Starting phenix.real_space_refine on Tue Nov 19 08:38:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fd2_50325/11_2024/9fd2_50325.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fd2_50325/11_2024/9fd2_50325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fd2_50325/11_2024/9fd2_50325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fd2_50325/11_2024/9fd2_50325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fd2_50325/11_2024/9fd2_50325.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fd2_50325/11_2024/9fd2_50325.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.029 sd= 1.373 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 10 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 295 5.16 5 C 32497 2.51 5 N 9113 2.21 5 O 9929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51949 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11161 Classifications: {'peptide': 1409} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1339} Chain breaks: 4 Chain: "B" Number of atoms: 9048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1130, 9048 Classifications: {'peptide': 1130} Link IDs: {'PTRANS': 53, 'TRANS': 1076} Chain breaks: 3 Chain: "C" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "f" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "N" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 831 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "M" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1091 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "a" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2951 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 12, 'TRANS': 364} Chain breaks: 2 Chain: "b" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6405 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 787} Chain breaks: 3 Chain: "c" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 302 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain breaks: 1 Chain: "g" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1721 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "e" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4820 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 21, 'TRANS': 568} Chain breaks: 7 Chain: "d" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2040 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 233} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" 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 464 SG CYS A 71 87.568 124.711 103.478 1.00 86.93 S ATOM 486 SG CYS A 74 90.507 123.960 101.078 1.00 85.00 S ATOM 533 SG CYS A 81 86.953 123.152 100.005 1.00 84.53 S ATOM 768 SG CYS A 111 91.009 85.430 128.656 1.00115.03 S ATOM 796 SG CYS A 114 94.722 85.705 129.059 1.00117.26 S ATOM 1109 SG CYS A 154 93.106 82.269 128.841 1.00119.29 S ATOM 1132 SG CYS A 184 92.482 84.432 131.947 1.00117.22 S ATOM 19779 SG CYS B1119 101.212 112.284 103.984 1.00 81.33 S ATOM 19801 SG CYS B1122 98.070 110.386 104.857 1.00 80.71 S ATOM 19916 SG CYS B1137 98.618 113.792 106.337 1.00 88.98 S ATOM 19937 SG CYS B1140 100.810 110.873 107.490 1.00 90.33 S ATOM 20903 SG CYS C 88 60.188 142.805 42.522 1.00 76.08 S ATOM 20916 SG CYS C 90 59.291 144.736 45.594 1.00 79.19 S ATOM 20951 SG CYS C 94 56.902 144.570 43.000 1.00 71.51 S ATOM 20973 SG CYS C 97 57.318 141.342 44.760 1.00 70.13 S ATOM 28331 SG CYS I 17 30.302 54.003 124.480 1.00 80.11 S ATOM 28355 SG CYS I 20 31.441 57.496 125.345 1.00 81.70 S ATOM 28516 SG CYS I 39 34.124 54.930 124.564 1.00 81.27 S ATOM 28541 SG CYS I 42 31.957 54.516 127.684 1.00 81.12 S ATOM 28893 SG CYS I 86 18.923 51.567 81.947 1.00 99.21 S ATOM 28917 SG CYS I 89 15.321 52.664 81.527 1.00 99.28 S ATOM 29121 SG CYS I 114 18.112 55.278 81.620 1.00 92.37 S ATOM 29156 SG CYS I 119 17.114 53.405 84.762 1.00 97.90 S ATOM 29266 SG CYS J 7 42.743 113.225 46.728 1.00 54.83 S ATOM 29290 SG CYS J 10 43.452 114.031 43.018 1.00 56.51 S ATOM 29554 SG CYS J 44 42.463 110.498 44.234 1.00 56.78 S ATOM 29560 SG CYS J 45 39.993 113.420 44.054 1.00 56.41 S ATOM 30722 SG CYS L 19 33.199 136.557 82.838 1.00 77.76 S ATOM 30741 SG CYS L 22 30.239 138.826 82.175 1.00 79.16 S ATOM 30858 SG CYS L 36 32.777 139.834 84.777 1.00 79.35 S ATOM 30884 SG CYS L 39 30.420 136.785 85.331 1.00 79.03 S ATOM 31109 SG CYS f 26 56.398 84.000 141.884 1.00 89.48 S ATOM 31133 SG CYS f 29 58.893 86.768 142.543 1.00 82.44 S ATOM 31294 SG CYS f 50 60.125 83.370 141.413 1.00 87.19 S ATOM 31314 SG CYS f 53 58.700 83.761 144.910 1.00 81.46 S ATOM 51171 SG CYS d 567 64.758 21.550 99.884 1.00167.28 S ATOM 51249 SG CYS d 577 61.240 21.164 101.418 1.00164.04 S ATOM 51320 SG CYS d 585 62.875 24.658 101.136 1.00157.27 S Time building chain proxies: 25.53, per 1000 atoms: 0.49 Number of scatterers: 51949 At special positions: 0 Unit cell: (164.3, 178.08, 238.5, 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 10 29.99 S 295 16.00 P 104 15.00 Mg 1 11.99 O 9929 8.00 N 9113 7.00 C 32497 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: 11.13 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN d1001 " pdb="ZN ZN d1001 " - pdb=" ND1 HIS d 588 " pdb="ZN ZN d1001 " - pdb=" SG CYS d 567 " pdb="ZN ZN d1001 " - pdb=" SG CYS d 585 " pdb="ZN ZN d1001 " - pdb=" SG CYS d 577 " pdb=" ZN f1001 " pdb="ZN ZN f1001 " - pdb=" SG CYS f 53 " pdb="ZN ZN f1001 " - pdb=" SG CYS f 26 " pdb="ZN ZN f1001 " - pdb=" SG CYS f 29 " pdb="ZN ZN f1001 " - pdb=" SG CYS f 50 " Number of angles added : 54 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11700 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 78 sheets defined 36.9% alpha, 21.0% beta 44 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 17.39 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.654A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.752A pdb=" N LYS A 344 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.057A pdb=" N HIS A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.874A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.844A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.672A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 869 removed outlier: 4.193A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.789A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 3.622A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.812A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.363A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 Processing helix chain 'A' and resid 1314 through 1318 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.814A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'A' and resid 1466 through 1470 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.271A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.332A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.857A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 426 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.633A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.983A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.582A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.750A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.505A pdb=" N GLN B 683 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.391A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 removed outlier: 4.264A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.376A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.795A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.078A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.862A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.843A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 3.707A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.226A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.819A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 54 through 60 removed outlier: 4.413A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.974A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.369A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'f' and resid 41 through 43 No H-bonds generated for 'chain 'f' and resid 41 through 43' Processing helix chain 'f' and resid 66 through 82 Processing helix chain 'a' and resid 2 through 11 Processing helix chain 'a' and resid 14 through 29 removed outlier: 4.263A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG a 19 " --> pdb=" O PRO a 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 250 through 255 removed outlier: 3.841A pdb=" N GLN b 255 " --> pdb=" O ILE b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 366 through 370 removed outlier: 3.527A pdb=" N ARG b 369 " --> pdb=" O ASP b 366 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN b 370 " --> pdb=" O LEU b 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 366 through 370' Processing helix chain 'b' and resid 985 through 990 removed outlier: 3.582A pdb=" N ARG b 989 " --> pdb=" O THR b 985 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN b 990 " --> pdb=" O ASP b 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 985 through 990' Processing helix chain 'b' and resid 1044 through 1060 removed outlier: 3.538A pdb=" N ASN b1049 " --> pdb=" O GLU b1045 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU b1051 " --> pdb=" O TRP b1047 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS b1060 " --> pdb=" O ASN b1056 " (cutoff:3.500A) Processing helix chain 'b' and resid 1069 through 1074 Processing helix chain 'b' and resid 1090 through 1095 Processing helix chain 'b' and resid 1096 through 1098 No H-bonds generated for 'chain 'b' and resid 1096 through 1098' Processing helix chain 'b' and resid 1101 through 1109 removed outlier: 3.626A pdb=" N GLN b1106 " --> pdb=" O ARG b1102 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU b1107 " --> pdb=" O PRO b1103 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL b1108 " --> pdb=" O LYS b1104 " (cutoff:3.500A) Processing helix chain 'b' and resid 1125 through 1136 removed outlier: 3.877A pdb=" N GLU b1135 " --> pdb=" O LYS b1131 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU b1136 " --> pdb=" O VAL b1132 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 47 removed outlier: 3.620A pdb=" N LEU g 43 " --> pdb=" O ALA g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 53 removed outlier: 3.647A pdb=" N PHE g 52 " --> pdb=" O ARG g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 69 removed outlier: 3.772A pdb=" N SER g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 71 through 85 removed outlier: 4.081A pdb=" N ARG g 77 " --> pdb=" O THR g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 117 removed outlier: 3.802A pdb=" N LEU g 113 " --> pdb=" O ARG g 109 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS g 114 " --> pdb=" O THR g 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 121 through 132 removed outlier: 3.795A pdb=" N VAL g 125 " --> pdb=" O TYR g 121 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN g 126 " --> pdb=" O ALA g 122 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS g 127 " --> pdb=" O GLY g 123 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 136 removed outlier: 3.639A pdb=" N CYS g 136 " --> pdb=" O LEU g 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 133 through 136' Processing helix chain 'g' and resid 143 through 150 Processing helix chain 'g' and resid 156 through 163 removed outlier: 3.691A pdb=" N LEU g 160 " --> pdb=" O GLU g 156 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA g 163 " --> pdb=" O HIS g 159 " (cutoff:3.500A) Processing helix chain 'g' and resid 181 through 202 Processing helix chain 'g' and resid 203 through 206 removed outlier: 3.536A pdb=" N GLU g 206 " --> pdb=" O LYS g 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 203 through 206' Processing helix chain 'g' and resid 209 through 215 removed outlier: 3.521A pdb=" N LEU g 213 " --> pdb=" O LEU g 209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG g 215 " --> pdb=" O GLU g 211 " (cutoff:3.500A) Processing helix chain 'g' and resid 224 through 235 removed outlier: 3.631A pdb=" N HIS g 230 " --> pdb=" O THR g 226 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP g 231 " --> pdb=" O TYR g 227 " (cutoff:3.500A) Processing helix chain 'e' and resid 457 through 469 Processing helix chain 'e' and resid 500 through 505 removed outlier: 3.565A pdb=" N LYS e 505 " --> pdb=" O GLY e 501 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 524 removed outlier: 3.576A pdb=" N GLN e 524 " --> pdb=" O GLU e 520 " (cutoff:3.500A) Processing helix chain 'e' and resid 538 through 553 Processing helix chain 'e' and resid 577 through 589 Processing helix chain 'e' and resid 606 through 618 removed outlier: 4.261A pdb=" N LEU e 610 " --> pdb=" O LYS e 606 " (cutoff:3.500A) Processing helix chain 'e' and resid 625 through 631 Processing helix chain 'e' and resid 631 through 636 removed outlier: 3.944A pdb=" N ILE e 635 " --> pdb=" O MET e 631 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER e 636 " --> pdb=" O GLN e 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 631 through 636' Processing helix chain 'e' and resid 637 through 639 No H-bonds generated for 'chain 'e' and resid 637 through 639' Processing helix chain 'e' and resid 648 through 652 Processing helix chain 'e' and resid 656 through 664 Processing helix chain 'e' and resid 681 through 693 removed outlier: 3.577A pdb=" N LEU e 685 " --> pdb=" O ASN e 681 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU e 688 " --> pdb=" O GLU e 684 " (cutoff:3.500A) Processing helix chain 'e' and resid 699 through 707 Processing helix chain 'e' and resid 707 through 715 removed outlier: 3.606A pdb=" N GLY e 714 " --> pdb=" O PRO e 710 " (cutoff:3.500A) Processing helix chain 'e' and resid 720 through 737 removed outlier: 3.534A pdb=" N LYS e 725 " --> pdb=" O PRO e 721 " (cutoff:3.500A) Processing helix chain 'e' and resid 738 through 740 No H-bonds generated for 'chain 'e' and resid 738 through 740' Processing helix chain 'e' and resid 746 through 751 Processing helix chain 'e' and resid 769 through 782 Processing helix chain 'e' and resid 783 through 790 Processing helix chain 'e' and resid 794 through 808 removed outlier: 3.564A pdb=" N LEU e 802 " --> pdb=" O GLY e 798 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS e 806 " --> pdb=" O LEU e 802 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN e 807 " --> pdb=" O ARG e 803 " (cutoff:3.500A) Processing helix chain 'e' and resid 834 through 837 Processing helix chain 'e' and resid 838 through 852 removed outlier: 3.609A pdb=" N SER e 846 " --> pdb=" O ILE e 842 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS e 852 " --> pdb=" O LEU e 848 " (cutoff:3.500A) Processing helix chain 'e' and resid 853 through 855 No H-bonds generated for 'chain 'e' and resid 853 through 855' Processing helix chain 'e' and resid 864 through 878 removed outlier: 3.700A pdb=" N ASP e 869 " --> pdb=" O ARG e 865 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE e 870 " --> pdb=" O GLN e 866 " (cutoff:3.500A) Processing helix chain 'e' and resid 890 through 893 Processing helix chain 'e' and resid 894 through 904 removed outlier: 3.563A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU e 903 " --> pdb=" O THR e 899 " (cutoff:3.500A) Processing helix chain 'e' and resid 938 through 949 removed outlier: 3.869A pdb=" N ALA e 948 " --> pdb=" O ALA e 944 " (cutoff:3.500A) Processing helix chain 'e' and resid 967 through 988 removed outlier: 3.932A pdb=" N GLN e 980 " --> pdb=" O GLN e 976 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR e 983 " --> pdb=" O LYS e 979 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL e 986 " --> pdb=" O LEU e 982 " (cutoff:3.500A) Processing helix chain 'e' and resid 997 through 1003 removed outlier: 3.760A pdb=" N GLU e1003 " --> pdb=" O ASN e 999 " (cutoff:3.500A) Processing helix chain 'e' and resid 1016 through 1022 Processing helix chain 'e' and resid 1251 through 1256 Processing helix chain 'e' and resid 1268 through 1273 removed outlier: 3.572A pdb=" N MET e1272 " --> pdb=" O HIS e1268 " (cutoff:3.500A) Processing helix chain 'e' and resid 1387 through 1398 removed outlier: 3.637A pdb=" N LYS e1392 " --> pdb=" O SER e1388 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 14 Processing helix chain 'd' and resid 21 through 35 removed outlier: 3.929A pdb=" N SER d 34 " --> pdb=" O LYS d 30 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER d 35 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 51 Processing helix chain 'd' and resid 54 through 71 removed outlier: 3.543A pdb=" N ILE d 64 " --> pdb=" O SER d 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL d 70 " --> pdb=" O GLU d 66 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG d 71 " --> pdb=" O GLU d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 72 through 82 removed outlier: 3.592A pdb=" N VAL d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 92 Processing helix chain 'd' and resid 102 through 125 removed outlier: 3.519A pdb=" N ALA d 116 " --> pdb=" O ALA d 112 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY d 119 " --> pdb=" O ARG d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 141 Processing helix chain 'd' and resid 602 through 619 Processing helix chain 'd' and resid 660 through 666 removed outlier: 3.532A pdb=" N ALA d 665 " --> pdb=" O LEU d 661 " (cutoff:3.500A) Processing helix chain 'd' and resid 667 through 677 removed outlier: 3.871A pdb=" N ARG d 671 " --> pdb=" O THR d 667 " (cutoff:3.500A) Processing helix chain 'd' and resid 678 through 697 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.373A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.605A pdb=" N ARG A 190 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.727A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.621A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.172A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.563A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.411A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.411A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.715A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.841A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.812A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.753A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.510A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.015A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.015A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.212A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.523A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.502A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.591A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.615A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.615A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS L 46 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD6, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.551A pdb=" N MET B 796 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 948 " --> pdb=" O MET B 796 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD8, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.910A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AE1, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.539A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 44 through 55 removed outlier: 6.448A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.527A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.566A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.659A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 117 through 120 removed outlier: 4.482A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF1, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'f' and resid 35 through 40 removed outlier: 3.662A pdb=" N ASP f 40 " --> pdb=" O THR f 45 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 30 through 31 Processing sheet with id=AF5, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.528A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS a 88 " --> pdb=" O LEU a 70 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 102 through 107 removed outlier: 4.415A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN a 133 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 144 through 149 removed outlier: 3.580A pdb=" N SER a 146 " --> pdb=" O GLY a 162 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS a 180 " --> pdb=" O LEU a 170 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 189 through 194 removed outlier: 3.547A pdb=" N ILE a 224 " --> pdb=" O LEU a 213 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 252 through 253 Processing sheet with id=AG1, first strand: chain 'a' and resid 298 through 299 removed outlier: 6.306A pdb=" N ILE a 316 " --> pdb=" O MET a 329 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET a 329 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL a 318 " --> pdb=" O ILE a 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 6 through 10 removed outlier: 6.114A pdb=" N ILE b1037 " --> pdb=" O ALA b 9 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER b1042 " --> pdb=" O GLY b1026 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY b1026 " --> pdb=" O SER b1042 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL b1006 " --> pdb=" O GLY b1031 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 17 through 21 removed outlier: 5.744A pdb=" N VAL b 43 " --> pdb=" O PRO b 51 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR b 45 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU b 49 " --> pdb=" O THR b 45 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 61 through 67 removed outlier: 6.712A pdb=" N LEU b 80 " --> pdb=" O ALA b 62 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET b 64 " --> pdb=" O PHE b 78 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE b 78 " --> pdb=" O MET b 64 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU b 66 " --> pdb=" O LEU b 76 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU b 76 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN b 85 " --> pdb=" O THR b 81 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU b 90 " --> pdb=" O THR b 102 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR b 102 " --> pdb=" O GLU b 90 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS b 92 " --> pdb=" O ILE b 100 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE b 100 " --> pdb=" O LYS b 92 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER b 94 " --> pdb=" O ILE b 98 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE b 98 " --> pdb=" O SER b 94 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N GLN c 45 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG b 103 " --> pdb=" O GLN c 45 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE c 47 " --> pdb=" O ARG b 103 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS b 105 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR c 49 " --> pdb=" O HIS b 105 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ASN b 107 " --> pdb=" O THR c 49 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS b 153 " --> pdb=" O PRO b 144 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 163 through 169 removed outlier: 4.394A pdb=" N HIS b 163 " --> pdb=" O GLN b 183 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL b 181 " --> pdb=" O ILE b 165 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL b 167 " --> pdb=" O CYS b 179 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS b 179 " --> pdb=" O VAL b 167 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE b 169 " --> pdb=" O THR b 177 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR b 177 " --> pdb=" O PHE b 169 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 163 through 169 removed outlier: 4.394A pdb=" N HIS b 163 " --> pdb=" O GLN b 183 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL b 181 " --> pdb=" O ILE b 165 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL b 167 " --> pdb=" O CYS b 179 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS b 179 " --> pdb=" O VAL b 167 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE b 169 " --> pdb=" O THR b 177 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR b 177 " --> pdb=" O PHE b 169 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG b 188 " --> pdb=" O VAL b 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL b 190 " --> pdb=" O GLU b 210 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 218 through 221 removed outlier: 3.787A pdb=" N LEU b 246 " --> pdb=" O TYR b 239 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 258 through 263 removed outlier: 6.786A pdb=" N GLY b 274 " --> pdb=" O VAL b 259 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS b 261 " --> pdb=" O LEU b 272 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU b 272 " --> pdb=" O HIS b 261 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG b 263 " --> pdb=" O ARG b 270 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ARG b 270 " --> pdb=" O ARG b 263 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG b 279 " --> pdb=" O ASP b 275 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU b 280 " --> pdb=" O LEU b 304 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU b 304 " --> pdb=" O LEU b 280 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET b 282 " --> pdb=" O VAL b 302 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL b 302 " --> pdb=" O MET b 282 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU b 284 " --> pdb=" O LEU b 300 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU b 300 " --> pdb=" O LEU b 284 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU b 286 " --> pdb=" O LYS b 298 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 313 through 318 removed outlier: 6.851A pdb=" N VAL b 321 " --> pdb=" O LEU b 317 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS b 335 " --> pdb=" O ALA b 349 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA b 349 " --> pdb=" O LYS b 335 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 362 through 365 removed outlier: 3.634A pdb=" N HIS b 711 " --> pdb=" O ARG b 391 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 720 through 727 removed outlier: 6.261A pdb=" N LEU b 736 " --> pdb=" O ARG b 722 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE b 724 " --> pdb=" O GLY b 734 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY b 734 " --> pdb=" O ILE b 724 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR b 726 " --> pdb=" O CYS b 732 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N CYS b 732 " --> pdb=" O TYR b 726 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 720 through 727 removed outlier: 6.261A pdb=" N LEU b 736 " --> pdb=" O ARG b 722 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE b 724 " --> pdb=" O GLY b 734 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY b 734 " --> pdb=" O ILE b 724 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR b 726 " --> pdb=" O CYS b 732 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N CYS b 732 " --> pdb=" O TYR b 726 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N HIS b 789 " --> pdb=" O GLN b 806 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN b 806 " --> pdb=" O HIS b 789 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU b 791 " --> pdb=" O ALA b 804 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA b 804 " --> pdb=" O LEU b 791 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE b 793 " --> pdb=" O LEU b 802 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 811 through 819 removed outlier: 6.890A pdb=" N GLY b 832 " --> pdb=" O LEU b 814 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU b 816 " --> pdb=" O ILE b 830 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE b 830 " --> pdb=" O LEU b 816 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER b 818 " --> pdb=" O TYR b 828 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR b 828 " --> pdb=" O SER b 818 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN b 845 " --> pdb=" O MET b 835 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL b 850 " --> pdb=" O VAL b 861 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 811 through 819 removed outlier: 6.890A pdb=" N GLY b 832 " --> pdb=" O LEU b 814 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU b 816 " --> pdb=" O ILE b 830 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE b 830 " --> pdb=" O LEU b 816 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER b 818 " --> pdb=" O TYR b 828 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR b 828 " --> pdb=" O SER b 818 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN b 845 " --> pdb=" O MET b 835 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 870 through 876 removed outlier: 4.307A pdb=" N SER b 872 " --> pdb=" O SER b 883 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG b 900 " --> pdb=" O GLU b 892 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 911 through 917 removed outlier: 7.551A pdb=" N VAL b 930 " --> pdb=" O ARG b 947 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG b 947 " --> pdb=" O VAL b 930 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU b 932 " --> pdb=" O ILE b 945 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN b 941 " --> pdb=" O LYS b 936 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 954 through 959 removed outlier: 3.988A pdb=" N ALA b 956 " --> pdb=" O ALA b 968 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN b 978 " --> pdb=" O GLU b 994 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU b 994 " --> pdb=" O GLN b 978 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 1076 through 1078 Processing sheet with id=AI1, first strand: chain 'g' and resid 59 through 61 Processing sheet with id=AI2, first strand: chain 'g' and resid 140 through 142 Processing sheet with id=AI3, first strand: chain 'g' and resid 207 through 208 removed outlier: 4.112A pdb=" N LEU g 207 " --> pdb=" O LEU g 249 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU g 249 " --> pdb=" O LEU g 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG g 250 " --> pdb=" O ASP g 239 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 594 through 597 removed outlier: 6.399A pdb=" N ALA e 595 " --> pdb=" O ILE e 622 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER e 624 " --> pdb=" O ALA e 595 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU e 597 " --> pdb=" O SER e 624 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR e 569 " --> pdb=" O LEU e 621 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR e 623 " --> pdb=" O THR e 569 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE e 571 " --> pdb=" O THR e 623 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL e 643 " --> pdb=" O ILE e 671 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU e 673 " --> pdb=" O VAL e 643 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU e 645 " --> pdb=" O LEU e 673 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE e 529 " --> pdb=" O LEU e 743 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 882 through 884 removed outlier: 7.050A pdb=" N LEU e 883 " --> pdb=" O LEU e 911 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU e 860 " --> pdb=" O PHE e 910 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU e 859 " --> pdb=" O VAL e 930 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN e 760 " --> pdb=" O VAL e 959 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG e 961 " --> pdb=" O ASN e 760 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN e 762 " --> pdb=" O ARG e 961 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLU e 761 " --> pdb=" O LYS e1267 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS e1267 " --> pdb=" O GLU e 761 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL e 763 " --> pdb=" O VAL e1265 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL e1265 " --> pdb=" O VAL e 763 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE e 765 " --> pdb=" O HIS e1263 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'd' and resid 584 through 585 2108 hydrogen bonds defined for protein. 5862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 30.47 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16434 1.34 - 1.46: 9256 1.46 - 1.58: 26807 1.58 - 1.70: 204 1.70 - 1.82: 459 Bond restraints: 53160 Sorted by residual: bond pdb=" C SER B 106 " pdb=" N PRO B 107 " ideal model delta sigma weight residual 1.333 1.357 -0.024 1.01e-02 9.80e+03 5.48e+00 bond pdb=" CA GLU A1097 " pdb=" C GLU A1097 " ideal model delta sigma weight residual 1.520 1.548 -0.028 1.23e-02 6.61e+03 5.09e+00 bond pdb=" CA TYR d 43 " pdb=" C TYR d 43 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.27e-02 6.20e+03 4.90e+00 bond pdb=" N THR d 51 " pdb=" CA THR d 51 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.90e+00 bond pdb=" CA ILE e 931 " pdb=" C ILE e 931 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.01e-02 9.80e+03 3.78e+00 ... (remaining 53155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 70937 2.01 - 4.02: 1157 4.02 - 6.04: 122 6.04 - 8.05: 25 8.05 - 10.06: 9 Bond angle restraints: 72250 Sorted by residual: angle pdb=" O3' DG T 43 " pdb=" P DG T 44 " pdb=" O5' DG T 44 " ideal model delta sigma weight residual 104.00 110.20 -6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" P DG T 43 " pdb=" O5' DG T 43 " pdb=" C5' DG T 43 " ideal model delta sigma weight residual 120.00 125.96 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CA PHE g 128 " pdb=" CB PHE g 128 " pdb=" CG PHE g 128 " ideal model delta sigma weight residual 113.80 117.71 -3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 108.17 113.61 -5.44 1.40e+00 5.10e-01 1.51e+01 angle pdb=" N ALA e 965 " pdb=" CA ALA e 965 " pdb=" C ALA e 965 " ideal model delta sigma weight residual 110.23 115.83 -5.60 1.45e+00 4.76e-01 1.49e+01 ... (remaining 72245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 30504 34.91 - 69.81: 1547 69.81 - 104.72: 79 104.72 - 139.63: 1 139.63 - 174.54: 4 Dihedral angle restraints: 32135 sinusoidal: 14037 harmonic: 18098 Sorted by residual: dihedral pdb=" CD ARG E 162 " pdb=" NE ARG E 162 " pdb=" CZ ARG E 162 " pdb=" NH1 ARG E 162 " ideal model delta sinusoidal sigma weight residual 0.00 -65.15 65.15 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CD ARG A 532 " pdb=" NE ARG A 532 " pdb=" CZ ARG A 532 " pdb=" NH1 ARG A 532 " ideal model delta sinusoidal sigma weight residual 0.00 -61.71 61.71 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CD ARG d 44 " pdb=" NE ARG d 44 " pdb=" CZ ARG d 44 " pdb=" NH1 ARG d 44 " ideal model delta sinusoidal sigma weight residual 0.00 -52.86 52.86 1 1.00e+01 1.00e-02 3.80e+01 ... (remaining 32132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 6693 0.057 - 0.114: 1247 0.114 - 0.171: 110 0.171 - 0.228: 2 0.228 - 0.285: 3 Chirality restraints: 8055 Sorted by residual: chirality pdb=" P DA T 47 " pdb=" OP1 DA T 47 " pdb=" OP2 DA T 47 " pdb=" O5' DA T 47 " both_signs ideal model delta sigma weight residual True 2.35 -2.63 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" P DG T 44 " pdb=" OP1 DG T 44 " pdb=" OP2 DG T 44 " pdb=" O5' DG T 44 " both_signs ideal model delta sigma weight residual True 2.35 -2.63 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" P DG T 43 " pdb=" OP1 DG T 43 " pdb=" OP2 DG T 43 " pdb=" O5' DG T 43 " both_signs ideal model delta sigma weight residual True 2.35 -2.59 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 8052 not shown) Planarity restraints: 8982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 162 " 0.998 9.50e-02 1.11e+02 4.47e-01 1.21e+02 pdb=" NE ARG E 162 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG E 162 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 162 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 162 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 532 " 0.965 9.50e-02 1.11e+02 4.33e-01 1.13e+02 pdb=" NE ARG A 532 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 532 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 532 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 532 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 44 " -0.885 9.50e-02 1.11e+02 3.97e-01 9.54e+01 pdb=" NE ARG d 44 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG d 44 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG d 44 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG d 44 " -0.025 2.00e-02 2.50e+03 ... (remaining 8979 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 336 2.50 - 3.10: 36760 3.10 - 3.70: 83559 3.70 - 4.30: 119379 4.30 - 4.90: 195219 Nonbonded interactions: 435253 Sorted by model distance: nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.905 2.170 nonbonded pdb=" O3' A M 10 " pdb="MG MG A2003 " model vdw 1.970 2.170 nonbonded pdb=" OG SER A 508 " pdb=" OE1 GLU A 510 " model vdw 1.986 3.040 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.991 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 2.013 2.170 ... (remaining 435248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.630 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 129.850 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 53160 Z= 0.227 Angle : 0.612 10.062 72250 Z= 0.349 Chirality : 0.043 0.285 8055 Planarity : 0.015 0.447 8982 Dihedral : 18.708 174.535 20435 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.38 % Allowed : 27.55 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 6148 helix: 0.89 (0.12), residues: 2001 sheet: -0.36 (0.15), residues: 1162 loop : -0.74 (0.11), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP d 120 HIS 0.009 0.001 HIS B 370 PHE 0.028 0.001 PHE d 86 TYR 0.032 0.001 TYR d 128 ARG 0.009 0.000 ARG b 900 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 1364 time to evaluate : 5.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7797 (ttp) cc_final: 0.7585 (ttt) REVERT: A 1011 GLU cc_start: 0.7144 (mp0) cc_final: 0.6908 (mp0) REVERT: A 1159 CYS cc_start: 0.6940 (m) cc_final: 0.6682 (m) REVERT: B 198 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6463 (mt-10) REVERT: B 199 LYS cc_start: 0.7560 (pttm) cc_final: 0.7329 (ptmm) REVERT: C 62 GLU cc_start: 0.7781 (mp0) cc_final: 0.7556 (mp0) REVERT: E 186 LYS cc_start: 0.7125 (pttt) cc_final: 0.6818 (pttt) REVERT: K 26 LYS cc_start: 0.7773 (mppt) cc_final: 0.7314 (mppt) REVERT: a 35 ASP cc_start: 0.6585 (p0) cc_final: 0.6358 (p0) REVERT: a 172 ASP cc_start: 0.7579 (t0) cc_final: 0.7229 (t0) REVERT: a 174 LYS cc_start: 0.7258 (ttmm) cc_final: 0.6335 (ttmm) REVERT: g 41 SER cc_start: 0.8435 (t) cc_final: 0.7963 (m) REVERT: g 72 ARG cc_start: 0.6572 (mtm-85) cc_final: 0.6312 (mtm-85) REVERT: g 128 PHE cc_start: 0.8063 (t80) cc_final: 0.7830 (t80) REVERT: g 196 LEU cc_start: 0.6954 (tp) cc_final: 0.6101 (mt) REVERT: g 227 TYR cc_start: 0.8143 (t80) cc_final: 0.7883 (t80) REVERT: e 796 PHE cc_start: 0.7012 (m-80) cc_final: 0.6711 (m-80) REVERT: e 883 LEU cc_start: 0.8189 (tp) cc_final: 0.7982 (tt) REVERT: e 933 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6148 (p0) REVERT: d 23 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7242 (mt-10) REVERT: d 26 LYS cc_start: 0.8707 (mttt) cc_final: 0.8311 (mttt) REVERT: d 44 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7876 (ttt180) outliers start: 21 outliers final: 13 residues processed: 1372 average time/residue: 0.7664 time to fit residues: 1677.6211 Evaluate side-chains 1356 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1342 time to evaluate : 5.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain b residue 355 ASN Chi-restraints excluded: chain b residue 386 SER Chi-restraints excluded: chain b residue 809 GLN Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 933 ASP Chi-restraints excluded: chain e residue 1007 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 0.0980 chunk 472 optimal weight: 2.9990 chunk 262 optimal weight: 0.1980 chunk 161 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 489 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 364 optimal weight: 0.9990 chunk 566 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN A 885 GLN A1180 ASN A1299 GLN B 23 GLN B 552 ASN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN B1053 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN K 89 ASN f 82 ASN ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN b 790 ASN c 45 GLN ** g 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 193 GLN ** e 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 773 HIS e 778 ASN e 956 GLN d 38 GLN d 74 GLN d 580 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 53160 Z= 0.214 Angle : 0.567 19.064 72250 Z= 0.298 Chirality : 0.043 0.180 8055 Planarity : 0.004 0.060 8982 Dihedral : 13.145 174.764 8002 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.38 % Allowed : 24.37 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 6148 helix: 1.13 (0.12), residues: 2038 sheet: -0.25 (0.15), residues: 1144 loop : -0.68 (0.11), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 175 HIS 0.008 0.001 HIS B 370 PHE 0.018 0.001 PHE b1030 TYR 0.024 0.001 TYR d 128 ARG 0.008 0.001 ARG A1167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 1413 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7847 (tp40) cc_final: 0.7028 (tm-30) REVERT: A 143 HIS cc_start: 0.6520 (m170) cc_final: 0.6045 (m170) REVERT: A 244 ARG cc_start: 0.7459 (mtp85) cc_final: 0.7204 (mtp85) REVERT: A 483 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7511 (mpt180) REVERT: A 510 GLU cc_start: 0.6680 (mp0) cc_final: 0.6347 (mp0) REVERT: A 701 ASP cc_start: 0.7387 (m-30) cc_final: 0.6980 (m-30) REVERT: A 1159 CYS cc_start: 0.7105 (m) cc_final: 0.6642 (m) REVERT: A 1221 MET cc_start: 0.6648 (mmp) cc_final: 0.6116 (mmp) REVERT: A 1403 ASP cc_start: 0.7022 (m-30) cc_final: 0.6746 (m-30) REVERT: B 198 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6377 (mt-10) REVERT: B 199 LYS cc_start: 0.7820 (pttm) cc_final: 0.7545 (pttm) REVERT: B 257 VAL cc_start: 0.8106 (t) cc_final: 0.7682 (p) REVERT: B 384 ASP cc_start: 0.7186 (p0) cc_final: 0.6763 (p0) REVERT: B 391 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7617 (mttm) REVERT: B 585 ASN cc_start: 0.7399 (m-40) cc_final: 0.6906 (m110) REVERT: B 798 ARG cc_start: 0.7349 (tpp-160) cc_final: 0.7065 (tpp-160) REVERT: B 1054 MET cc_start: 0.6762 (mtm) cc_final: 0.6509 (mpp) REVERT: B 1109 GLU cc_start: 0.7039 (mp0) cc_final: 0.6799 (mp0) REVERT: C 62 GLU cc_start: 0.7772 (mp0) cc_final: 0.6984 (mp0) REVERT: C 201 GLU cc_start: 0.7168 (pm20) cc_final: 0.6847 (pm20) REVERT: E 73 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7903 (m-10) REVERT: E 162 ARG cc_start: 0.7383 (tpt90) cc_final: 0.7061 (tmt-80) REVERT: E 187 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6908 (mtp-110) REVERT: I 37 TYR cc_start: 0.8105 (m-80) cc_final: 0.7855 (m-80) REVERT: J 16 ASN cc_start: 0.8339 (p0) cc_final: 0.8095 (p0) REVERT: a 35 ASP cc_start: 0.6648 (p0) cc_final: 0.6278 (p0) REVERT: a 36 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6983 (mtm180) REVERT: a 111 ASP cc_start: 0.7054 (t0) cc_final: 0.6782 (t0) REVERT: a 118 SER cc_start: 0.8227 (m) cc_final: 0.7913 (t) REVERT: a 172 ASP cc_start: 0.7817 (t0) cc_final: 0.7259 (t0) REVERT: a 174 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6362 (ttmm) REVERT: a 295 LEU cc_start: 0.7999 (tp) cc_final: 0.7658 (tt) REVERT: b 265 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: b 892 GLU cc_start: 0.6698 (pm20) cc_final: 0.6329 (pm20) REVERT: b 928 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6967 (mtm-85) REVERT: b 1130 ILE cc_start: 0.8649 (tt) cc_final: 0.8226 (pt) REVERT: g 41 SER cc_start: 0.8323 (t) cc_final: 0.7841 (m) REVERT: g 60 VAL cc_start: 0.7920 (m) cc_final: 0.7717 (p) REVERT: g 71 ASP cc_start: 0.6025 (OUTLIER) cc_final: 0.5683 (p0) REVERT: g 128 PHE cc_start: 0.8040 (t80) cc_final: 0.7776 (t80) REVERT: g 175 TRP cc_start: 0.7026 (m-90) cc_final: 0.6553 (m-90) REVERT: e 580 GLN cc_start: 0.6600 (tm130) cc_final: 0.6365 (tm130) REVERT: e 584 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6805 (mm-30) REVERT: e 607 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7854 (mtmm) REVERT: e 625 TYR cc_start: 0.7865 (m-80) cc_final: 0.7602 (m-80) REVERT: e 639 ASP cc_start: 0.6625 (t0) cc_final: 0.6379 (t0) REVERT: e 640 TRP cc_start: 0.7586 (m100) cc_final: 0.7117 (m100) REVERT: e 660 LEU cc_start: 0.7886 (mp) cc_final: 0.7637 (mp) REVERT: e 759 LYS cc_start: 0.6507 (mttm) cc_final: 0.6258 (mttm) REVERT: e 789 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6766 (pp) REVERT: e 796 PHE cc_start: 0.6953 (m-80) cc_final: 0.6667 (m-80) REVERT: e 866 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6764 (mm-40) REVERT: e 876 ARG cc_start: 0.6723 (mmt-90) cc_final: 0.6466 (mpt180) REVERT: e 883 LEU cc_start: 0.8209 (tp) cc_final: 0.7955 (tt) REVERT: e 933 ASP cc_start: 0.6418 (p0) cc_final: 0.6095 (p0) REVERT: e 985 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7695 (ttm110) REVERT: e 997 LYS cc_start: 0.6831 (tmtt) cc_final: 0.6626 (tmtt) REVERT: d 23 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7002 (mt-10) REVERT: d 24 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7328 (mmtt) REVERT: d 26 LYS cc_start: 0.8506 (mttt) cc_final: 0.7981 (mttt) REVERT: d 36 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7062 (mt-10) REVERT: d 118 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6385 (mp0) outliers start: 186 outliers final: 100 residues processed: 1508 average time/residue: 0.7149 time to fit residues: 1718.5923 Evaluate side-chains 1477 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1369 time to evaluate : 5.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1242 ASP Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain a residue 36 ARG Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1065 VAL Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain g residue 71 ASP Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 797 SER Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 74 GLN Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 126 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 471 optimal weight: 0.8980 chunk 385 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 567 optimal weight: 1.9990 chunk 613 optimal weight: 4.9990 chunk 505 optimal weight: 0.6980 chunk 562 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 455 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1310 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN I 32 ASN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 641 HIS d 49 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 580 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 53160 Z= 0.229 Angle : 0.554 19.781 72250 Z= 0.290 Chirality : 0.043 0.165 8055 Planarity : 0.004 0.047 8982 Dihedral : 13.093 174.509 7986 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.09 % Allowed : 24.59 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 6148 helix: 1.24 (0.12), residues: 2036 sheet: -0.25 (0.15), residues: 1153 loop : -0.68 (0.11), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 175 HIS 0.007 0.001 HIS B 370 PHE 0.026 0.001 PHE B 309 TYR 0.025 0.001 TYR e 510 ARG 0.007 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 1416 time to evaluate : 5.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6529 (m170) cc_final: 0.5988 (m170) REVERT: A 197 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: A 319 ASP cc_start: 0.6944 (t0) cc_final: 0.6633 (t70) REVERT: A 322 LEU cc_start: 0.7898 (mt) cc_final: 0.7659 (mp) REVERT: A 701 ASP cc_start: 0.7343 (m-30) cc_final: 0.6863 (m-30) REVERT: A 740 GLN cc_start: 0.6511 (tt0) cc_final: 0.6215 (tt0) REVERT: A 1159 CYS cc_start: 0.7143 (m) cc_final: 0.6670 (m) REVERT: A 1221 MET cc_start: 0.6888 (mmp) cc_final: 0.6489 (mmp) REVERT: A 1245 CYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7379 (m) REVERT: A 1403 ASP cc_start: 0.6991 (m-30) cc_final: 0.6636 (m-30) REVERT: A 1472 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7257 (t70) REVERT: B 198 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6324 (mt-10) REVERT: B 257 VAL cc_start: 0.8140 (t) cc_final: 0.7705 (p) REVERT: B 384 ASP cc_start: 0.7188 (p0) cc_final: 0.6738 (p0) REVERT: B 391 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7674 (mttm) REVERT: B 585 ASN cc_start: 0.7433 (m-40) cc_final: 0.6938 (m-40) REVERT: B 681 ASP cc_start: 0.7658 (m-30) cc_final: 0.7451 (m-30) REVERT: B 798 ARG cc_start: 0.7413 (tpp-160) cc_final: 0.7162 (tpp-160) REVERT: B 1054 MET cc_start: 0.6980 (mtm) cc_final: 0.6641 (mpp) REVERT: B 1109 GLU cc_start: 0.7041 (mp0) cc_final: 0.6785 (mp0) REVERT: C 62 GLU cc_start: 0.7743 (mp0) cc_final: 0.6962 (mp0) REVERT: C 94 CYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6547 (p) REVERT: C 201 GLU cc_start: 0.7244 (pm20) cc_final: 0.6857 (pm20) REVERT: E 73 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: E 129 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 162 ARG cc_start: 0.7385 (tpt90) cc_final: 0.7128 (tmt-80) REVERT: E 165 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7352 (pp) REVERT: H 90 TYR cc_start: 0.8159 (t80) cc_final: 0.7899 (t80) REVERT: K 26 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7537 (mtpt) REVERT: L 24 THR cc_start: 0.8503 (m) cc_final: 0.8224 (m) REVERT: a 35 ASP cc_start: 0.6723 (p0) cc_final: 0.6493 (p0) REVERT: a 172 ASP cc_start: 0.7886 (t0) cc_final: 0.7289 (t0) REVERT: a 174 LYS cc_start: 0.7364 (ttmm) cc_final: 0.6459 (ttmm) REVERT: a 206 SER cc_start: 0.8416 (t) cc_final: 0.8016 (p) REVERT: a 208 ASP cc_start: 0.7149 (p0) cc_final: 0.6721 (p0) REVERT: b 265 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: b 314 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7804 (pp) REVERT: b 840 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6659 (tm-30) REVERT: b 1051 LEU cc_start: 0.8579 (mt) cc_final: 0.8362 (mt) REVERT: b 1102 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7550 (mmm160) REVERT: b 1130 ILE cc_start: 0.8664 (tt) cc_final: 0.8232 (pt) REVERT: g 41 SER cc_start: 0.8401 (t) cc_final: 0.7931 (m) REVERT: g 74 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7502 (t) REVERT: g 128 PHE cc_start: 0.8048 (t80) cc_final: 0.7822 (t80) REVERT: g 175 TRP cc_start: 0.7126 (m-90) cc_final: 0.6760 (m-90) REVERT: g 196 LEU cc_start: 0.7394 (mt) cc_final: 0.7122 (mm) REVERT: g 203 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7848 (mtpt) REVERT: e 533 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7106 (tm-30) REVERT: e 580 GLN cc_start: 0.6617 (tm130) cc_final: 0.6346 (tm130) REVERT: e 584 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6738 (mm-30) REVERT: e 639 ASP cc_start: 0.6622 (t0) cc_final: 0.6388 (t0) REVERT: e 641 HIS cc_start: 0.7734 (t-170) cc_final: 0.7506 (t-170) REVERT: e 660 LEU cc_start: 0.7923 (mp) cc_final: 0.7694 (mp) REVERT: e 704 MET cc_start: 0.7895 (mmm) cc_final: 0.7681 (mmp) REVERT: e 789 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6847 (pp) REVERT: e 847 LEU cc_start: 0.7555 (mt) cc_final: 0.7310 (mt) REVERT: e 866 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6775 (mm-40) REVERT: e 867 MET cc_start: 0.7345 (tpt) cc_final: 0.6453 (tpt) REVERT: e 876 ARG cc_start: 0.6756 (mmt-90) cc_final: 0.6544 (mpt180) REVERT: e 885 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5781 (ptm) REVERT: e 894 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7693 (mtt180) REVERT: e 933 ASP cc_start: 0.6486 (p0) cc_final: 0.6125 (p0) REVERT: e 937 ASN cc_start: 0.7842 (t0) cc_final: 0.7583 (t0) REVERT: e 963 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7707 (tp) REVERT: e 997 LYS cc_start: 0.6809 (tmtt) cc_final: 0.6572 (tmtt) REVERT: e 1268 HIS cc_start: 0.8077 (t70) cc_final: 0.7784 (t70) REVERT: d 23 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7068 (mt-10) REVERT: d 24 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7286 (mmtt) REVERT: d 26 LYS cc_start: 0.8404 (mttt) cc_final: 0.8003 (mttt) REVERT: d 36 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6995 (mt-10) REVERT: d 118 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6470 (mp0) REVERT: d 123 LYS cc_start: 0.8241 (mttt) cc_final: 0.7936 (mttt) REVERT: d 671 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7562 (mtm110) outliers start: 225 outliers final: 145 residues processed: 1543 average time/residue: 0.7495 time to fit residues: 1860.1193 Evaluate side-chains 1535 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1377 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1242 ASP Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 301 ARG Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 314 LEU Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain b residue 1129 LEU Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 92 GLN Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 539 THR Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 963 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 126 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 0.8980 chunk 426 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 chunk 381 optimal weight: 2.9990 chunk 569 optimal weight: 1.9990 chunk 603 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 539 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN G 60 GLN I 32 ASN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 GLN e 679 GLN e 878 GLN d 49 GLN d 74 GLN d 580 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 53160 Z= 0.251 Angle : 0.563 20.358 72250 Z= 0.294 Chirality : 0.044 0.173 8055 Planarity : 0.004 0.048 8982 Dihedral : 13.104 174.425 7983 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.58 % Allowed : 24.86 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.11), residues: 6148 helix: 1.22 (0.12), residues: 2037 sheet: -0.28 (0.15), residues: 1195 loop : -0.71 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 851 HIS 0.007 0.001 HIS B 370 PHE 0.022 0.001 PHE b 851 TYR 0.038 0.001 TYR e 510 ARG 0.008 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1666 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 1414 time to evaluate : 5.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6453 (m170) cc_final: 0.5958 (m170) REVERT: A 197 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5991 (mp0) REVERT: A 322 LEU cc_start: 0.7970 (mt) cc_final: 0.7695 (mp) REVERT: A 358 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7468 (mmm160) REVERT: A 408 ARG cc_start: 0.7388 (tpp80) cc_final: 0.6904 (ttp80) REVERT: A 740 GLN cc_start: 0.6480 (tt0) cc_final: 0.6164 (tt0) REVERT: A 804 HIS cc_start: 0.8097 (m90) cc_final: 0.7874 (m90) REVERT: A 953 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 1159 CYS cc_start: 0.7104 (m) cc_final: 0.6624 (m) REVERT: A 1403 ASP cc_start: 0.6987 (m-30) cc_final: 0.6566 (m-30) REVERT: A 1472 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7267 (t70) REVERT: B 198 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6380 (mt-10) REVERT: B 291 ASP cc_start: 0.7286 (t0) cc_final: 0.6897 (t0) REVERT: B 360 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7562 (mtmm) REVERT: B 384 ASP cc_start: 0.7157 (p0) cc_final: 0.6731 (p0) REVERT: B 391 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7765 (mttp) REVERT: B 433 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6905 (mm) REVERT: B 582 GLN cc_start: 0.7220 (tm130) cc_final: 0.6745 (tm130) REVERT: B 585 ASN cc_start: 0.7454 (m-40) cc_final: 0.6954 (m-40) REVERT: B 844 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7239 (tp) REVERT: B 959 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: B 1010 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7613 (mttp) REVERT: B 1054 MET cc_start: 0.6997 (mtm) cc_final: 0.6540 (mpp) REVERT: B 1109 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 1150 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7303 (mtp-110) REVERT: C 62 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: C 94 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6570 (p) REVERT: C 164 TYR cc_start: 0.8068 (m-80) cc_final: 0.7166 (m-80) REVERT: C 201 GLU cc_start: 0.7266 (pm20) cc_final: 0.6886 (pm20) REVERT: C 221 ASP cc_start: 0.8173 (t0) cc_final: 0.7937 (t0) REVERT: E 73 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: E 129 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7725 (tm-30) REVERT: E 162 ARG cc_start: 0.7374 (tpt90) cc_final: 0.7083 (tmt-80) REVERT: E 165 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7427 (pp) REVERT: H 74 GLU cc_start: 0.6278 (tm-30) cc_final: 0.6037 (tm-30) REVERT: H 111 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6723 (mtp85) REVERT: K 26 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: K 32 LEU cc_start: 0.7468 (mm) cc_final: 0.7265 (mt) REVERT: L 24 THR cc_start: 0.8519 (m) cc_final: 0.8207 (m) REVERT: L 41 TYR cc_start: 0.8166 (t80) cc_final: 0.7928 (t80) REVERT: a 35 ASP cc_start: 0.6710 (p0) cc_final: 0.6491 (p0) REVERT: a 50 ASP cc_start: 0.7736 (t0) cc_final: 0.7498 (t0) REVERT: a 118 SER cc_start: 0.8195 (m) cc_final: 0.7961 (t) REVERT: a 128 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: a 172 ASP cc_start: 0.7923 (t0) cc_final: 0.7381 (t0) REVERT: a 174 LYS cc_start: 0.7422 (ttmm) cc_final: 0.6542 (ttmm) REVERT: a 208 ASP cc_start: 0.7163 (p0) cc_final: 0.6947 (p0) REVERT: a 295 LEU cc_start: 0.7928 (tp) cc_final: 0.7622 (tt) REVERT: b 90 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6528 (tm-30) REVERT: b 129 ARG cc_start: 0.8099 (ptt-90) cc_final: 0.7831 (ptp-170) REVERT: b 265 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: b 892 GLU cc_start: 0.6566 (pm20) cc_final: 0.6326 (pm20) REVERT: b 894 THR cc_start: 0.8905 (p) cc_final: 0.8060 (p) REVERT: b 928 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6911 (mtm-85) REVERT: b 989 ARG cc_start: 0.7653 (ptp-170) cc_final: 0.7244 (ptp-110) REVERT: b 1102 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7502 (mmm160) REVERT: b 1130 ILE cc_start: 0.8615 (tt) cc_final: 0.8211 (pt) REVERT: g 41 SER cc_start: 0.8574 (t) cc_final: 0.7859 (m) REVERT: g 42 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7245 (mm-30) REVERT: g 45 GLN cc_start: 0.7676 (mm110) cc_final: 0.7443 (mm110) REVERT: g 74 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7506 (t) REVERT: g 128 PHE cc_start: 0.8044 (t80) cc_final: 0.7823 (t80) REVERT: g 175 TRP cc_start: 0.7139 (m-90) cc_final: 0.6694 (m-90) REVERT: g 227 TYR cc_start: 0.8303 (t80) cc_final: 0.8015 (t80) REVERT: e 533 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7089 (tm-30) REVERT: e 580 GLN cc_start: 0.6617 (tm130) cc_final: 0.6337 (tm130) REVERT: e 584 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6750 (mm-30) REVERT: e 641 HIS cc_start: 0.7733 (t-170) cc_final: 0.7464 (t-170) REVERT: e 660 LEU cc_start: 0.7941 (mp) cc_final: 0.7711 (mp) REVERT: e 704 MET cc_start: 0.7900 (mmm) cc_final: 0.7689 (mmp) REVERT: e 772 GLN cc_start: 0.6814 (tt0) cc_final: 0.6502 (tp40) REVERT: e 789 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6663 (pp) REVERT: e 876 ARG cc_start: 0.6712 (mmt-90) cc_final: 0.6505 (mmt180) REVERT: e 933 ASP cc_start: 0.6542 (p0) cc_final: 0.6148 (p0) REVERT: e 937 ASN cc_start: 0.7768 (t0) cc_final: 0.7551 (t0) REVERT: e 963 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7676 (tp) REVERT: e 997 LYS cc_start: 0.6810 (tmtt) cc_final: 0.6544 (tmtt) REVERT: e 1268 HIS cc_start: 0.8101 (t70) cc_final: 0.7758 (t70) REVERT: d 10 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6796 (tm-30) REVERT: d 23 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7116 (mt-10) REVERT: d 24 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7203 (mmtt) REVERT: d 26 LYS cc_start: 0.8396 (mttt) cc_final: 0.7997 (mttt) REVERT: d 36 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7174 (mt-10) REVERT: d 118 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6441 (mp0) REVERT: d 669 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7093 (ttm170) REVERT: d 671 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7395 (mtm110) outliers start: 252 outliers final: 183 residues processed: 1548 average time/residue: 0.7088 time to fit residues: 1752.5371 Evaluate side-chains 1591 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1390 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1242 ASP Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 128 ASP Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 355 ASN Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 737 SER Chi-restraints excluded: chain b residue 765 VAL Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1065 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain b residue 1129 LEU Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 539 THR Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 811 LEU Chi-restraints excluded: chain e residue 838 SER Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 963 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1251 VAL Chi-restraints excluded: chain e residue 1387 SER Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 74 GLN Chi-restraints excluded: chain d residue 126 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 0.5980 chunk 342 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 449 optimal weight: 0.0370 chunk 248 optimal weight: 1.9990 chunk 514 optimal weight: 9.9990 chunk 416 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 307 optimal weight: 0.4980 chunk 541 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 410 ASN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN E 35 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 902 ASN d 580 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 53160 Z= 0.362 Angle : 0.603 21.126 72250 Z= 0.316 Chirality : 0.046 0.210 8055 Planarity : 0.004 0.053 8982 Dihedral : 13.174 174.620 7983 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.27 % Allowed : 24.86 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 6148 helix: 1.09 (0.12), residues: 2026 sheet: -0.41 (0.15), residues: 1192 loop : -0.78 (0.11), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP e 851 HIS 0.009 0.001 HIS B 370 PHE 0.026 0.002 PHE b1030 TYR 0.029 0.002 TYR e 510 ARG 0.007 0.001 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 290 poor density : 1402 time to evaluate : 5.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7823 (ttm110) cc_final: 0.7605 (ttm110) REVERT: A 143 HIS cc_start: 0.6456 (m170) cc_final: 0.5907 (m170) REVERT: A 197 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: A 294 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6009 (pp20) REVERT: A 319 ASP cc_start: 0.6936 (t0) cc_final: 0.6580 (t70) REVERT: A 320 ASN cc_start: 0.8024 (t0) cc_final: 0.7681 (t0) REVERT: A 322 LEU cc_start: 0.7971 (mt) cc_final: 0.7723 (mp) REVERT: A 358 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7485 (mmm160) REVERT: A 473 ARG cc_start: 0.7474 (mtt90) cc_final: 0.7245 (mtt90) REVERT: A 510 GLU cc_start: 0.6669 (mp0) cc_final: 0.6298 (mp0) REVERT: A 707 LYS cc_start: 0.7620 (mmtp) cc_final: 0.7263 (mmtp) REVERT: A 740 GLN cc_start: 0.6495 (tt0) cc_final: 0.6189 (tt0) REVERT: A 953 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 1159 CYS cc_start: 0.7167 (m) cc_final: 0.6682 (m) REVERT: A 1403 ASP cc_start: 0.7013 (m-30) cc_final: 0.6497 (m-30) REVERT: A 1472 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7277 (t70) REVERT: B 198 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6402 (mt-10) REVERT: B 291 ASP cc_start: 0.7300 (t0) cc_final: 0.7096 (t70) REVERT: B 360 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7595 (mtmm) REVERT: B 384 ASP cc_start: 0.7081 (p0) cc_final: 0.6526 (p0) REVERT: B 385 ARG cc_start: 0.6755 (mtt-85) cc_final: 0.6265 (mtt-85) REVERT: B 433 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6923 (mm) REVERT: B 582 GLN cc_start: 0.7216 (tm130) cc_final: 0.6696 (tm130) REVERT: B 585 ASN cc_start: 0.7495 (m-40) cc_final: 0.6932 (m110) REVERT: B 844 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7290 (tp) REVERT: B 959 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: B 1054 MET cc_start: 0.7050 (mtm) cc_final: 0.6485 (mpp) REVERT: B 1109 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: C 62 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: C 201 GLU cc_start: 0.7319 (pm20) cc_final: 0.6990 (pm20) REVERT: C 221 ASP cc_start: 0.8187 (t0) cc_final: 0.7939 (t0) REVERT: E 50 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6784 (pp20) REVERT: E 73 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7771 (m-10) REVERT: E 129 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7559 (tm-30) REVERT: E 162 ARG cc_start: 0.7349 (tpt90) cc_final: 0.7080 (tmt-80) REVERT: E 165 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7520 (pp) REVERT: F 80 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7519 (mmm) REVERT: H 74 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5920 (tm-30) REVERT: K 26 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7560 (mtpt) REVERT: K 32 LEU cc_start: 0.7505 (mm) cc_final: 0.7295 (mt) REVERT: L 24 THR cc_start: 0.8517 (m) cc_final: 0.8200 (m) REVERT: L 55 PHE cc_start: 0.8243 (m-80) cc_final: 0.7164 (m-80) REVERT: a 35 ASP cc_start: 0.6822 (p0) cc_final: 0.6616 (p0) REVERT: a 50 ASP cc_start: 0.7771 (t0) cc_final: 0.7505 (t0) REVERT: a 65 ASP cc_start: 0.7749 (p0) cc_final: 0.7543 (p0) REVERT: a 172 ASP cc_start: 0.7923 (t0) cc_final: 0.7371 (t0) REVERT: a 174 LYS cc_start: 0.7546 (ttmm) cc_final: 0.6619 (ttmm) REVERT: a 208 ASP cc_start: 0.7190 (p0) cc_final: 0.6952 (p0) REVERT: a 265 THR cc_start: 0.8334 (p) cc_final: 0.8093 (p) REVERT: a 295 LEU cc_start: 0.7916 (tp) cc_final: 0.7604 (tt) REVERT: b 90 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6536 (tm-30) REVERT: b 129 ARG cc_start: 0.8081 (ptt-90) cc_final: 0.7783 (ptp-170) REVERT: b 314 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7746 (pp) REVERT: b 890 LEU cc_start: 0.8061 (tp) cc_final: 0.7765 (tt) REVERT: b 892 GLU cc_start: 0.6599 (pm20) cc_final: 0.6389 (pm20) REVERT: b 928 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6969 (mtm-85) REVERT: b 1102 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7501 (mmm160) REVERT: b 1130 ILE cc_start: 0.8629 (tt) cc_final: 0.8276 (pt) REVERT: g 41 SER cc_start: 0.8586 (t) cc_final: 0.8295 (t) REVERT: g 42 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7265 (mm-30) REVERT: g 45 GLN cc_start: 0.7690 (mm110) cc_final: 0.7432 (mm110) REVERT: g 74 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7651 (t) REVERT: g 128 PHE cc_start: 0.8046 (t80) cc_final: 0.7820 (t80) REVERT: g 227 TYR cc_start: 0.8364 (t80) cc_final: 0.8087 (t80) REVERT: e 533 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7042 (tm-30) REVERT: e 580 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6377 (tm130) REVERT: e 584 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6786 (mm-30) REVERT: e 641 HIS cc_start: 0.7673 (t-170) cc_final: 0.7373 (t-170) REVERT: e 660 LEU cc_start: 0.7955 (mp) cc_final: 0.7730 (mp) REVERT: e 704 MET cc_start: 0.7933 (mmm) cc_final: 0.7722 (mmp) REVERT: e 789 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6570 (pp) REVERT: e 867 MET cc_start: 0.7280 (tpt) cc_final: 0.6355 (tpt) REVERT: e 876 ARG cc_start: 0.6781 (mmt-90) cc_final: 0.6532 (mmt180) REVERT: e 933 ASP cc_start: 0.6848 (p0) cc_final: 0.6389 (p0) REVERT: e 963 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7655 (tp) REVERT: e 997 LYS cc_start: 0.6964 (tmtt) cc_final: 0.6657 (tmtt) REVERT: e 1268 HIS cc_start: 0.8129 (t70) cc_final: 0.7870 (t70) REVERT: d 10 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6754 (tm-30) REVERT: d 23 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7082 (mt-10) REVERT: d 24 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7362 (mmtt) REVERT: d 26 LYS cc_start: 0.8462 (mttt) cc_final: 0.8042 (mttt) REVERT: d 36 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7262 (mt-10) REVERT: d 118 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6468 (mp0) REVERT: d 120 TRP cc_start: 0.8263 (m-10) cc_final: 0.8049 (m100) REVERT: d 129 LYS cc_start: 0.7802 (mttt) cc_final: 0.7573 (mttm) REVERT: d 671 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7408 (mtm110) outliers start: 290 outliers final: 214 residues processed: 1555 average time/residue: 0.6934 time to fit residues: 1725.8285 Evaluate side-chains 1617 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 1383 time to evaluate : 5.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1242 ASP Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 128 ASP Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 362 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 301 ARG Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 314 LEU Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 720 SER Chi-restraints excluded: chain b residue 737 SER Chi-restraints excluded: chain b residue 765 VAL Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 808 LEU Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1065 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 223 LEU Chi-restraints excluded: chain g residue 233 ILE Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 539 THR Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 580 GLN Chi-restraints excluded: chain e residue 582 VAL Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 796 PHE Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 909 VAL Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 924 THR Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 963 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1251 VAL Chi-restraints excluded: chain e residue 1259 SER Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 126 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.5980 chunk 543 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 603 optimal weight: 0.1980 chunk 501 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 316 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 287 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN H 126 GLN K 69 HIS a 33 ASN ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN e 772 GLN e 790 ASN ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 53160 Z= 0.200 Angle : 0.557 21.378 72250 Z= 0.289 Chirality : 0.043 0.161 8055 Planarity : 0.004 0.048 8982 Dihedral : 13.068 174.092 7983 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.73 % Allowed : 25.61 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 6148 helix: 1.23 (0.12), residues: 2032 sheet: -0.30 (0.15), residues: 1178 loop : -0.74 (0.11), residues: 2938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b1047 HIS 0.008 0.001 HIS a 229 PHE 0.024 0.001 PHE B 309 TYR 0.025 0.001 TYR e 510 ARG 0.008 0.000 ARG a 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 1393 time to evaluate : 5.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7151 (ttm-80) REVERT: A 108 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7574 (ttm110) REVERT: A 143 HIS cc_start: 0.6429 (m170) cc_final: 0.5906 (m170) REVERT: A 197 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5963 (mp0) REVERT: A 244 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7111 (mtp85) REVERT: A 246 GLU cc_start: 0.7412 (pm20) cc_final: 0.7000 (pm20) REVERT: A 294 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5968 (pp20) REVERT: A 319 ASP cc_start: 0.6941 (t0) cc_final: 0.6606 (t70) REVERT: A 322 LEU cc_start: 0.7979 (mt) cc_final: 0.7734 (mp) REVERT: A 358 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7461 (mmm160) REVERT: A 360 ASP cc_start: 0.6932 (m-30) cc_final: 0.6545 (m-30) REVERT: A 408 ARG cc_start: 0.7367 (tpp80) cc_final: 0.6467 (ttp80) REVERT: A 473 ARG cc_start: 0.7502 (mtt90) cc_final: 0.7255 (mtt90) REVERT: A 483 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7466 (mpt180) REVERT: A 707 LYS cc_start: 0.7530 (mmtp) cc_final: 0.7175 (mmtp) REVERT: A 733 LEU cc_start: 0.7354 (tt) cc_final: 0.7122 (tt) REVERT: A 740 GLN cc_start: 0.6483 (tt0) cc_final: 0.6150 (tt0) REVERT: A 953 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6671 (mm-30) REVERT: A 1159 CYS cc_start: 0.7144 (m) cc_final: 0.6650 (m) REVERT: A 1403 ASP cc_start: 0.6977 (m-30) cc_final: 0.6443 (m-30) REVERT: A 1472 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7270 (t70) REVERT: B 53 MET cc_start: 0.6950 (mpp) cc_final: 0.6711 (mpp) REVERT: B 198 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6425 (mt-10) REVERT: B 291 ASP cc_start: 0.7275 (t0) cc_final: 0.7057 (t70) REVERT: B 384 ASP cc_start: 0.7057 (p0) cc_final: 0.6599 (p0) REVERT: B 385 ARG cc_start: 0.6725 (mtt-85) cc_final: 0.6177 (mtt-85) REVERT: B 433 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6900 (mm) REVERT: B 552 ASN cc_start: 0.7372 (m-40) cc_final: 0.7139 (m110) REVERT: B 557 SER cc_start: 0.8492 (p) cc_final: 0.8225 (p) REVERT: B 582 GLN cc_start: 0.7260 (tm130) cc_final: 0.6732 (tm130) REVERT: B 585 ASN cc_start: 0.7481 (m-40) cc_final: 0.6923 (m110) REVERT: B 844 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7254 (tp) REVERT: B 1010 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7611 (mttp) REVERT: B 1054 MET cc_start: 0.7061 (mtm) cc_final: 0.6568 (mpp) REVERT: B 1109 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 1150 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.7257 (mtp-110) REVERT: C 62 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: C 94 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6567 (p) REVERT: C 201 GLU cc_start: 0.7295 (pm20) cc_final: 0.6999 (pm20) REVERT: E 50 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6756 (pp20) REVERT: E 73 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: E 129 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 162 ARG cc_start: 0.7312 (tpt90) cc_final: 0.7023 (tmt-80) REVERT: H 42 ASP cc_start: 0.7390 (m-30) cc_final: 0.7145 (m-30) REVERT: K 26 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7477 (mtpt) REVERT: L 24 THR cc_start: 0.8543 (m) cc_final: 0.8223 (m) REVERT: L 55 PHE cc_start: 0.8259 (m-80) cc_final: 0.7043 (m-80) REVERT: a 33 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7045 (m-40) REVERT: a 35 ASP cc_start: 0.6767 (p0) cc_final: 0.6555 (p0) REVERT: a 50 ASP cc_start: 0.7670 (t0) cc_final: 0.7451 (t0) REVERT: a 65 ASP cc_start: 0.7669 (p0) cc_final: 0.7456 (p0) REVERT: a 118 SER cc_start: 0.8231 (m) cc_final: 0.7959 (t) REVERT: a 172 ASP cc_start: 0.7897 (t0) cc_final: 0.7474 (t0) REVERT: a 174 LYS cc_start: 0.7545 (ttmm) cc_final: 0.6558 (ttmm) REVERT: a 265 THR cc_start: 0.8217 (p) cc_final: 0.8006 (p) REVERT: a 295 LEU cc_start: 0.7892 (tp) cc_final: 0.7603 (tt) REVERT: a 346 PHE cc_start: 0.8102 (m-80) cc_final: 0.7843 (m-80) REVERT: b 1 MET cc_start: 0.5656 (mmm) cc_final: 0.5410 (mmm) REVERT: b 90 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6428 (tm-30) REVERT: b 129 ARG cc_start: 0.8102 (ptt-90) cc_final: 0.7787 (ptp-170) REVERT: b 726 TYR cc_start: 0.7603 (t80) cc_final: 0.7333 (t80) REVERT: b 890 LEU cc_start: 0.7988 (tp) cc_final: 0.7635 (tt) REVERT: b 898 GLU cc_start: 0.6801 (tp30) cc_final: 0.6453 (tp30) REVERT: b 928 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7258 (mmm-85) REVERT: b 943 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6745 (tm-30) REVERT: b 1130 ILE cc_start: 0.8630 (tt) cc_final: 0.8282 (pt) REVERT: g 41 SER cc_start: 0.8580 (t) cc_final: 0.8225 (t) REVERT: g 42 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7111 (mm-30) REVERT: g 45 GLN cc_start: 0.7622 (mm110) cc_final: 0.7315 (mm110) REVERT: g 74 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7545 (t) REVERT: g 128 PHE cc_start: 0.8037 (t80) cc_final: 0.7805 (t80) REVERT: g 227 TYR cc_start: 0.8276 (t80) cc_final: 0.7994 (t80) REVERT: e 533 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7028 (tm-30) REVERT: e 580 GLN cc_start: 0.6605 (tm130) cc_final: 0.6290 (tm130) REVERT: e 584 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6736 (mm-30) REVERT: e 641 HIS cc_start: 0.7640 (t-170) cc_final: 0.7323 (t-170) REVERT: e 660 LEU cc_start: 0.7962 (mp) cc_final: 0.7741 (mp) REVERT: e 704 MET cc_start: 0.7875 (mmm) cc_final: 0.7674 (mmp) REVERT: e 789 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6571 (pp) REVERT: e 841 MET cc_start: 0.7237 (mmp) cc_final: 0.6915 (mmp) REVERT: e 847 LEU cc_start: 0.7685 (mt) cc_final: 0.7410 (mp) REVERT: e 867 MET cc_start: 0.7179 (tpt) cc_final: 0.6314 (tpt) REVERT: e 876 ARG cc_start: 0.6730 (mmt-90) cc_final: 0.6499 (mmt180) REVERT: e 914 THR cc_start: 0.7247 (p) cc_final: 0.6926 (t) REVERT: e 933 ASP cc_start: 0.6690 (p0) cc_final: 0.6279 (p0) REVERT: e 939 SER cc_start: 0.8071 (m) cc_final: 0.7710 (p) REVERT: e 960 TYR cc_start: 0.7204 (m-80) cc_final: 0.6721 (m-10) REVERT: e 985 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7631 (ttm110) REVERT: e 1268 HIS cc_start: 0.8100 (t70) cc_final: 0.7813 (t70) REVERT: d 10 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6744 (tm-30) REVERT: d 23 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7186 (mt-10) REVERT: d 26 LYS cc_start: 0.8480 (mttt) cc_final: 0.8086 (mttt) REVERT: d 36 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7189 (mt-10) REVERT: d 115 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7392 (mtm110) REVERT: d 118 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6450 (mp0) REVERT: d 120 TRP cc_start: 0.8278 (m-10) cc_final: 0.8035 (m100) REVERT: d 671 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7409 (mtm110) outliers start: 260 outliers final: 191 residues processed: 1544 average time/residue: 0.7153 time to fit residues: 1770.6260 Evaluate side-chains 1583 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1374 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1242 ASP Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1014 MET Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1065 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 233 ILE Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 539 THR Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 699 THR Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 772 GLN Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 838 SER Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 909 VAL Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 924 THR Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 1004 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 115 ARG Chi-restraints excluded: chain d residue 126 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 343 optimal weight: 1.9990 chunk 440 optimal weight: 0.0050 chunk 341 optimal weight: 3.9990 chunk 508 optimal weight: 0.9980 chunk 337 optimal weight: 0.7980 chunk 601 optimal weight: 8.9990 chunk 376 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN G 60 GLN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 976 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 53160 Z= 0.259 Angle : 0.573 21.307 72250 Z= 0.298 Chirality : 0.044 0.172 8055 Planarity : 0.004 0.048 8982 Dihedral : 13.077 174.322 7983 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.00 % Allowed : 25.70 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6148 helix: 1.24 (0.12), residues: 2022 sheet: -0.31 (0.15), residues: 1182 loop : -0.75 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP e 851 HIS 0.008 0.001 HIS a 229 PHE 0.022 0.001 PHE B 309 TYR 0.023 0.001 TYR e 510 ARG 0.009 0.000 ARG B 812 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 1384 time to evaluate : 5.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7161 (ttm-80) REVERT: A 22 GLN cc_start: 0.7854 (tp40) cc_final: 0.7614 (tp-100) REVERT: A 108 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7581 (ttm110) REVERT: A 143 HIS cc_start: 0.6431 (m170) cc_final: 0.5909 (m170) REVERT: A 197 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: A 244 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6864 (ttt-90) REVERT: A 246 GLU cc_start: 0.7431 (pm20) cc_final: 0.7231 (pm20) REVERT: A 294 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5967 (pp20) REVERT: A 319 ASP cc_start: 0.6942 (t0) cc_final: 0.6594 (t70) REVERT: A 322 LEU cc_start: 0.7987 (mt) cc_final: 0.7749 (mp) REVERT: A 358 ARG cc_start: 0.7774 (mmt-90) cc_final: 0.7462 (mmm160) REVERT: A 360 ASP cc_start: 0.6911 (m-30) cc_final: 0.6583 (m-30) REVERT: A 473 ARG cc_start: 0.7508 (mtt90) cc_final: 0.7263 (mtt90) REVERT: A 483 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7478 (mpt180) REVERT: A 510 GLU cc_start: 0.6637 (mp0) cc_final: 0.6288 (mp0) REVERT: A 707 LYS cc_start: 0.7601 (mmtp) cc_final: 0.7196 (mmtp) REVERT: A 733 LEU cc_start: 0.7377 (tt) cc_final: 0.7129 (tt) REVERT: A 740 GLN cc_start: 0.6484 (tt0) cc_final: 0.6187 (tt0) REVERT: A 953 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6761 (mm-30) REVERT: A 960 ARG cc_start: 0.7219 (ttp80) cc_final: 0.7008 (ttp80) REVERT: A 1159 CYS cc_start: 0.7264 (m) cc_final: 0.6785 (m) REVERT: A 1403 ASP cc_start: 0.6980 (m-30) cc_final: 0.6400 (m-30) REVERT: A 1472 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7262 (t70) REVERT: B 37 LYS cc_start: 0.7425 (mptt) cc_final: 0.7035 (mmtp) REVERT: B 198 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6413 (mt-10) REVERT: B 281 ASP cc_start: 0.6747 (t70) cc_final: 0.6477 (t70) REVERT: B 291 ASP cc_start: 0.7289 (t0) cc_final: 0.6871 (t0) REVERT: B 360 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7566 (mtmm) REVERT: B 384 ASP cc_start: 0.7029 (p0) cc_final: 0.6579 (p0) REVERT: B 385 ARG cc_start: 0.6719 (mtt-85) cc_final: 0.6161 (mtt-85) REVERT: B 433 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6945 (mm) REVERT: B 552 ASN cc_start: 0.7386 (m-40) cc_final: 0.7139 (m110) REVERT: B 582 GLN cc_start: 0.7231 (tm130) cc_final: 0.6670 (tm130) REVERT: B 585 ASN cc_start: 0.7489 (m-40) cc_final: 0.6933 (m110) REVERT: B 844 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7290 (tp) REVERT: B 1010 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7617 (mttp) REVERT: B 1054 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6537 (mpp) REVERT: B 1109 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: B 1150 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7321 (mtp-110) REVERT: C 62 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: C 94 CYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6588 (p) REVERT: C 201 GLU cc_start: 0.7302 (pm20) cc_final: 0.6999 (pm20) REVERT: E 50 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6763 (pp20) REVERT: E 73 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7754 (m-10) REVERT: E 129 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7579 (tm-30) REVERT: H 42 ASP cc_start: 0.7391 (m-30) cc_final: 0.7138 (m-30) REVERT: H 100 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6675 (mt-10) REVERT: H 102 ASP cc_start: 0.7393 (p0) cc_final: 0.7185 (p0) REVERT: K 26 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: L 24 THR cc_start: 0.8524 (m) cc_final: 0.8196 (m) REVERT: L 41 TYR cc_start: 0.8196 (t80) cc_final: 0.7959 (t80) REVERT: L 55 PHE cc_start: 0.8253 (m-80) cc_final: 0.7103 (m-80) REVERT: f 57 PHE cc_start: 0.7702 (t80) cc_final: 0.7166 (t80) REVERT: a 50 ASP cc_start: 0.7703 (t0) cc_final: 0.7454 (t0) REVERT: a 65 ASP cc_start: 0.7686 (p0) cc_final: 0.7472 (p0) REVERT: a 172 ASP cc_start: 0.7905 (t0) cc_final: 0.7499 (t0) REVERT: a 174 LYS cc_start: 0.7546 (ttmm) cc_final: 0.6584 (ttmm) REVERT: a 265 THR cc_start: 0.8239 (p) cc_final: 0.8015 (p) REVERT: b 726 TYR cc_start: 0.7588 (t80) cc_final: 0.7292 (t80) REVERT: b 890 LEU cc_start: 0.8001 (tp) cc_final: 0.7745 (tt) REVERT: b 898 GLU cc_start: 0.6855 (tp30) cc_final: 0.6519 (tp30) REVERT: b 928 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6933 (mtm-85) REVERT: b 943 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6747 (tm-30) REVERT: b 1083 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7082 (mt-10) REVERT: b 1130 ILE cc_start: 0.8628 (tt) cc_final: 0.8270 (pt) REVERT: g 41 SER cc_start: 0.8583 (t) cc_final: 0.8222 (t) REVERT: g 42 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7157 (mm-30) REVERT: g 45 GLN cc_start: 0.7619 (mm110) cc_final: 0.7321 (mm110) REVERT: g 74 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7592 (t) REVERT: g 128 PHE cc_start: 0.8066 (t80) cc_final: 0.7828 (t80) REVERT: g 174 TRP cc_start: 0.7022 (m-90) cc_final: 0.6697 (m-90) REVERT: g 227 TYR cc_start: 0.8315 (t80) cc_final: 0.8043 (t80) REVERT: e 494 ASP cc_start: 0.3965 (OUTLIER) cc_final: 0.3761 (p0) REVERT: e 580 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.6295 (tm130) REVERT: e 584 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6754 (mm-30) REVERT: e 641 HIS cc_start: 0.7644 (t-170) cc_final: 0.7309 (t-170) REVERT: e 660 LEU cc_start: 0.7967 (mp) cc_final: 0.7753 (mp) REVERT: e 704 MET cc_start: 0.7908 (mmm) cc_final: 0.7705 (mmp) REVERT: e 747 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6981 (mttp) REVERT: e 800 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8254 (mm) REVERT: e 804 LYS cc_start: 0.7812 (mttt) cc_final: 0.7588 (mttt) REVERT: e 876 ARG cc_start: 0.6738 (mmt-90) cc_final: 0.6499 (mmt180) REVERT: e 914 THR cc_start: 0.7261 (p) cc_final: 0.6923 (t) REVERT: e 933 ASP cc_start: 0.6846 (p0) cc_final: 0.6417 (p0) REVERT: e 939 SER cc_start: 0.8108 (m) cc_final: 0.7685 (p) REVERT: e 985 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7652 (ttm110) REVERT: d 10 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6761 (tm-30) REVERT: d 23 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7630 (mt-10) REVERT: d 33 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6941 (mtpp) REVERT: d 36 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7161 (mt-10) REVERT: d 115 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7434 (mtm110) REVERT: d 118 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6621 (mp0) REVERT: d 120 TRP cc_start: 0.8286 (m-10) cc_final: 0.8030 (m100) REVERT: d 129 LYS cc_start: 0.7655 (mttt) cc_final: 0.7342 (mttm) REVERT: d 671 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7425 (mtm110) outliers start: 275 outliers final: 216 residues processed: 1545 average time/residue: 0.7662 time to fit residues: 1917.9151 Evaluate side-chains 1605 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1366 time to evaluate : 5.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1324 GLU Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 195 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 362 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 218 MET Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 256 SER Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 735 VAL Chi-restraints excluded: chain b residue 765 VAL Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 808 LEU Chi-restraints excluded: chain b residue 809 GLN Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1014 MET Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1065 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 233 ILE Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 494 ASP Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 580 GLN Chi-restraints excluded: chain e residue 582 VAL Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 689 PHE Chi-restraints excluded: chain e residue 699 THR Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 800 ILE Chi-restraints excluded: chain e residue 838 SER Chi-restraints excluded: chain e residue 858 VAL Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 909 VAL Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 924 THR Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 1004 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1259 SER Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 115 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 409 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 472 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A1310 HIS B 287 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 854 GLN ** e1268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 53160 Z= 0.298 Angle : 0.596 21.467 72250 Z= 0.309 Chirality : 0.045 0.280 8055 Planarity : 0.004 0.052 8982 Dihedral : 13.096 174.299 7981 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.03 % Allowed : 25.86 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 6148 helix: 1.19 (0.12), residues: 2022 sheet: -0.35 (0.15), residues: 1180 loop : -0.78 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b1047 HIS 0.008 0.001 HIS a 229 PHE 0.023 0.002 PHE b1030 TYR 0.023 0.002 TYR e 510 ARG 0.010 0.000 ARG B 812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 1392 time to evaluate : 5.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7176 (ttm110) REVERT: A 22 GLN cc_start: 0.7873 (tp40) cc_final: 0.7639 (tp-100) REVERT: A 108 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7585 (ttm110) REVERT: A 117 LEU cc_start: 0.8159 (tp) cc_final: 0.7959 (tt) REVERT: A 143 HIS cc_start: 0.6417 (m170) cc_final: 0.5930 (m170) REVERT: A 197 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: A 244 ARG cc_start: 0.7430 (mtp85) cc_final: 0.6828 (ttt-90) REVERT: A 246 GLU cc_start: 0.7462 (pm20) cc_final: 0.7197 (pm20) REVERT: A 294 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5897 (pp20) REVERT: A 319 ASP cc_start: 0.6914 (t0) cc_final: 0.6576 (t70) REVERT: A 320 ASN cc_start: 0.7996 (t0) cc_final: 0.7735 (t0) REVERT: A 322 LEU cc_start: 0.7998 (mt) cc_final: 0.7773 (mp) REVERT: A 358 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7430 (mmm160) REVERT: A 360 ASP cc_start: 0.6925 (m-30) cc_final: 0.6596 (m-30) REVERT: A 473 ARG cc_start: 0.7510 (mtt90) cc_final: 0.7261 (mtt90) REVERT: A 483 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7444 (mpt180) REVERT: A 510 GLU cc_start: 0.6629 (mp0) cc_final: 0.6268 (mp0) REVERT: A 707 LYS cc_start: 0.7592 (mmtp) cc_final: 0.7151 (mmtp) REVERT: A 733 LEU cc_start: 0.7403 (tt) cc_final: 0.7140 (tt) REVERT: A 740 GLN cc_start: 0.6494 (tt0) cc_final: 0.6201 (tt0) REVERT: A 953 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6781 (mm-30) REVERT: A 1011 GLU cc_start: 0.7056 (mp0) cc_final: 0.6827 (mp0) REVERT: A 1159 CYS cc_start: 0.7268 (m) cc_final: 0.6805 (m) REVERT: A 1403 ASP cc_start: 0.7020 (m-30) cc_final: 0.6444 (m-30) REVERT: A 1472 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7266 (t70) REVERT: B 37 LYS cc_start: 0.7481 (mptt) cc_final: 0.7259 (mptt) REVERT: B 198 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6374 (mt-10) REVERT: B 281 ASP cc_start: 0.6766 (t70) cc_final: 0.6518 (t70) REVERT: B 291 ASP cc_start: 0.7297 (t0) cc_final: 0.6872 (t0) REVERT: B 360 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7577 (mtmm) REVERT: B 384 ASP cc_start: 0.7013 (p0) cc_final: 0.6568 (p0) REVERT: B 385 ARG cc_start: 0.6722 (mtt-85) cc_final: 0.6150 (mtt-85) REVERT: B 433 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6948 (mm) REVERT: B 552 ASN cc_start: 0.7380 (m-40) cc_final: 0.7139 (m110) REVERT: B 582 GLN cc_start: 0.7241 (tm130) cc_final: 0.6658 (tm130) REVERT: B 585 ASN cc_start: 0.7497 (m-40) cc_final: 0.6937 (m110) REVERT: B 844 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7289 (tp) REVERT: B 1010 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7614 (mttp) REVERT: B 1054 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6562 (mpp) REVERT: B 1109 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: C 27 ASP cc_start: 0.7132 (m-30) cc_final: 0.6761 (m-30) REVERT: C 62 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: C 94 CYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6636 (p) REVERT: C 201 GLU cc_start: 0.7317 (pm20) cc_final: 0.7012 (pm20) REVERT: E 30 GLN cc_start: 0.7476 (tp-100) cc_final: 0.7187 (tp40) REVERT: E 50 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6759 (pp20) REVERT: E 73 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: E 129 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7549 (tm-30) REVERT: E 162 ARG cc_start: 0.7302 (tpt90) cc_final: 0.7020 (tmt-80) REVERT: E 177 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7741 (t70) REVERT: H 100 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6709 (mt-10) REVERT: H 102 ASP cc_start: 0.7357 (p0) cc_final: 0.7144 (p0) REVERT: K 26 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7490 (mtpt) REVERT: L 24 THR cc_start: 0.8525 (m) cc_final: 0.8187 (m) REVERT: L 41 TYR cc_start: 0.8199 (t80) cc_final: 0.7961 (t80) REVERT: L 55 PHE cc_start: 0.8248 (m-80) cc_final: 0.7521 (m-80) REVERT: f 57 PHE cc_start: 0.7700 (t80) cc_final: 0.7170 (t80) REVERT: a 36 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7032 (mtm180) REVERT: a 50 ASP cc_start: 0.7794 (t0) cc_final: 0.7477 (t0) REVERT: a 65 ASP cc_start: 0.7719 (p0) cc_final: 0.7501 (p0) REVERT: a 172 ASP cc_start: 0.7889 (t0) cc_final: 0.7470 (t0) REVERT: a 178 CYS cc_start: 0.7497 (t) cc_final: 0.7175 (t) REVERT: a 208 ASP cc_start: 0.7176 (p0) cc_final: 0.6910 (p0) REVERT: a 265 THR cc_start: 0.8256 (p) cc_final: 0.8003 (p) REVERT: b 64 MET cc_start: 0.7444 (ptm) cc_final: 0.7214 (ptm) REVERT: b 129 ARG cc_start: 0.8143 (ptt-90) cc_final: 0.7846 (ptp-170) REVERT: b 314 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7723 (pp) REVERT: b 890 LEU cc_start: 0.8008 (tp) cc_final: 0.7672 (tt) REVERT: b 898 GLU cc_start: 0.6847 (tp30) cc_final: 0.6531 (tp30) REVERT: b 928 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6964 (mmm-85) REVERT: b 943 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6729 (tm-30) REVERT: b 989 ARG cc_start: 0.7747 (ptp-110) cc_final: 0.7416 (ptp90) REVERT: b 1083 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7096 (mt-10) REVERT: b 1130 ILE cc_start: 0.8619 (tt) cc_final: 0.8270 (pt) REVERT: g 41 SER cc_start: 0.8563 (t) cc_final: 0.8143 (t) REVERT: g 42 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7155 (mm-30) REVERT: g 45 GLN cc_start: 0.7625 (mm110) cc_final: 0.7330 (mm110) REVERT: g 74 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7591 (t) REVERT: g 128 PHE cc_start: 0.8047 (t80) cc_final: 0.7823 (t80) REVERT: g 227 TYR cc_start: 0.8335 (t80) cc_final: 0.8068 (t80) REVERT: e 494 ASP cc_start: 0.4006 (OUTLIER) cc_final: 0.3783 (p0) REVERT: e 580 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.6298 (tm130) REVERT: e 584 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6744 (mm-30) REVERT: e 641 HIS cc_start: 0.7644 (t-170) cc_final: 0.7311 (t-170) REVERT: e 660 LEU cc_start: 0.7981 (mp) cc_final: 0.7763 (mp) REVERT: e 704 MET cc_start: 0.7879 (mmm) cc_final: 0.7632 (mmp) REVERT: e 747 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6960 (mttp) REVERT: e 789 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6780 (pp) REVERT: e 799 LEU cc_start: 0.8179 (mt) cc_final: 0.7966 (mt) REVERT: e 804 LYS cc_start: 0.7781 (mttt) cc_final: 0.7458 (mttt) REVERT: e 829 GLU cc_start: 0.5742 (tm-30) cc_final: 0.4917 (tm-30) REVERT: e 847 LEU cc_start: 0.7653 (mt) cc_final: 0.7397 (mp) REVERT: e 867 MET cc_start: 0.7282 (tpt) cc_final: 0.6238 (tpt) REVERT: e 876 ARG cc_start: 0.6763 (mmt-90) cc_final: 0.6528 (mmt180) REVERT: e 914 THR cc_start: 0.7307 (p) cc_final: 0.6948 (t) REVERT: e 933 ASP cc_start: 0.6886 (p0) cc_final: 0.6443 (p0) REVERT: e 939 SER cc_start: 0.8099 (m) cc_final: 0.7682 (p) REVERT: e 960 TYR cc_start: 0.7128 (m-80) cc_final: 0.6732 (m-10) REVERT: d 10 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6806 (tm-30) REVERT: d 23 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7645 (mt-10) REVERT: d 33 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7180 (mtpp) REVERT: d 36 GLU cc_start: 0.7728 (mt-10) cc_final: 0.6979 (mt-10) REVERT: d 115 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7523 (mtm110) REVERT: d 120 TRP cc_start: 0.8288 (m-10) cc_final: 0.8027 (m100) REVERT: d 129 LYS cc_start: 0.7705 (mttt) cc_final: 0.7485 (mttm) REVERT: d 671 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7473 (mtm110) outliers start: 277 outliers final: 223 residues processed: 1550 average time/residue: 0.7547 time to fit residues: 1897.9554 Evaluate side-chains 1623 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 1374 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 36 ARG Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 195 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 362 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 218 MET Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 256 SER Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 314 LEU Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 735 VAL Chi-restraints excluded: chain b residue 765 VAL Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 808 LEU Chi-restraints excluded: chain b residue 809 GLN Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1014 MET Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1065 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 233 ILE Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 494 ASP Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 580 GLN Chi-restraints excluded: chain e residue 582 VAL Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 689 PHE Chi-restraints excluded: chain e residue 699 THR Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 838 SER Chi-restraints excluded: chain e residue 854 GLN Chi-restraints excluded: chain e residue 858 VAL Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 909 VAL Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 924 THR Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 1004 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1259 SER Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 115 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 0.1980 chunk 576 optimal weight: 1.9990 chunk 525 optimal weight: 0.9980 chunk 560 optimal weight: 1.9990 chunk 337 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 440 optimal weight: 0.0060 chunk 171 optimal weight: 2.9990 chunk 506 optimal weight: 0.9980 chunk 530 optimal weight: 6.9990 chunk 558 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A1310 HIS B 287 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 525 GLN e 669 HIS ** e 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 854 GLN ** e1268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 53160 Z= 0.183 Angle : 0.569 21.030 72250 Z= 0.293 Chirality : 0.043 0.212 8055 Planarity : 0.004 0.047 8982 Dihedral : 13.011 173.726 7981 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.42 % Allowed : 26.63 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 6148 helix: 1.29 (0.12), residues: 2044 sheet: -0.23 (0.15), residues: 1148 loop : -0.74 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP e 851 HIS 0.008 0.001 HIS a 229 PHE 0.019 0.001 PHE B 320 TYR 0.022 0.001 TYR e 510 ARG 0.011 0.000 ARG B1150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1616 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1373 time to evaluate : 5.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7145 (ttm-80) REVERT: A 22 GLN cc_start: 0.7791 (tp40) cc_final: 0.7523 (tp-100) REVERT: A 108 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7574 (ttm110) REVERT: A 143 HIS cc_start: 0.6369 (m170) cc_final: 0.5880 (m170) REVERT: A 197 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5899 (mp0) REVERT: A 244 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6778 (ttt-90) REVERT: A 246 GLU cc_start: 0.7472 (pm20) cc_final: 0.7120 (pm20) REVERT: A 294 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5874 (pp20) REVERT: A 317 MET cc_start: 0.7795 (ttp) cc_final: 0.7583 (ttt) REVERT: A 320 ASN cc_start: 0.7946 (t0) cc_final: 0.7619 (t0) REVERT: A 322 LEU cc_start: 0.7991 (mt) cc_final: 0.7746 (mp) REVERT: A 358 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.7393 (mmm160) REVERT: A 360 ASP cc_start: 0.6933 (m-30) cc_final: 0.6526 (m-30) REVERT: A 473 ARG cc_start: 0.7512 (mtt90) cc_final: 0.7264 (mtt90) REVERT: A 483 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7487 (mpt180) REVERT: A 707 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7102 (mmtp) REVERT: A 733 LEU cc_start: 0.7373 (tt) cc_final: 0.7139 (tt) REVERT: A 798 ILE cc_start: 0.7472 (mm) cc_final: 0.7218 (mm) REVERT: A 953 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6768 (mm-30) REVERT: A 1011 GLU cc_start: 0.7009 (mp0) cc_final: 0.6767 (mp0) REVERT: A 1159 CYS cc_start: 0.7268 (m) cc_final: 0.6792 (m) REVERT: A 1403 ASP cc_start: 0.7008 (m-30) cc_final: 0.6444 (m-30) REVERT: A 1472 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7254 (t70) REVERT: B 16 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6729 (mm-30) REVERT: B 160 TYR cc_start: 0.7455 (m-80) cc_final: 0.7056 (m-80) REVERT: B 198 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6374 (mt-10) REVERT: B 281 ASP cc_start: 0.6683 (t70) cc_final: 0.6444 (t70) REVERT: B 291 ASP cc_start: 0.7277 (t0) cc_final: 0.7045 (t70) REVERT: B 385 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.6109 (mtt-85) REVERT: B 433 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6927 (mm) REVERT: B 552 ASN cc_start: 0.7328 (m-40) cc_final: 0.7084 (m110) REVERT: B 582 GLN cc_start: 0.7226 (tm130) cc_final: 0.6634 (tm130) REVERT: B 585 ASN cc_start: 0.7490 (m-40) cc_final: 0.6927 (m110) REVERT: B 844 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7263 (tp) REVERT: B 1010 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7633 (mttp) REVERT: B 1054 MET cc_start: 0.6993 (mtm) cc_final: 0.6581 (mpp) REVERT: B 1109 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: C 27 ASP cc_start: 0.7074 (m-30) cc_final: 0.6765 (m-30) REVERT: C 62 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: C 94 CYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6513 (p) REVERT: C 164 TYR cc_start: 0.8112 (m-80) cc_final: 0.7019 (m-80) REVERT: C 201 GLU cc_start: 0.7279 (pm20) cc_final: 0.6963 (pm20) REVERT: E 50 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6760 (pp20) REVERT: E 73 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: E 129 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7549 (tm-30) REVERT: E 165 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7481 (pp) REVERT: E 177 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (t70) REVERT: H 42 ASP cc_start: 0.7362 (m-30) cc_final: 0.7103 (m-30) REVERT: H 100 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6703 (mt-10) REVERT: H 102 ASP cc_start: 0.7354 (p0) cc_final: 0.7116 (p0) REVERT: K 26 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7469 (mtpt) REVERT: L 24 THR cc_start: 0.8508 (m) cc_final: 0.8178 (m) REVERT: L 41 TYR cc_start: 0.8181 (t80) cc_final: 0.7949 (t80) REVERT: L 55 PHE cc_start: 0.8269 (m-80) cc_final: 0.7060 (m-80) REVERT: f 28 PHE cc_start: 0.8542 (m-80) cc_final: 0.8294 (m-80) REVERT: f 45 THR cc_start: 0.8464 (t) cc_final: 0.8127 (m) REVERT: a 36 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7208 (mtm180) REVERT: a 65 ASP cc_start: 0.7631 (p0) cc_final: 0.7425 (p0) REVERT: a 124 LEU cc_start: 0.8036 (tp) cc_final: 0.7718 (tt) REVERT: b 129 ARG cc_start: 0.8126 (ptt-90) cc_final: 0.7840 (ptp-170) REVERT: b 314 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7738 (pp) REVERT: b 890 LEU cc_start: 0.7963 (tp) cc_final: 0.7636 (tt) REVERT: b 898 GLU cc_start: 0.6822 (tp30) cc_final: 0.6511 (tp30) REVERT: b 928 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6921 (mmm-85) REVERT: b 943 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6732 (tm-30) REVERT: b 989 ARG cc_start: 0.7721 (ptp-110) cc_final: 0.7313 (ptp-110) REVERT: b 1130 ILE cc_start: 0.8644 (tt) cc_final: 0.8269 (pt) REVERT: g 41 SER cc_start: 0.8556 (t) cc_final: 0.7988 (t) REVERT: g 42 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7213 (mm-30) REVERT: g 74 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7436 (t) REVERT: g 128 PHE cc_start: 0.8037 (t80) cc_final: 0.7813 (t80) REVERT: g 227 TYR cc_start: 0.8265 (t80) cc_final: 0.7998 (t80) REVERT: g 248 LEU cc_start: 0.8303 (tp) cc_final: 0.8020 (tp) REVERT: e 494 ASP cc_start: 0.3957 (OUTLIER) cc_final: 0.3720 (p0) REVERT: e 580 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6248 (tm130) REVERT: e 584 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6730 (mm-30) REVERT: e 641 HIS cc_start: 0.7641 (t-170) cc_final: 0.7329 (t-170) REVERT: e 653 ASN cc_start: 0.8074 (t0) cc_final: 0.7819 (t0) REVERT: e 704 MET cc_start: 0.7878 (mmm) cc_final: 0.7591 (mmp) REVERT: e 747 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7102 (mttp) REVERT: e 789 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6827 (pp) REVERT: e 866 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6741 (mm-40) REVERT: e 867 MET cc_start: 0.7219 (tpt) cc_final: 0.6250 (tpt) REVERT: e 914 THR cc_start: 0.7275 (p) cc_final: 0.6924 (t) REVERT: e 933 ASP cc_start: 0.6882 (p0) cc_final: 0.6433 (p0) REVERT: e 937 ASN cc_start: 0.7972 (t0) cc_final: 0.7649 (m-40) REVERT: e 939 SER cc_start: 0.7975 (m) cc_final: 0.7583 (p) REVERT: e 960 TYR cc_start: 0.7015 (m-80) cc_final: 0.6668 (m-10) REVERT: e 985 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7505 (ttm110) REVERT: d 10 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6793 (tm-30) REVERT: d 23 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7583 (mt-10) REVERT: d 115 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7478 (mtm110) REVERT: d 120 TRP cc_start: 0.8308 (m-10) cc_final: 0.7961 (m100) REVERT: d 671 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7553 (mtm110) outliers start: 243 outliers final: 201 residues processed: 1513 average time/residue: 0.7072 time to fit residues: 1714.8517 Evaluate side-chains 1584 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 1359 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 36 ARG Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 362 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 218 MET Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 253 ILE Chi-restraints excluded: chain b residue 256 SER Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 314 LEU Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 735 VAL Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 809 GLN Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1014 MET Chi-restraints excluded: chain b residue 1036 MET Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 494 ASP Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 570 VAL Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 580 GLN Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 699 THR Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 789 LEU Chi-restraints excluded: chain e residue 838 SER Chi-restraints excluded: chain e residue 858 VAL Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 909 VAL Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 954 LYS Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 1004 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1259 SER Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 3.9990 chunk 592 optimal weight: 0.9990 chunk 361 optimal weight: 0.8980 chunk 281 optimal weight: 8.9990 chunk 411 optimal weight: 0.4980 chunk 621 optimal weight: 5.9990 chunk 572 optimal weight: 6.9990 chunk 495 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 382 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN K 69 HIS ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 343 GLN b 262 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 45 GLN e 679 GLN ** e 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 53160 Z= 0.285 Angle : 0.607 21.064 72250 Z= 0.312 Chirality : 0.045 0.232 8055 Planarity : 0.004 0.060 8982 Dihedral : 13.050 174.090 7981 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.23 % Allowed : 26.83 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 6148 helix: 1.23 (0.12), residues: 2032 sheet: -0.30 (0.15), residues: 1167 loop : -0.79 (0.11), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP e 936 HIS 0.007 0.001 HIS B 370 PHE 0.036 0.002 PHE B 309 TYR 0.023 0.002 TYR e 510 ARG 0.015 0.001 ARG B1150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12296 Ramachandran restraints generated. 6148 Oldfield, 0 Emsley, 6148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1598 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 1365 time to evaluate : 5.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7148 (ttm110) REVERT: A 22 GLN cc_start: 0.7811 (tp40) cc_final: 0.7544 (tp-100) REVERT: A 29 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6219 (p0) REVERT: A 108 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7584 (ttm110) REVERT: A 117 LEU cc_start: 0.8172 (tp) cc_final: 0.7950 (tt) REVERT: A 143 HIS cc_start: 0.6349 (m170) cc_final: 0.5858 (m170) REVERT: A 197 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: A 244 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6779 (ttt-90) REVERT: A 246 GLU cc_start: 0.7461 (pm20) cc_final: 0.7146 (pm20) REVERT: A 294 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5865 (pp20) REVERT: A 319 ASP cc_start: 0.6961 (t0) cc_final: 0.6667 (t70) REVERT: A 320 ASN cc_start: 0.7937 (t0) cc_final: 0.7701 (t0) REVERT: A 360 ASP cc_start: 0.6961 (m-30) cc_final: 0.6569 (m-30) REVERT: A 473 ARG cc_start: 0.7517 (mtt90) cc_final: 0.7268 (mtt90) REVERT: A 483 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7473 (mpt180) REVERT: A 510 GLU cc_start: 0.6660 (mp0) cc_final: 0.6278 (mp0) REVERT: A 707 LYS cc_start: 0.7582 (mmtp) cc_final: 0.7177 (mmtp) REVERT: A 733 LEU cc_start: 0.7427 (tt) cc_final: 0.7171 (tt) REVERT: A 953 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6792 (mm-30) REVERT: A 1011 GLU cc_start: 0.7053 (mp0) cc_final: 0.6775 (mp0) REVERT: A 1159 CYS cc_start: 0.7209 (m) cc_final: 0.6749 (m) REVERT: A 1343 LEU cc_start: 0.7742 (tp) cc_final: 0.7456 (tp) REVERT: A 1403 ASP cc_start: 0.7027 (m-30) cc_final: 0.6464 (m-30) REVERT: A 1472 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7268 (t70) REVERT: B 130 LYS cc_start: 0.7386 (tttm) cc_final: 0.7102 (tttm) REVERT: B 160 TYR cc_start: 0.7480 (m-80) cc_final: 0.7176 (m-80) REVERT: B 198 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6327 (mt-10) REVERT: B 204 THR cc_start: 0.8017 (m) cc_final: 0.7586 (p) REVERT: B 281 ASP cc_start: 0.6727 (t70) cc_final: 0.6495 (t70) REVERT: B 291 ASP cc_start: 0.7289 (t0) cc_final: 0.7057 (t70) REVERT: B 385 ARG cc_start: 0.6716 (mtt-85) cc_final: 0.6076 (mtt-85) REVERT: B 433 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6939 (mm) REVERT: B 552 ASN cc_start: 0.7326 (m-40) cc_final: 0.7083 (m110) REVERT: B 582 GLN cc_start: 0.7238 (tm130) cc_final: 0.6646 (tm130) REVERT: B 585 ASN cc_start: 0.7498 (m-40) cc_final: 0.6936 (m110) REVERT: B 844 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7289 (tp) REVERT: B 1010 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7600 (mttp) REVERT: B 1054 MET cc_start: 0.7031 (mtm) cc_final: 0.6635 (mpp) REVERT: B 1109 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 27 ASP cc_start: 0.7127 (m-30) cc_final: 0.6854 (m-30) REVERT: C 62 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: C 94 CYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6595 (p) REVERT: C 164 TYR cc_start: 0.8141 (m-80) cc_final: 0.7129 (m-80) REVERT: C 201 GLU cc_start: 0.7325 (pm20) cc_final: 0.7020 (pm20) REVERT: E 50 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: E 73 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: E 129 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7584 (tm-30) REVERT: E 162 ARG cc_start: 0.7293 (tpt90) cc_final: 0.7012 (tmt-80) REVERT: E 177 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7718 (t70) REVERT: H 100 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6692 (mt-10) REVERT: H 102 ASP cc_start: 0.7340 (p0) cc_final: 0.7118 (p0) REVERT: K 26 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7486 (mtpt) REVERT: K 32 LEU cc_start: 0.7504 (mm) cc_final: 0.7294 (mt) REVERT: L 24 THR cc_start: 0.8526 (m) cc_final: 0.8191 (m) REVERT: L 41 TYR cc_start: 0.8197 (t80) cc_final: 0.7959 (t80) REVERT: L 55 PHE cc_start: 0.8250 (m-80) cc_final: 0.7114 (m-80) REVERT: f 28 PHE cc_start: 0.8563 (m-80) cc_final: 0.8312 (m-80) REVERT: f 45 THR cc_start: 0.8487 (t) cc_final: 0.8144 (m) REVERT: f 57 PHE cc_start: 0.7681 (t80) cc_final: 0.7190 (t80) REVERT: a 36 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7119 (mtm180) REVERT: a 65 ASP cc_start: 0.7684 (p0) cc_final: 0.7473 (p0) REVERT: a 124 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7757 (tt) REVERT: a 178 CYS cc_start: 0.7534 (t) cc_final: 0.7246 (t) REVERT: b 129 ARG cc_start: 0.8117 (ptt-90) cc_final: 0.7823 (ptp-170) REVERT: b 314 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7711 (pp) REVERT: b 890 LEU cc_start: 0.8003 (tp) cc_final: 0.7643 (tt) REVERT: b 894 THR cc_start: 0.8764 (p) cc_final: 0.8530 (t) REVERT: b 896 GLU cc_start: 0.6580 (pm20) cc_final: 0.6317 (pm20) REVERT: b 928 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7004 (mtm-85) REVERT: b 943 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6730 (tm-30) REVERT: b 1094 ILE cc_start: 0.8653 (pp) cc_final: 0.8175 (mm) REVERT: b 1130 ILE cc_start: 0.8605 (tt) cc_final: 0.8289 (pt) REVERT: g 41 SER cc_start: 0.8428 (t) cc_final: 0.8001 (t) REVERT: g 42 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7164 (mm-30) REVERT: g 74 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7521 (t) REVERT: g 128 PHE cc_start: 0.8071 (t80) cc_final: 0.7838 (t80) REVERT: g 227 TYR cc_start: 0.8327 (t80) cc_final: 0.8060 (t80) REVERT: g 248 LEU cc_start: 0.8320 (tp) cc_final: 0.8032 (tp) REVERT: e 494 ASP cc_start: 0.3875 (OUTLIER) cc_final: 0.3649 (p0) REVERT: e 580 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6301 (tm130) REVERT: e 584 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6768 (mm-30) REVERT: e 641 HIS cc_start: 0.7649 (t-170) cc_final: 0.7333 (t-170) REVERT: e 653 ASN cc_start: 0.8130 (t0) cc_final: 0.7827 (t0) REVERT: e 704 MET cc_start: 0.7907 (mmm) cc_final: 0.7637 (mmp) REVERT: e 747 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6898 (mttp) REVERT: e 829 GLU cc_start: 0.5920 (tm-30) cc_final: 0.5044 (tm-30) REVERT: e 867 MET cc_start: 0.7209 (tpt) cc_final: 0.6293 (tpt) REVERT: e 914 THR cc_start: 0.7287 (p) cc_final: 0.6950 (t) REVERT: e 933 ASP cc_start: 0.6891 (p0) cc_final: 0.6447 (p0) REVERT: e 939 SER cc_start: 0.8081 (m) cc_final: 0.7616 (p) REVERT: e 960 TYR cc_start: 0.6912 (m-80) cc_final: 0.6613 (m-10) REVERT: e 985 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7625 (ttm110) REVERT: d 10 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6852 (tm-30) REVERT: d 23 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7579 (mt-10) REVERT: d 115 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7486 (mtm110) REVERT: d 120 TRP cc_start: 0.8308 (m-10) cc_final: 0.8011 (m100) REVERT: d 129 LYS cc_start: 0.7625 (mttt) cc_final: 0.7419 (mttm) REVERT: d 671 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7482 (mtm110) outliers start: 233 outliers final: 196 residues processed: 1500 average time/residue: 0.6877 time to fit residues: 1650.3772 Evaluate side-chains 1582 residues out of total 5502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1362 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 36 ARG Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 124 LEU Chi-restraints excluded: chain a residue 142 GLU Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 245 ASN Chi-restraints excluded: chain a residue 292 LYS Chi-restraints excluded: chain a residue 308 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 362 VAL Chi-restraints excluded: chain a residue 369 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 98 ILE Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 159 LEU Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 218 MET Chi-restraints excluded: chain b residue 222 VAL Chi-restraints excluded: chain b residue 256 SER Chi-restraints excluded: chain b residue 265 ASP Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 302 VAL Chi-restraints excluded: chain b residue 312 GLU Chi-restraints excluded: chain b residue 314 LEU Chi-restraints excluded: chain b residue 367 LEU Chi-restraints excluded: chain b residue 390 ILE Chi-restraints excluded: chain b residue 735 VAL Chi-restraints excluded: chain b residue 797 HIS Chi-restraints excluded: chain b residue 809 GLN Chi-restraints excluded: chain b residue 823 LYS Chi-restraints excluded: chain b residue 831 VAL Chi-restraints excluded: chain b residue 833 THR Chi-restraints excluded: chain b residue 895 THR Chi-restraints excluded: chain b residue 916 THR Chi-restraints excluded: chain b residue 928 ARG Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 985 THR Chi-restraints excluded: chain b residue 1039 LEU Chi-restraints excluded: chain b residue 1050 LEU Chi-restraints excluded: chain b residue 1061 VAL Chi-restraints excluded: chain b residue 1081 LYS Chi-restraints excluded: chain b residue 1100 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 206 GLU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain g residue 221 VAL Chi-restraints excluded: chain g residue 251 LEU Chi-restraints excluded: chain e residue 494 ASP Chi-restraints excluded: chain e residue 516 ARG Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 570 VAL Chi-restraints excluded: chain e residue 577 VAL Chi-restraints excluded: chain e residue 580 GLN Chi-restraints excluded: chain e residue 582 VAL Chi-restraints excluded: chain e residue 600 THR Chi-restraints excluded: chain e residue 624 SER Chi-restraints excluded: chain e residue 634 ASP Chi-restraints excluded: chain e residue 643 VAL Chi-restraints excluded: chain e residue 689 PHE Chi-restraints excluded: chain e residue 699 THR Chi-restraints excluded: chain e residue 747 LYS Chi-restraints excluded: chain e residue 838 SER Chi-restraints excluded: chain e residue 858 VAL Chi-restraints excluded: chain e residue 870 ILE Chi-restraints excluded: chain e residue 885 MET Chi-restraints excluded: chain e residue 909 VAL Chi-restraints excluded: chain e residue 921 VAL Chi-restraints excluded: chain e residue 929 VAL Chi-restraints excluded: chain e residue 932 TYR Chi-restraints excluded: chain e residue 956 GLN Chi-restraints excluded: chain e residue 1004 LEU Chi-restraints excluded: chain e residue 1007 LEU Chi-restraints excluded: chain e residue 1017 GLU Chi-restraints excluded: chain e residue 1259 SER Chi-restraints excluded: chain e residue 1398 HIS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 6.9990 chunk 527 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 456 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 495 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 509 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A1310 HIS B 287 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN K 69 HIS f 23 GLN ** a 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 ASN a 343 GLN b 262 ASN b 790 ASN ** b 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125788 restraints weight = 74584.948| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.08 r_work: 0.3220 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 53160 Z= 0.323 Angle : 0.626 21.339 72250 Z= 0.323 Chirality : 0.046 0.238 8055 Planarity : 0.004 0.059 8982 Dihedral : 13.089 174.037 7981 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.23 % Allowed : 26.97 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 6148 helix: 1.13 (0.12), residues: 2030 sheet: -0.39 (0.15), residues: 1174 loop : -0.80 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP e 936 HIS 0.008 0.001 HIS B 370 PHE 0.048 0.002 PHE B 309 TYR 0.028 0.002 TYR b 726 ARG 0.015 0.001 ARG B1150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23874.24 seconds wall clock time: 457 minutes 58.31 seconds (27478.31 seconds total)