ideal model delta sinusoidal sigma weight residual -140.00 22.11 -162.11 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3562 0.038 - 0.075: 1127 0.075 - 0.113: 401 0.113 - 0.150: 94 0.150 - 0.188: 6 Chirality restraints: 5190 Sorted by residual: 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 -2.44 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CG LEU A 472 " pdb=" CB LEU A 472 " pdb=" CD1 LEU A 472 " pdb=" CD2 LEU A 472 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CB VAL B 482 " pdb=" CA VAL B 482 " pdb=" CG1 VAL B 482 " pdb=" CG2 VAL B 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-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 3.37e-02 1.13e+01 pdb=" C LEU A 710 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 909 " 0.043 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 910 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 910 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 910 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 984 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C LYS A 984 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 984 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 985 " 0.011 2.00e-02 2.50e+03 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 87 2.39 - 3.01: 18960 3.01 - 3.64: 49282 3.64 - 4.27: 75452 4.27 - 4.90: 126815 Nonbonded interactions: 270596 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.757 2.170 nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.910 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.916 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1802 " model vdw 2.037 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.133 2.170 ... (remaining 270591 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 group one per residue 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: 2.190 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.530 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 33905 Z= 0.327 Angle : 0.644 21.163 46198 Z= 0.430 Chirality : 0.043 0.188 5190 Planarity : 0.004 0.066 5630 Dihedral : 14.987 162.114 13127 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3854 helix: 1.59 (0.15), residues: 1299 sheet: -0.32 (0.21), residues: 637 loop : -0.55 (0.15), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1012 TYR 0.029 0.001 TYR B 797 PHE 0.017 0.001 PHE B 37 TRP 0.012 0.001 TRP C 192 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.33 (33873) covalent geometry : angle 0.63812 / 0.43 (46153) hydrogen bonds : bond 0.18929 / 12.69 ( 1420) hydrogen bonds : angle 7.06557 / 4.99 ( 3940) metal coordination : bond 0.00690 / 0.47 ( 32) metal coordination : angle 2.85345 / 1.84 ( 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 615 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.7771 (tp30) cc_final: 0.7489 (tp30) REVERT: A 293 GLU cc_start: 0.8497 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 453 MET cc_start: 0.8770 (mpp) cc_final: 0.8498 (mpp) REVERT: A 487 MET cc_start: 0.9230 (mtp) cc_final: 0.9017 (mtm) REVERT: A 494 SER cc_start: 0.8178 (m) cc_final: 0.7849 (p) REVERT: A 618 GLU cc_start: 0.7976 (pm20) cc_final: 0.7704 (pm20) REVERT: A 636 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 698 GLN cc_start: 0.8279 (tt0) cc_final: 0.7988 (mm110) REVERT: A 708 MET cc_start: 0.6666 (mtt) cc_final: 0.6348 (mtm) REVERT: A 739 ASP cc_start: 0.8498 (m-30) cc_final: 0.8212 (t0) REVERT: A 1109 LYS cc_start: 0.9347 (mtmm) cc_final: 0.9137 (mttm) REVERT: A 1285 MET cc_start: 0.8312 (mmt) cc_final: 0.8076 (mmm) REVERT: A 1382 THR cc_start: 0.9101 (m) cc_final: 0.8640 (p) REVERT: A 1411 GLU cc_start: 0.8618 (tp30) cc_final: 0.7813 (tm-30) REVERT: A 1444 MET cc_start: 0.8238 (mmt) cc_final: 0.8031 (mmt) REVERT: B 289 LEU cc_start: 0.8915 (mt) cc_final: 0.8672 (mm) REVERT: B 308 TRP cc_start: 0.8984 (p-90) cc_final: 0.8615 (p-90) REVERT: B 311 LEU cc_start: 0.8778 (mt) cc_final: 0.8541 (mt) REVERT: B 322 PHE cc_start: 0.7251 (t80) cc_final: 0.7017 (t80) REVERT: B 327 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8205 (ttm170) REVERT: B 398 ARG cc_start: 0.8553 (mpt-90) cc_final: 0.8156 (mtt90) REVERT: B 595 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7607 (ttp-170) REVERT: B 620 ARG cc_start: 0.9195 (ptp-170) cc_final: 0.8791 (mtp-110) REVERT: B 641 GLU cc_start: 0.8499 (tt0) cc_final: 0.8243 (pt0) REVERT: B 662 MET cc_start: 0.8769 (mtm) cc_final: 0.8483 (mtm) REVERT: B 666 TYR cc_start: 0.8545 (t80) cc_final: 0.8285 (m-10) REVERT: B 733 HIS cc_start: 0.5226 (t-90) cc_final: 0.5003 (p-80) REVERT: B 1032 SER cc_start: 0.9191 (m) cc_final: 0.8776 (t) REVERT: B 1072 MET cc_start: 0.9139 (mtp) cc_final: 0.8822 (mtp) REVERT: C 55 THR cc_start: 0.9119 (m) cc_final: 0.8703 (p) REVERT: C 187 LYS cc_start: 0.8816 (mttt) cc_final: 0.8556 (mttm) REVERT: C 207 CYS cc_start: 0.8757 (m) cc_final: 0.8272 (m) REVERT: C 214 ASN cc_start: 0.8822 (m110) cc_final: 0.8393 (m110) REVERT: D 35 LEU cc_start: 0.8778 (mt) cc_final: 0.8346 (tp) REVERT: D 58 VAL cc_start: 0.8660 (t) cc_final: 0.8346 (p) REVERT: D 60 LYS cc_start: 0.7706 (tttt) cc_final: 0.7235 (ptpp) REVERT: D 61 GLU cc_start: 0.8505 (pt0) cc_final: 0.8229 (tp30) REVERT: D 65 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7104 (tt0) REVERT: E 106 GLN cc_start: 0.8230 (mm-40) cc_final: 0.8017 (mp10) REVERT: E 192 ARG cc_start: 0.9136 (ttt180) cc_final: 0.8548 (ttp80) REVERT: E 201 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8807 (mmtt) REVERT: F 72 LYS cc_start: 0.6332 (mmtt) cc_final: 0.6047 (pttp) REVERT: F 76 LYS cc_start: 0.8871 (tptt) cc_final: 0.8663 (tptt) REVERT: G 3 PHE cc_start: 0.6848 (m-80) cc_final: 0.6086 (m-80) REVERT: G 21 ARG cc_start: 0.8838 (mtt180) cc_final: 0.8584 (ttt-90) REVERT: G 32 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8242 (tm-30) REVERT: G 33 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7423 (mt-10) REVERT: G 35 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6171 (mt-10) REVERT: G 151 ILE cc_start: 0.6090 (mt) cc_final: 0.5855 (tp) REVERT: H 7 ASP cc_start: 0.8623 (t0) cc_final: 0.8402 (p0) REVERT: H 22 LYS cc_start: 0.8461 (mttp) cc_final: 0.8230 (mtpp) REVERT: H 52 GLN cc_start: 0.8655 (mt0) cc_final: 0.8444 (mp10) REVERT: H 92 ASP cc_start: 0.8993 (m-30) cc_final: 0.8592 (t0) REVERT: H 128 ASN cc_start: 0.8789 (t0) cc_final: 0.8504 (t0) REVERT: H 137 GLN cc_start: 0.8532 (tt0) cc_final: 0.7467 (tm-30) REVERT: H 139 ASN cc_start: 0.8916 (m-40) cc_final: 0.8535 (m-40) REVERT: I 13 MET cc_start: 0.4350 (ptt) cc_final: 0.4040 (pmm) REVERT: I 70 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7159 (ttm-80) REVERT: J 49 MET cc_start: 0.9253 (tpp) cc_final: 0.8038 (tpp) REVERT: K 17 SER cc_start: 0.9140 (m) cc_final: 0.8809 (p) REVERT: K 26 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8413 (mtmm) REVERT: K 49 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8762 (mm-30) REVERT: K 54 ARG cc_start: 0.8888 (mtm180) cc_final: 0.8617 (mmm-85) REVERT: K 64 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8496 (mt-10) REVERT: K 72 LYS cc_start: 0.8716 (mttt) cc_final: 0.8265 (mtmt) REVERT: K 77 THR cc_start: 0.9013 (p) cc_final: 0.8812 (p) REVERT: L 63 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7204 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.2422 time to fit residues: 228.8796 Evaluate side-chains 403 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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: 6.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN A 363 GLN A 994 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 357 GLN B 443 ASN B 538 ASN D 138 ASN E 8 ASN E 113 GLN G 153 GLN L 66 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.118649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079106 restraints weight = 60635.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.081887 restraints weight = 28381.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083641 restraints weight = 18348.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.084676 restraints weight = 14346.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085128 restraints weight = 12547.394| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33905 Z= 0.194 Angle : 0.641 15.420 46198 Z= 0.335 Chirality : 0.046 0.288 5190 Planarity : 0.005 0.056 5630 Dihedral : 16.958 159.068 5346 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 1.02 % Allowed : 6.12 % Favored : 92.87 % 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: 1.36 (0.14), residues: 1343 sheet: -0.33 (0.21), residues: 629 loop : -0.59 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1012 TYR 0.019 0.001 TYR B 797 PHE 0.020 0.002 PHE A 219 TRP 0.010 0.001 TRP C 201 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (33873) covalent geometry : angle 0.62314 / 0.33 (46153) hydrogen bonds : bond 0.04981 / 3.29 ( 1420) hydrogen bonds : angle 5.30487 / 3.76 ( 3940) metal coordination : bond 0.00891 / 0.59 ( 32) metal coordination : angle 4.91170 / 3.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 414 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8779 (tpp) cc_final: 0.8491 (tpp) REVERT: A 293 GLU cc_start: 0.8297 (tt0) cc_final: 0.7924 (tm-30) REVERT: A 618 GLU cc_start: 0.7759 (pm20) cc_final: 0.7510 (pm20) REVERT: A 833 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7678 (tt0) REVERT: A 1382 THR cc_start: 0.9473 (m) cc_final: 0.9149 (p) REVERT: A 1411 GLU cc_start: 0.8426 (tp30) cc_final: 0.7665 (tm-30) REVERT: B 289 LEU cc_start: 0.9260 (mt) cc_final: 0.8956 (mm) REVERT: B 470 LYS cc_start: 0.8786 (mppt) cc_final: 0.8495 (mttt) REVERT: B 1032 SER cc_start: 0.9103 (m) cc_final: 0.8880 (t) REVERT: B 1072 MET cc_start: 0.8832 (mtp) cc_final: 0.8565 (mtp) REVERT: C 55 THR cc_start: 0.9311 (m) cc_final: 0.9100 (p) REVERT: C 187 LYS cc_start: 0.9359 (mttt) cc_final: 0.9115 (mttm) REVERT: D 35 LEU cc_start: 0.8575 (mt) cc_final: 0.8161 (tp) REVERT: D 60 LYS cc_start: 0.7812 (tttt) cc_final: 0.7514 (tptm) REVERT: D 65 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7319 (tt0) REVERT: F 72 LYS cc_start: 0.7256 (mmtt) cc_final: 0.7021 (pttp) REVERT: G 2 PHE cc_start: 0.7181 (m-80) cc_final: 0.6830 (m-80) REVERT: G 3 PHE cc_start: 0.7588 (m-80) cc_final: 0.6757 (m-80) REVERT: G 33 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7583 (mt-10) REVERT: G 69 GLU cc_start: 0.8235 (tt0) cc_final: 0.7887 (tt0) REVERT: G 82 PHE cc_start: 0.7761 (m-80) cc_final: 0.7109 (m-80) REVERT: H 136 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8513 (mmmt) REVERT: I 1 MET cc_start: 0.7126 (mpp) cc_final: 0.5585 (mtt) REVERT: J 49 MET cc_start: 0.8788 (tpp) cc_final: 0.8527 (tpp) REVERT: K 64 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8154 (mt-10) outliers start: 35 outliers final: 17 residues processed: 436 average time/residue: 0.2200 time to fit residues: 153.2762 Evaluate side-chains 359 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 342 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 304 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN D 138 ASN E 8 ASN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.121858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081620 restraints weight = 59914.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084563 restraints weight = 28039.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086413 restraints weight = 18088.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087484 restraints weight = 14137.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088090 restraints weight = 12384.682| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1873 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= 0.219 Angle : 0.618 14.489 46198 Z= 0.323 Chirality : 0.045 0.280 5190 Planarity : 0.004 0.052 5630 Dihedral : 16.834 158.442 5346 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 1.34 % Allowed : 8.04 % Favored : 90.62 % 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 (0.14), residues: 3854 helix: 1.33 (0.14), residues: 1343 sheet: -0.41 (0.21), residues: 632 loop : -0.64 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 66 TYR 0.018 0.001 TYR A 836 PHE 0.020 0.002 PHE A 219 TRP 0.010 0.001 TRP C 192 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (33873) covalent geometry : angle 0.60292 / 0.32 (46153) hydrogen bonds : bond 0.04403 / 2.93 ( 1420) hydrogen bonds : angle 4.98298 / 3.54 ( 3940) metal coordination : bond 0.00917 / 0.62 ( 32) metal coordination : angle 4.44772 / 2.89 ( 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 416 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 370 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8784 (tpp) cc_final: 0.8545 (tpp) REVERT: A 293 GLU cc_start: 0.8326 (tt0) cc_final: 0.7966 (tm-30) REVERT: A 618 GLU cc_start: 0.7785 (pm20) cc_final: 0.7531 (pm20) REVERT: A 1382 THR cc_start: 0.9511 (m) cc_final: 0.9171 (p) REVERT: A 1411 GLU cc_start: 0.8409 (tp30) cc_final: 0.7608 (tm-30) REVERT: B 470 LYS cc_start: 0.8784 (mppt) cc_final: 0.8485 (mtpt) REVERT: B 705 MET cc_start: 0.9222 (tpp) cc_final: 0.8943 (tpp) REVERT: B 1032 SER cc_start: 0.9092 (m) cc_final: 0.8881 (t) REVERT: B 1072 MET cc_start: 0.8813 (mtp) cc_final: 0.8501 (mtp) REVERT: C 187 LYS cc_start: 0.9351 (mttt) cc_final: 0.9110 (mttm) REVERT: C 209 TYR cc_start: 0.9172 (m-80) cc_final: 0.8919 (m-80) REVERT: D 35 LEU cc_start: 0.8590 (mt) cc_final: 0.8162 (tp) REVERT: D 60 LYS cc_start: 0.7696 (tttt) cc_final: 0.7444 (tptm) REVERT: D 65 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7312 (tt0) REVERT: F 72 LYS cc_start: 0.7242 (mmtt) cc_final: 0.7002 (pttp) REVERT: F 81 THR cc_start: 0.9370 (m) cc_final: 0.9125 (p) REVERT: G 3 PHE cc_start: 0.7448 (m-80) cc_final: 0.6839 (m-80) REVERT: G 21 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7625 (mtp85) REVERT: G 69 GLU cc_start: 0.8216 (tt0) cc_final: 0.7787 (tt0) REVERT: G 79 PHE cc_start: 0.6414 (t80) cc_final: 0.6213 (t80) REVERT: G 82 PHE cc_start: 0.7744 (m-80) cc_final: 0.6968 (m-80) REVERT: G 153 GLN cc_start: 0.6609 (mm110) cc_final: 0.6156 (mp10) REVERT: H 129 TYR cc_start: 0.8026 (p90) cc_final: 0.7761 (p90) REVERT: I 1 MET cc_start: 0.7100 (mpp) cc_final: 0.5591 (mtt) REVERT: I 92 ARG cc_start: 0.5751 (mtm110) cc_final: 0.4968 (mtm180) REVERT: K 64 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8107 (mt-10) outliers start: 46 outliers final: 27 residues processed: 402 average time/residue: 0.2356 time to fit residues: 149.8162 Evaluate side-chains 371 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 344 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU 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: 3.9990 chunk 138 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 286 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN E 8 ASN I 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081009 restraints weight = 60117.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083839 restraints weight = 28040.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085641 restraints weight = 18064.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086710 restraints weight = 14076.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087302 restraints weight = 12290.856| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33905 Z= 0.185 Angle : 0.580 10.046 46198 Z= 0.304 Chirality : 0.044 0.251 5190 Planarity : 0.004 0.088 5630 Dihedral : 16.779 157.898 5346 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 1.57 % Allowed : 8.97 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3854 helix: 1.40 (0.14), residues: 1342 sheet: -0.46 (0.21), residues: 625 loop : -0.66 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 70 TYR 0.030 0.001 TYR A1153 PHE 0.025 0.001 PHE A 444 TRP 0.010 0.001 TRP C 192 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (33873) covalent geometry : angle 0.56878 / 0.30 (46153) hydrogen bonds : bond 0.03918 / 2.62 ( 1420) hydrogen bonds : angle 4.74043 / 3.37 ( 3940) metal coordination : bond 0.00851 / 0.57 ( 32) metal coordination : angle 3.73550 / 2.43 ( 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 421 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 367 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8401 (mmm) cc_final: 0.8151 (mmp) REVERT: A 293 GLU cc_start: 0.8337 (tt0) cc_final: 0.8081 (tm-30) REVERT: A 618 GLU cc_start: 0.7738 (pm20) cc_final: 0.7520 (pm20) REVERT: A 833 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7714 (tt0) REVERT: A 1373 ASP cc_start: 0.8191 (m-30) cc_final: 0.7918 (m-30) REVERT: A 1382 THR cc_start: 0.9467 (m) cc_final: 0.9081 (p) REVERT: A 1411 GLU cc_start: 0.8381 (tp30) cc_final: 0.7574 (tm-30) REVERT: B 705 MET cc_start: 0.9229 (tpp) cc_final: 0.8888 (tpp) REVERT: B 1032 SER cc_start: 0.9097 (m) cc_final: 0.8877 (t) REVERT: B 1072 MET cc_start: 0.8851 (mtp) cc_final: 0.8587 (mtp) REVERT: B 1085 ILE cc_start: 0.9657 (mm) cc_final: 0.9455 (mm) REVERT: C 187 LYS cc_start: 0.9339 (mttt) cc_final: 0.9100 (mttm) REVERT: C 209 TYR cc_start: 0.9171 (m-80) cc_final: 0.8881 (m-80) REVERT: D 35 LEU cc_start: 0.8583 (mt) cc_final: 0.8139 (tp) REVERT: D 60 LYS cc_start: 0.7714 (tttt) cc_final: 0.7450 (tptm) REVERT: D 65 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7252 (tt0) REVERT: F 72 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6942 (pttp) REVERT: F 81 THR cc_start: 0.9355 (m) cc_final: 0.9104 (p) REVERT: G 3 PHE cc_start: 0.7515 (m-80) cc_final: 0.7111 (m-80) REVERT: G 69 GLU cc_start: 0.8139 (tt0) cc_final: 0.7692 (tt0) REVERT: G 153 GLN cc_start: 0.6694 (mm110) cc_final: 0.6282 (mp10) REVERT: I 1 MET cc_start: 0.7283 (mpp) cc_final: 0.5843 (mtt) REVERT: I 70 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7574 (tpp-160) REVERT: I 92 ARG cc_start: 0.5805 (mtm110) cc_final: 0.4932 (mtm180) REVERT: K 64 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8097 (mt-10) outliers start: 54 outliers final: 34 residues processed: 403 average time/residue: 0.2274 time to fit residues: 145.8501 Evaluate side-chains 380 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 346 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 0.0020 chunk 140 optimal weight: 3.9990 chunk 136 optimal weight: 0.0670 chunk 106 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 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 = 0.3767 r_free = 0.3767 target = 0.122368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.083014 restraints weight = 59954.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085971 restraints weight = 27702.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087808 restraints weight = 17701.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088892 restraints weight = 13756.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089520 restraints weight = 11989.663| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33905 Z= 0.110 Angle : 0.535 9.989 46198 Z= 0.282 Chirality : 0.043 0.248 5190 Planarity : 0.004 0.043 5630 Dihedral : 16.660 157.858 5346 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 1.08 % Allowed : 10.02 % Favored : 88.91 % 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: 0.24 (0.14), residues: 3854 helix: 1.48 (0.14), residues: 1355 sheet: -0.33 (0.21), residues: 617 loop : -0.61 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.013 0.001 TYR A1153 PHE 0.022 0.001 PHE A 444 TRP 0.009 0.001 TRP C 192 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (33873) covalent geometry : angle 0.52572 / 0.28 (46153) hydrogen bonds : bond 0.03493 / 2.33 ( 1420) hydrogen bonds : angle 4.51443 / 3.21 ( 3940) metal coordination : bond 0.00453 / 0.30 ( 32) metal coordination : angle 3.16945 / 2.10 ( 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 423 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 386 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8296 (tt0) cc_final: 0.8078 (tm-30) REVERT: A 444 PHE cc_start: 0.9182 (t80) cc_final: 0.8958 (t80) REVERT: A 800 VAL cc_start: 0.9345 (t) cc_final: 0.9034 (m) REVERT: A 833 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7557 (tt0) REVERT: A 1382 THR cc_start: 0.9431 (m) cc_final: 0.9082 (p) REVERT: A 1411 GLU cc_start: 0.8333 (tp30) cc_final: 0.7507 (tm-30) REVERT: A 1444 MET cc_start: 0.8460 (mmt) cc_final: 0.7870 (mmm) REVERT: B 705 MET cc_start: 0.9180 (tpp) cc_final: 0.8889 (tpp) REVERT: B 1032 SER cc_start: 0.9022 (m) cc_final: 0.8807 (t) REVERT: C 55 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9113 (p) REVERT: C 187 LYS cc_start: 0.9346 (mttt) cc_final: 0.9129 (mttm) REVERT: C 209 TYR cc_start: 0.9147 (m-80) cc_final: 0.8803 (m-80) REVERT: D 35 LEU cc_start: 0.8589 (mt) cc_final: 0.8145 (tp) REVERT: D 60 LYS cc_start: 0.7771 (tttt) cc_final: 0.7486 (tptm) REVERT: D 65 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7355 (tt0) REVERT: G 3 PHE cc_start: 0.7465 (m-80) cc_final: 0.7114 (m-80) REVERT: G 69 GLU cc_start: 0.8074 (tt0) cc_final: 0.7658 (tt0) REVERT: G 153 GLN cc_start: 0.6670 (mm110) cc_final: 0.6228 (mp10) REVERT: H 45 GLU cc_start: 0.8348 (tt0) cc_final: 0.7990 (tt0) REVERT: I 1 MET cc_start: 0.7190 (mpp) cc_final: 0.5840 (mtt) REVERT: I 92 ARG cc_start: 0.5811 (mtm110) cc_final: 0.4946 (mtm180) REVERT: K 64 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8062 (mt-10) outliers start: 37 outliers final: 24 residues processed: 413 average time/residue: 0.2251 time to fit residues: 148.9858 Evaluate side-chains 374 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 349 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 0.0040 chunk 89 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN D 138 ASN ** H 128 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 = 0.3730 r_free = 0.3730 target = 0.119740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080660 restraints weight = 60222.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083491 restraints weight = 28048.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085265 restraints weight = 18045.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086312 restraints weight = 14067.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086886 restraints weight = 12285.647| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33905 Z= 0.209 Angle : 0.575 10.360 46198 Z= 0.300 Chirality : 0.044 0.249 5190 Planarity : 0.004 0.045 5630 Dihedral : 16.690 158.809 5346 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 1.81 % Allowed : 10.57 % Favored : 87.62 % 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: 0.22 (0.14), residues: 3854 helix: 1.46 (0.14), residues: 1351 sheet: -0.36 (0.21), residues: 617 loop : -0.60 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.013 0.001 TYR A 836 PHE 0.022 0.002 PHE J 8 TRP 0.047 0.001 TRP B 561 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (33873) covalent geometry : angle 0.56580 / 0.30 (46153) hydrogen bonds : bond 0.03773 / 2.52 ( 1420) hydrogen bonds : angle 4.55013 / 3.23 ( 3940) metal coordination : bond 0.00815 / 0.55 ( 32) metal coordination : angle 3.41559 / 2.25 ( 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 402 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 340 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8428 (m-30) cc_final: 0.8133 (m-30) REVERT: A 293 GLU cc_start: 0.8342 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 444 PHE cc_start: 0.9197 (t80) cc_final: 0.8906 (t80) REVERT: A 833 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7599 (tt0) REVERT: A 1382 THR cc_start: 0.9468 (m) cc_final: 0.9082 (p) REVERT: A 1411 GLU cc_start: 0.8400 (tp30) cc_final: 0.7563 (tm-30) REVERT: A 1444 MET cc_start: 0.8495 (mmt) cc_final: 0.7914 (mmm) REVERT: B 705 MET cc_start: 0.9196 (tpp) cc_final: 0.8856 (tpp) REVERT: B 1032 SER cc_start: 0.9116 (m) cc_final: 0.8901 (t) REVERT: C 55 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9155 (p) REVERT: C 187 LYS cc_start: 0.9371 (mttt) cc_final: 0.9151 (mttm) REVERT: C 209 TYR cc_start: 0.9194 (m-80) cc_final: 0.8902 (m-80) REVERT: D 35 LEU cc_start: 0.8585 (mt) cc_final: 0.8142 (tp) REVERT: D 60 LYS cc_start: 0.7761 (tttt) cc_final: 0.7487 (tptm) REVERT: D 65 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7335 (tt0) REVERT: F 81 THR cc_start: 0.9348 (m) cc_final: 0.9057 (p) REVERT: G 3 PHE cc_start: 0.7501 (m-80) cc_final: 0.7177 (m-80) REVERT: G 69 GLU cc_start: 0.8105 (tt0) cc_final: 0.7703 (tt0) REVERT: G 153 GLN cc_start: 0.6665 (mm110) cc_final: 0.6259 (mp10) REVERT: H 22 LYS cc_start: 0.9078 (mttp) cc_final: 0.8833 (mtpp) REVERT: H 45 GLU cc_start: 0.8346 (tt0) cc_final: 0.7844 (tt0) REVERT: H 92 ASP cc_start: 0.8190 (t0) cc_final: 0.7987 (t0) REVERT: I 1 MET cc_start: 0.7273 (mpp) cc_final: 0.6068 (mtt) REVERT: I 13 MET cc_start: 0.4474 (pmm) cc_final: 0.4269 (pmm) REVERT: I 70 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7633 (ttm-80) REVERT: I 92 ARG cc_start: 0.5770 (mtm110) cc_final: 0.4969 (mtm180) REVERT: K 64 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8075 (mt-10) outliers start: 62 outliers final: 43 residues processed: 380 average time/residue: 0.2319 time to fit residues: 140.6713 Evaluate side-chains 369 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 325 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 354 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082170 restraints weight = 60215.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085047 restraints weight = 27821.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086850 restraints weight = 17809.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.087938 restraints weight = 13858.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088528 restraints weight = 12061.807| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33905 Z= 0.135 Angle : 0.544 10.184 46198 Z= 0.286 Chirality : 0.043 0.249 5190 Planarity : 0.004 0.049 5630 Dihedral : 16.643 158.766 5346 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 1.46 % Allowed : 11.42 % Favored : 87.13 % 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: 0.27 (0.14), residues: 3854 helix: 1.52 (0.14), residues: 1351 sheet: -0.35 (0.21), residues: 607 loop : -0.58 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.014 0.001 TYR H 129 PHE 0.021 0.001 PHE A 219 TRP 0.028 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (33873) covalent geometry : angle 0.53504 / 0.29 (46153) hydrogen bonds : bond 0.03511 / 2.34 ( 1420) hydrogen bonds : angle 4.45133 / 3.16 ( 3940) metal coordination : bond 0.00501 / 0.33 ( 32) metal coordination : angle 3.25891 / 2.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 355 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8412 (m-30) cc_final: 0.8173 (m-30) REVERT: A 293 GLU cc_start: 0.8305 (tt0) cc_final: 0.8099 (tm-30) REVERT: A 833 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7594 (tt0) REVERT: A 1382 THR cc_start: 0.9448 (m) cc_final: 0.9106 (p) REVERT: A 1411 GLU cc_start: 0.8345 (tp30) cc_final: 0.7437 (tm-30) REVERT: A 1444 MET cc_start: 0.8475 (mmt) cc_final: 0.7975 (mmm) REVERT: B 628 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9242 (p) REVERT: B 705 MET cc_start: 0.9168 (tpp) cc_final: 0.8863 (tpp) REVERT: B 1032 SER cc_start: 0.9037 (m) cc_final: 0.8827 (t) REVERT: C 55 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9142 (p) REVERT: C 187 LYS cc_start: 0.9353 (mttt) cc_final: 0.9151 (mttm) REVERT: C 209 TYR cc_start: 0.9152 (m-80) cc_final: 0.8803 (m-80) REVERT: D 35 LEU cc_start: 0.8513 (mt) cc_final: 0.8053 (tp) REVERT: D 60 LYS cc_start: 0.7775 (tttt) cc_final: 0.7517 (tptm) REVERT: D 65 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7333 (tt0) REVERT: F 81 THR cc_start: 0.9359 (m) cc_final: 0.9088 (p) REVERT: G 3 PHE cc_start: 0.7553 (m-80) cc_final: 0.7243 (m-80) REVERT: G 24 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7243 (tm-30) REVERT: G 69 GLU cc_start: 0.8096 (tt0) cc_final: 0.7736 (tt0) REVERT: G 153 GLN cc_start: 0.6669 (mm110) cc_final: 0.6245 (mp10) REVERT: H 41 ASP cc_start: 0.8589 (m-30) cc_final: 0.8356 (m-30) REVERT: H 45 GLU cc_start: 0.8344 (tt0) cc_final: 0.7814 (tt0) REVERT: H 110 ASP cc_start: 0.7919 (p0) cc_final: 0.7576 (p0) REVERT: I 1 MET cc_start: 0.7347 (mpp) cc_final: 0.6119 (mtt) REVERT: I 70 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7650 (ttm-80) REVERT: I 92 ARG cc_start: 0.5794 (mtm110) cc_final: 0.5001 (mtm180) REVERT: K 64 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8054 (mt-10) outliers start: 50 outliers final: 38 residues processed: 391 average time/residue: 0.2370 time to fit residues: 147.5106 Evaluate side-chains 384 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 363 optimal weight: 6.9990 chunk 243 optimal weight: 0.0270 chunk 331 optimal weight: 2.9990 chunk 139 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 overall best weight: 1.0052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 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 = 0.3759 r_free = 0.3759 target = 0.122025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082695 restraints weight = 60222.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085616 restraints weight = 27874.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087440 restraints weight = 17819.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088528 restraints weight = 13849.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088999 restraints weight = 12067.749| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33905 Z= 0.121 Angle : 0.531 9.301 46198 Z= 0.279 Chirality : 0.042 0.249 5190 Planarity : 0.004 0.048 5630 Dihedral : 16.590 159.230 5346 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 1.34 % Allowed : 11.88 % Favored : 86.78 % 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: 1.54 (0.15), residues: 1357 sheet: -0.32 (0.21), residues: 605 loop : -0.58 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 66 TYR 0.013 0.001 TYR E 187 PHE 0.021 0.001 PHE J 8 TRP 0.022 0.001 TRP B 561 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33873) covalent geometry : angle 0.52236 / 0.28 (46153) hydrogen bonds : bond 0.03365 / 2.24 ( 1420) hydrogen bonds : angle 4.35261 / 3.08 ( 3940) metal coordination : bond 0.00464 / 0.31 ( 32) metal coordination : angle 3.09371 / 2.05 ( 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 400 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8437 (m-30) cc_final: 0.8126 (m-30) REVERT: A 293 GLU cc_start: 0.8278 (tt0) cc_final: 0.8074 (tm-30) REVERT: A 833 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7627 (tt0) REVERT: A 1375 MET cc_start: 0.9109 (mtp) cc_final: 0.8847 (mtp) REVERT: A 1382 THR cc_start: 0.9457 (m) cc_final: 0.9117 (p) REVERT: A 1411 GLU cc_start: 0.8356 (tp30) cc_final: 0.7493 (tm-30) REVERT: A 1444 MET cc_start: 0.8448 (mmt) cc_final: 0.8017 (mmm) REVERT: B 597 MET cc_start: 0.8702 (tpt) cc_final: 0.8376 (tpp) REVERT: B 628 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9250 (p) REVERT: B 705 MET cc_start: 0.9161 (tpp) cc_final: 0.8858 (tpp) REVERT: B 1032 SER cc_start: 0.9045 (m) cc_final: 0.8828 (t) REVERT: C 55 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9137 (p) REVERT: C 209 TYR cc_start: 0.9149 (m-80) cc_final: 0.8794 (m-80) REVERT: D 35 LEU cc_start: 0.8540 (mt) cc_final: 0.8054 (tp) REVERT: D 60 LYS cc_start: 0.7800 (tttt) cc_final: 0.7537 (tptm) REVERT: D 65 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7321 (tt0) REVERT: F 81 THR cc_start: 0.9364 (m) cc_final: 0.9110 (p) REVERT: G 3 PHE cc_start: 0.7525 (m-80) cc_final: 0.7205 (m-80) REVERT: G 24 GLN cc_start: 0.7263 (tm-30) cc_final: 0.7054 (tm-30) REVERT: G 69 GLU cc_start: 0.8090 (tt0) cc_final: 0.7718 (tt0) REVERT: G 153 GLN cc_start: 0.6642 (mm110) cc_final: 0.6235 (mp10) REVERT: H 110 ASP cc_start: 0.7999 (p0) cc_final: 0.7699 (p0) REVERT: I 1 MET cc_start: 0.7301 (mpp) cc_final: 0.6082 (mtt) REVERT: I 92 ARG cc_start: 0.5817 (mtm110) cc_final: 0.4969 (mtm180) REVERT: J 23 ASN cc_start: 0.8658 (m-40) cc_final: 0.8423 (m-40) REVERT: K 64 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8044 (mt-10) outliers start: 46 outliers final: 41 residues processed: 387 average time/residue: 0.2241 time to fit residues: 138.9606 Evaluate side-chains 381 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 338 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 4.9990 chunk 377 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN A 363 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN B 215 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.121005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082020 restraints weight = 59873.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084927 restraints weight = 27634.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086759 restraints weight = 17647.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087814 restraints weight = 13726.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088409 restraints weight = 11982.935| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 33905 Z= 0.298 Angle : 0.654 14.276 46198 Z= 0.338 Chirality : 0.046 0.248 5190 Planarity : 0.004 0.060 5630 Dihedral : 16.712 160.333 5346 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 1.51 % Allowed : 11.97 % Favored : 86.52 % 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: 0.09 (0.14), residues: 3854 helix: 1.37 (0.14), residues: 1345 sheet: -0.40 (0.20), residues: 634 loop : -0.70 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 591 TYR 0.025 0.002 TYR H 141 PHE 0.023 0.002 PHE G 2 TRP 0.014 0.001 TRP B 561 HIS 0.011 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.30 (33873) covalent geometry : angle 0.64173 / 0.34 (46153) hydrogen bonds : bond 0.04107 / 2.75 ( 1420) hydrogen bonds : angle 4.61525 / 3.28 ( 3940) metal coordination : bond 0.01216 / 0.82 ( 32) metal coordination : angle 4.05001 / 2.60 ( 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 390 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8409 (m-30) cc_final: 0.8159 (m-30) REVERT: A 293 GLU cc_start: 0.8334 (tt0) cc_final: 0.8119 (tm-30) REVERT: A 1382 THR cc_start: 0.9513 (m) cc_final: 0.9130 (p) REVERT: A 1411 GLU cc_start: 0.8405 (tp30) cc_final: 0.7610 (tm-30) REVERT: A 1444 MET cc_start: 0.8486 (mmt) cc_final: 0.8045 (mmm) REVERT: B 628 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9268 (p) REVERT: B 1032 SER cc_start: 0.9121 (m) cc_final: 0.8913 (t) REVERT: C 55 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9187 (p) REVERT: C 209 TYR cc_start: 0.9199 (m-80) cc_final: 0.8905 (m-80) REVERT: D 35 LEU cc_start: 0.8564 (mt) cc_final: 0.8118 (tp) REVERT: D 60 LYS cc_start: 0.7811 (tttt) cc_final: 0.7530 (tptm) REVERT: D 65 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7289 (tt0) REVERT: D 67 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7503 (mtp85) REVERT: F 81 THR cc_start: 0.9350 (m) cc_final: 0.9078 (p) REVERT: G 3 PHE cc_start: 0.7511 (m-80) cc_final: 0.7202 (m-80) REVERT: G 24 GLN cc_start: 0.7373 (tm-30) cc_final: 0.7063 (tm-30) REVERT: G 69 GLU cc_start: 0.8170 (tt0) cc_final: 0.7822 (tt0) REVERT: G 153 GLN cc_start: 0.6729 (mm110) cc_final: 0.6281 (mp10) REVERT: H 110 ASP cc_start: 0.7963 (p0) cc_final: 0.7647 (p0) REVERT: I 70 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7813 (ttm-80) REVERT: I 92 ARG cc_start: 0.5743 (mtm110) cc_final: 0.4978 (mtm180) REVERT: K 64 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8076 (mt-10) outliers start: 52 outliers final: 36 residues processed: 374 average time/residue: 0.2238 time to fit residues: 134.1894 Evaluate side-chains 362 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 176 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 314 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 321 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN ** D 138 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 = 0.3809 r_free = 0.3809 target = 0.124865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085393 restraints weight = 59722.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088448 restraints weight = 27262.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090359 restraints weight = 17302.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091493 restraints weight = 13411.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092080 restraints weight = 11669.332| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33905 Z= 0.115 Angle : 0.549 11.185 46198 Z= 0.289 Chirality : 0.042 0.246 5190 Planarity : 0.004 0.060 5630 Dihedral : 16.597 159.637 5346 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.16 % Allowed : 12.55 % Favored : 86.28 % 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: 0.23 (0.14), residues: 3854 helix: 1.50 (0.14), residues: 1356 sheet: -0.40 (0.21), residues: 612 loop : -0.62 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 591 TYR 0.021 0.001 TYR G 44 PHE 0.022 0.001 PHE J 8 TRP 0.020 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (33873) covalent geometry : angle 0.53922 / 0.29 (46153) hydrogen bonds : bond 0.03462 / 2.30 ( 1420) hydrogen bonds : angle 4.38379 / 3.10 ( 3940) metal coordination : bond 0.00446 / 0.30 ( 32) metal coordination : angle 3.27544 / 2.14 ( 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 379 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8393 (m-30) cc_final: 0.8103 (m-30) REVERT: A 833 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7621 (tt0) REVERT: A 1284 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7929 (mtm) REVERT: A 1382 THR cc_start: 0.9467 (m) cc_final: 0.9095 (p) REVERT: A 1411 GLU cc_start: 0.8329 (tp30) cc_final: 0.7546 (tm-30) REVERT: A 1444 MET cc_start: 0.8425 (mmt) cc_final: 0.8002 (mmm) REVERT: B 628 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9263 (p) REVERT: B 705 MET cc_start: 0.9119 (tpp) cc_final: 0.8857 (tpp) REVERT: C 55 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9161 (p) REVERT: C 209 TYR cc_start: 0.9115 (m-80) cc_final: 0.8760 (m-80) REVERT: D 35 LEU cc_start: 0.8571 (mt) cc_final: 0.8108 (tp) REVERT: D 60 LYS cc_start: 0.7780 (tttt) cc_final: 0.7534 (tptm) REVERT: D 65 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7321 (tt0) REVERT: D 67 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7458 (mtp85) REVERT: F 81 THR cc_start: 0.9341 (m) cc_final: 0.9102 (p) REVERT: G 3 PHE cc_start: 0.7637 (m-80) cc_final: 0.7351 (m-80) REVERT: G 69 GLU cc_start: 0.8125 (tt0) cc_final: 0.7774 (tt0) REVERT: G 106 MET cc_start: 0.6535 (mpp) cc_final: 0.6222 (mpp) REVERT: G 153 GLN cc_start: 0.6691 (mm110) cc_final: 0.6266 (mp10) REVERT: H 41 ASP cc_start: 0.8550 (m-30) cc_final: 0.8335 (m-30) REVERT: I 1 MET cc_start: 0.7090 (mpp) cc_final: 0.5997 (mtt) REVERT: I 92 ARG cc_start: 0.5862 (mtm110) cc_final: 0.5035 (mtm180) REVERT: J 23 ASN cc_start: 0.8631 (m-40) cc_final: 0.8403 (m-40) REVERT: K 64 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8040 (mt-10) outliers start: 40 outliers final: 32 residues processed: 370 average time/residue: 0.2137 time to fit residues: 127.6701 Evaluate side-chains 360 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 354 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 374 optimal weight: 0.0670 chunk 155 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS C 203 GLN ** D 138 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 = 0.3822 r_free = 0.3822 target = 0.125764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086490 restraints weight = 59477.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089558 restraints weight = 27143.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091485 restraints weight = 17212.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092605 restraints weight = 13329.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093162 restraints weight = 11596.230| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33905 Z= 0.113 Angle : 0.534 10.856 46198 Z= 0.281 Chirality : 0.042 0.249 5190 Planarity : 0.004 0.059 5630 Dihedral : 16.506 160.534 5346 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.00 % Rotamer: Outliers : 1.14 % Allowed : 12.96 % Favored : 85.91 % 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: 0.32 (0.14), residues: 3854 helix: 1.58 (0.14), residues: 1354 sheet: -0.31 (0.21), residues: 604 loop : -0.57 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 21 TYR 0.015 0.001 TYR E 187 PHE 0.024 0.001 PHE G 2 TRP 0.020 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (33873) covalent geometry : angle 0.52571 / 0.28 (46153) hydrogen bonds : bond 0.03280 / 2.18 ( 1420) hydrogen bonds : angle 4.28141 / 3.03 ( 3940) metal coordination : bond 0.00383 / 0.25 ( 32) metal coordination : angle 3.10950 / 2.04 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.00 seconds wall clock time: 112 minutes 21.16 seconds (6741.16 seconds total)