Starting phenix.real_space_refine on Tue Aug 26 10:39:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqw_39508/08_2025/8yqw_39508_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqw_39508/08_2025/8yqw_39508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yqw_39508/08_2025/8yqw_39508_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqw_39508/08_2025/8yqw_39508_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yqw_39508/08_2025/8yqw_39508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqw_39508/08_2025/8yqw_39508.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.122 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 Mg 1 5.21 5 S 194 5.16 5 C 22974 2.51 5 N 6165 2.21 5 O 6686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36029 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11201 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1341} Chain breaks: 2 Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "B" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9553 Classifications: {'peptide': 1207} Link IDs: {'PTRANS': 53, 'TRANS': 1153} Chain breaks: 4 Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2897 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain: "D" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "H" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5704 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 664} Chain breaks: 4 Chain: "F" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2698 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 442 SG CYS A 59 106.915 75.902 66.860 1.00 48.41 S ATOM 463 SG CYS A 62 104.644 74.769 64.052 1.00 49.45 S ATOM 523 SG CYS A 69 103.742 77.840 66.118 1.00 44.12 S ATOM 767 SG CYS A 99 91.342 59.214 108.536 1.00 78.10 S ATOM 789 SG CYS A 102 92.000 55.749 107.049 1.00 79.14 S ATOM 1041 SG CYS A 134 89.140 56.123 109.297 1.00 86.49 S ATOM 1066 SG CYS A 137 92.759 56.516 110.683 1.00 92.96 S ATOM 21127 SG CYS B1180 96.585 60.990 67.526 1.00 44.48 S ATOM 21152 SG CYS B1183 96.464 61.701 71.154 1.00 47.49 S ATOM 21268 SG CYS B1198 99.168 63.110 69.400 1.00 57.40 S ATOM 21290 SG CYS B1201 99.266 59.238 69.486 1.00 51.20 S ATOM 26223 SG CYS H 7 70.366 134.935 46.166 1.00 28.65 S ATOM 26247 SG CYS H 10 69.143 135.185 42.501 1.00 31.37 S ATOM 26666 SG CYS H 65 66.700 134.806 45.495 1.00 40.77 S ATOM 26672 SG CYS H 66 68.639 138.019 44.545 1.00 41.79 S ATOM 27369 SG CYS G 73 35.823 132.883 108.721 1.00 63.98 S ATOM 27390 SG CYS G 76 37.341 136.330 109.172 1.00 70.76 S ATOM 27547 SG CYS G 96 39.496 133.523 107.948 1.00 62.58 S ATOM 27564 SG CYS G 98 38.260 133.469 111.561 1.00 65.68 S ATOM 26833 SG CYS G 4 66.652 100.598 138.515 1.00 69.96 S ATOM 26853 SG CYS G 7 70.034 101.306 136.869 1.00 75.84 S ATOM 26987 SG CYS G 24 68.140 98.240 135.822 1.00 73.87 S ATOM 26999 SG CYS G 26 69.593 98.407 139.324 1.00 87.42 S ATOM 31032 SG CYS J 937 20.863 95.127 101.308 1.00 69.06 S ATOM 31134 SG CYS J 950 18.675 92.853 99.091 1.00 87.16 S ATOM 31156 SG CYS J 953 17.766 96.532 99.551 1.00 78.99 S ATOM 30716 SG CYS J 898 20.817 115.247 73.294 1.00 71.19 S ATOM 30735 SG CYS J 901 18.200 117.829 74.420 1.00 61.41 S Time building chain proxies: 6.56, per 1000 atoms: 0.18 Number of scatterers: 36029 At special positions: 0 Unit cell: (148.672, 172.912, 172.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 194 16.00 Mg 1 11.99 O 6686 8.00 N 6165 7.00 C 22974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 59 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 62 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 69 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 102 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 137 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 99 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 134 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 98 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 4 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 24 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb=" ZN J1301 " pdb="ZN ZN J1301 " - pdb=" ND1 HIS J 943 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 953 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 950 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 937 " pdb=" ZN J1302 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 901 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1302 " - pdb=" ND1 HIS J 857 " Number of angles added : 36 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8536 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 50 sheets defined 44.3% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.864A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 4.021A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.506A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.694A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.692A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.304A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.690A pdb=" N GLU A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.583A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.117A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.669A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.519A pdb=" N MET A 582 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 4.279A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.737A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.688A pdb=" N PHE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 812 " --> pdb=" O GLY A 808 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.117A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 removed outlier: 3.518A pdb=" N LYS A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.737A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.661A pdb=" N GLU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.580A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1015 through 1033 removed outlier: 3.584A pdb=" N SER A1020 " --> pdb=" O CYS A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1051 through 1059 removed outlier: 4.319A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1063 Processing helix chain 'A' and resid 1075 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1102 through 1105 Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.556A pdb=" N ALA A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.884A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1230 through 1232 No H-bonds generated for 'chain 'A' and resid 1230 through 1232' Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.647A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1310 through 1314' Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 removed outlier: 3.501A pdb=" N GLY A1344 " --> pdb=" O ARG A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.748A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A1356 " --> pdb=" O HIS A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 4.125A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.736A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.732A pdb=" N MET E 141 " --> pdb=" O PRO E 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.575A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.721A pdb=" N LEU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.846A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.754A pdb=" N ASP B 79 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 80 " --> pdb=" O GLU B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 80' Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.829A pdb=" N PHE B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 4.055A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.830A pdb=" N HIS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.639A pdb=" N LYS B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 removed outlier: 3.505A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.640A pdb=" N ASN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.622A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 489 removed outlier: 3.601A pdb=" N ASN B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.645A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.825A pdb=" N GLU B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.593A pdb=" N LYS B 703 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 704 " --> pdb=" O TRP B 701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 705 " --> pdb=" O GLU B 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 705' Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.511A pdb=" N GLU B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.560A pdb=" N ILE B 778 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.658A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 912 through 916 removed outlier: 4.171A pdb=" N LYS B 915 " --> pdb=" O ASN B 912 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 916 " --> pdb=" O TYR B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 916' Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.892A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1077 removed outlier: 3.528A pdb=" N LEU B1075 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1160 through 1169 removed outlier: 3.635A pdb=" N ILE B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.641A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 258 Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.526A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 358 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.697A pdb=" N THR D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 67 through 79 removed outlier: 3.620A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.702A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.672A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 37 through 44 Proline residue: H 42 - end of helix Processing helix chain 'H' and resid 51 through 58 removed outlier: 3.548A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.554A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.847A pdb=" N MET G 49 " --> pdb=" O THR G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'J' and resid 75 through 83 removed outlier: 3.684A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.766A pdb=" N PHE J 142 " --> pdb=" O SER J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 163 Processing helix chain 'J' and resid 167 through 173 Processing helix chain 'J' and resid 192 through 212 Processing helix chain 'J' and resid 215 through 236 Processing helix chain 'J' and resid 673 through 683 removed outlier: 3.631A pdb=" N LEU J 683 " --> pdb=" O THR J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 697 removed outlier: 3.616A pdb=" N ASP J 697 " --> pdb=" O VAL J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 720 Processing helix chain 'J' and resid 722 through 729 removed outlier: 3.605A pdb=" N LEU J 727 " --> pdb=" O PRO J 723 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER J 728 " --> pdb=" O ALA J 724 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN J 729 " --> pdb=" O GLU J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 748 Processing helix chain 'J' and resid 769 through 791 Processing helix chain 'J' and resid 795 through 817 Processing helix chain 'J' and resid 845 through 849 Processing helix chain 'J' and resid 879 through 881 No H-bonds generated for 'chain 'J' and resid 879 through 881' Processing helix chain 'J' and resid 882 through 887 Processing helix chain 'J' and resid 907 through 911 removed outlier: 3.502A pdb=" N GLN J 910 " --> pdb=" O GLU J 907 " (cutoff:3.500A) Processing helix chain 'J' and resid 912 through 933 Processing helix chain 'J' and resid 956 through 960 removed outlier: 3.520A pdb=" N ILE J 960 " --> pdb=" O THR J 957 " (cutoff:3.500A) Processing helix chain 'J' and resid 966 through 977 Processing helix chain 'J' and resid 977 through 989 Processing helix chain 'J' and resid 1017 through 1028 Processing helix chain 'J' and resid 1030 through 1036 removed outlier: 4.021A pdb=" N ILE J1034 " --> pdb=" O SER J1030 " (cutoff:3.500A) Processing helix chain 'J' and resid 1044 through 1051 Processing helix chain 'J' and resid 1063 through 1085 removed outlier: 3.862A pdb=" N MET J1067 " --> pdb=" O ASP J1063 " (cutoff:3.500A) Processing helix chain 'J' and resid 1093 through 1101 removed outlier: 3.858A pdb=" N ARG J1098 " --> pdb=" O ILE J1094 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU J1099 " --> pdb=" O HIS J1095 " (cutoff:3.500A) Processing helix chain 'J' and resid 1104 through 1109 Processing helix chain 'J' and resid 1121 through 1133 removed outlier: 3.553A pdb=" N HIS J1128 " --> pdb=" O THR J1124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL J1131 " --> pdb=" O LYS J1127 " (cutoff:3.500A) Processing helix chain 'J' and resid 1133 through 1154 removed outlier: 3.774A pdb=" N LEU J1139 " --> pdb=" O ALA J1135 " (cutoff:3.500A) Processing helix chain 'J' and resid 1158 through 1182 removed outlier: 3.654A pdb=" N VAL J1162 " --> pdb=" O PRO J1158 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN J1163 " --> pdb=" O SER J1159 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE J1164 " --> pdb=" O TRP J1160 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU J1167 " --> pdb=" O ASN J1163 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE J1168 " --> pdb=" O ILE J1164 " (cutoff:3.500A) Processing helix chain 'J' and resid 1209 through 1213 Processing helix chain 'J' and resid 1242 through 1247 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 194 removed outlier: 4.433A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 239 through 248 removed outlier: 3.788A pdb=" N LYS F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 314 Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.579A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.814A pdb=" N ARG F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.305A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 removed outlier: 6.724A pdb=" N VAL B1233 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 11 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B1231 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 13 " --> pdb=" O ASN B1229 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B1229 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.311A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.687A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 6.026A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.904A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.667A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 837 through 838 removed outlier: 6.421A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 6.381A pdb=" N ASN A1267 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR A1295 " --> pdb=" O ASN A1267 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.528A pdb=" N ILE A1120 " --> pdb=" O ILE A1259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.501A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 3.552A pdb=" N ASP A1428 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 161 removed outlier: 6.294A pdb=" N GLN B 145 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B 140 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 147 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B 138 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG B 149 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 136 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER B 151 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 134 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA B 132 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 128 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR B 159 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLY B 126 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 84 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.248A pdb=" N LEU B 204 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 217 removed outlier: 6.838A pdb=" N TYR B 250 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG B 229 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 248 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 231 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 246 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 233 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER B 244 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.504A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 598 removed outlier: 5.586A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 removed outlier: 7.052A pdb=" N LEU B 981 " --> pdb=" O VAL B 968 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 968 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.166A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 894 through 896 removed outlier: 7.129A pdb=" N LYS B 905 " --> pdb=" O ASP B 952 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 932 through 934 removed outlier: 3.694A pdb=" N ILE B 934 " --> pdb=" O VAL B 955 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD6, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.343A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP C 46 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N HIS C 216 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS C 186 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG C 218 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE C 184 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY C 220 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 68 through 73 removed outlier: 5.127A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AE2, first strand: chain 'D' and resid 20 through 21 removed outlier: 5.298A pdb=" N ILE D 52 " --> pdb=" O TYR D 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 87 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 138 through 142 removed outlier: 4.557A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AE5, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AE6, first strand: chain 'J' and resid 100 through 101 removed outlier: 6.901A pdb=" N VAL J 92 " --> pdb=" O TYR J 128 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE J 91 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AE8, first strand: chain 'J' and resid 875 through 878 removed outlier: 3.504A pdb=" N ASP J 895 " --> pdb=" O VAL J 863 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS J 865 " --> pdb=" O LEU J 893 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU J 893 " --> pdb=" O LYS J 865 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 945 through 946 Processing sheet with id=AF1, first strand: chain 'F' and resid 2 through 13 removed outlier: 12.092A pdb=" N TYR F 69 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N ARG F 54 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N HIS F 71 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ILE F 52 " --> pdb=" O HIS F 71 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG F 73 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY F 50 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER F 75 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE F 48 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL F 77 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 38 " --> pdb=" O ILE F 45 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 2 through 13 Processing sheet with id=AF3, first strand: chain 'F' and resid 86 through 95 removed outlier: 6.543A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN F 95 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE F 154 " --> pdb=" O PRO F 115 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 237 through 238 removed outlier: 6.827A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 217 through 219 1588 hydrogen bonds defined for protein. 4383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6554 1.32 - 1.45: 8969 1.45 - 1.57: 20915 1.57 - 1.69: 0 1.69 - 1.81: 315 Bond restraints: 36753 Sorted by residual: bond pdb=" CA HIS B 527 " pdb=" C HIS B 527 " ideal model delta sigma weight residual 1.528 1.446 0.083 1.38e-02 5.25e+03 3.58e+01 bond pdb=" CA TYR J 733 " pdb=" C TYR J 733 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.31e-02 5.83e+03 2.84e+01 bond pdb=" CA GLN J 980 " pdb=" C GLN J 980 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.34e-02 5.57e+03 1.50e+01 bond pdb=" CA LYS J 740 " pdb=" C LYS J 740 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" N THR J 738 " pdb=" CA THR J 738 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.22e-02 6.72e+03 1.24e+01 ... (remaining 36748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 49441 2.66 - 5.32: 272 5.32 - 7.99: 24 7.99 - 10.65: 2 10.65 - 13.31: 4 Bond angle restraints: 49743 Sorted by residual: angle pdb=" N GLN J 747 " pdb=" CA GLN J 747 " pdb=" C GLN J 747 " ideal model delta sigma weight residual 113.30 100.64 12.66 1.34e+00 5.57e-01 8.93e+01 angle pdb=" N LEU J 748 " pdb=" CA LEU J 748 " pdb=" C LEU J 748 " ideal model delta sigma weight residual 113.20 101.98 11.22 1.21e+00 6.83e-01 8.60e+01 angle pdb=" C ARG J 750 " pdb=" CA ARG J 750 " pdb=" CB ARG J 750 " ideal model delta sigma weight residual 110.42 121.78 -11.36 1.99e+00 2.53e-01 3.26e+01 angle pdb=" N THR J 738 " pdb=" CA THR J 738 " pdb=" C THR J 738 " ideal model delta sigma weight residual 108.26 99.98 8.28 1.66e+00 3.63e-01 2.49e+01 angle pdb=" C PRO J 743 " pdb=" N ASP J 744 " pdb=" CA ASP J 744 " ideal model delta sigma weight residual 122.84 117.40 5.44 1.30e+00 5.92e-01 1.75e+01 ... (remaining 49738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 20664 17.88 - 35.76: 1443 35.76 - 53.63: 213 53.63 - 71.51: 56 71.51 - 89.39: 22 Dihedral angle restraints: 22398 sinusoidal: 9191 harmonic: 13207 Sorted by residual: dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" C ARG J 750 " pdb=" N ARG J 750 " pdb=" CA ARG J 750 " pdb=" CB ARG J 750 " ideal model delta harmonic sigma weight residual -122.60 -135.78 13.18 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" CA CYS B1201 " pdb=" C CYS B1201 " pdb=" N ASP B1202 " pdb=" CA ASP B1202 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 22395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5165 0.085 - 0.171: 448 0.171 - 0.256: 2 0.256 - 0.342: 0 0.342 - 0.427: 2 Chirality restraints: 5617 Sorted by residual: chirality pdb=" CA ARG J 750 " pdb=" N ARG J 750 " pdb=" C ARG J 750 " pdb=" CB ARG J 750 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA LEU J 751 " pdb=" N LEU J 751 " pdb=" C LEU J 751 " pdb=" CB LEU J 751 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA TYR J 741 " pdb=" N TYR J 741 " pdb=" C TYR J 741 " pdb=" CB TYR J 741 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5614 not shown) Planarity restraints: 6396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 417 " -0.024 2.00e-02 2.50e+03 2.30e-02 9.22e+00 pdb=" CG PHE A 417 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 417 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 417 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 417 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 417 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 417 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 283 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO F 284 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 284 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 284 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 732 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C PHE J 732 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE J 732 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR J 733 " -0.012 2.00e-02 2.50e+03 ... (remaining 6393 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 181 2.53 - 3.12: 26772 3.12 - 3.72: 55534 3.72 - 4.31: 84365 4.31 - 4.90: 139208 Nonbonded interactions: 306060 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A2001 " model vdw 1.939 2.170 nonbonded pdb=" OD2 ASP A 332 " pdb=" OH TYR B 859 " model vdw 2.090 3.040 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A2001 " model vdw 2.114 2.170 nonbonded pdb=" OE1 GLN J 747 " pdb=" NZ LYS J 772 " model vdw 2.146 3.120 nonbonded pdb=" OD1 ASP B1059 " pdb=" OG1 THR B1061 " model vdw 2.147 3.040 ... (remaining 306055 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 0.083 36784 Z= 0.188 Angle : 0.567 13.312 49779 Z= 0.307 Chirality : 0.046 0.427 5617 Planarity : 0.004 0.062 6396 Dihedral : 12.829 89.389 13862 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 0.35 % Allowed : 0.15 % Favored : 99.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.12), residues: 4469 helix: -0.34 (0.12), residues: 1692 sheet: -0.15 (0.21), residues: 619 loop : -0.29 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 842 TYR 0.034 0.001 TYR B 413 PHE 0.052 0.001 PHE A 417 TRP 0.016 0.002 TRP A 466 HIS 0.011 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00397 (36753) covalent geometry : angle 0.55624 (49743) hydrogen bonds : bond 0.20728 ( 1574) hydrogen bonds : angle 7.63395 ( 4383) metal coordination : bond 0.00567 ( 31) metal coordination : angle 4.08417 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 699 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8417 (ptmt) cc_final: 0.7891 (pptt) REVERT: A 110 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7984 (ptpp) REVERT: A 235 ARG cc_start: 0.7341 (ttm110) cc_final: 0.7081 (ttm-80) REVERT: A 955 LYS cc_start: 0.8141 (ptmt) cc_final: 0.7716 (mttp) REVERT: A 1266 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7287 (mmmt) REVERT: A 1296 ASN cc_start: 0.7814 (t0) cc_final: 0.7553 (t0) REVERT: E 104 ASP cc_start: 0.8689 (m-30) cc_final: 0.8427 (m-30) REVERT: B 97 GLU cc_start: 0.8094 (mt-10) cc_final: 0.6979 (tm-30) REVERT: B 98 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7724 (mtt180) REVERT: B 333 ILE cc_start: 0.7971 (mt) cc_final: 0.7729 (mp) REVERT: B 369 ASP cc_start: 0.8101 (m-30) cc_final: 0.7893 (m-30) REVERT: B 703 LYS cc_start: 0.8489 (pptt) cc_final: 0.8228 (pptt) REVERT: B 918 ASP cc_start: 0.7342 (t0) cc_final: 0.7129 (t70) REVERT: C 34 GLU cc_start: 0.7768 (pm20) cc_final: 0.7459 (pm20) REVERT: J 677 LEU cc_start: 0.6777 (tp) cc_final: 0.6513 (tp) REVERT: J 731 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5330 (mt-10) REVERT: J 851 ASP cc_start: 0.8188 (p0) cc_final: 0.7862 (p0) REVERT: J 915 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7244 (mttp) REVERT: J 1177 ILE cc_start: 0.8543 (mm) cc_final: 0.8328 (mt) REVERT: F 30 GLU cc_start: 0.7836 (tp30) cc_final: 0.7576 (tp30) REVERT: F 94 LYS cc_start: 0.7273 (ttpt) cc_final: 0.7029 (tmtt) REVERT: F 158 LYS cc_start: 0.6865 (mmtt) cc_final: 0.6348 (mtmm) REVERT: F 197 PHE cc_start: 0.6900 (t80) cc_final: 0.6150 (t80) outliers start: 14 outliers final: 2 residues processed: 707 average time/residue: 0.7164 time to fit residues: 597.0764 Evaluate side-chains 539 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 536 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 980 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 77 GLN A 264 GLN A 642 ASN A 663 HIS A 721 ASN A 814 ASN A 834 GLN A 914 ASN ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 GLN A1214 ASN A1256 ASN A1405 ASN B 290 GLN B 321 GLN B 328 ASN B 364 GLN B 443 ASN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS B 704 HIS ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN B1200 ASN B1227 ASN C 183 HIS D 144 GLN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN G 75 ASN J 980 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116056 restraints weight = 40903.401| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.78 r_work: 0.3155 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 36784 Z= 0.268 Angle : 0.645 17.044 49779 Z= 0.339 Chirality : 0.049 0.226 5617 Planarity : 0.005 0.071 6396 Dihedral : 5.089 49.908 4910 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 2.34 % Allowed : 8.95 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.12), residues: 4469 helix: 0.41 (0.12), residues: 1727 sheet: -0.26 (0.21), residues: 610 loop : -0.31 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 842 TYR 0.031 0.002 TYR A1030 PHE 0.041 0.002 PHE A 417 TRP 0.016 0.002 TRP A 466 HIS 0.014 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00655 (36753) covalent geometry : angle 0.63633 (49743) hydrogen bonds : bond 0.05841 ( 1574) hydrogen bonds : angle 5.45512 ( 4383) metal coordination : bond 0.00707 ( 31) metal coordination : angle 3.99711 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 541 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7847 (pttp) REVERT: A 67 LYS cc_start: 0.8187 (mppt) cc_final: 0.7941 (mppt) REVERT: A 101 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: A 128 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6749 (tt0) REVERT: A 171 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7054 (ttp-170) REVERT: A 382 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6569 (mm-40) REVERT: A 678 GLU cc_start: 0.7865 (tt0) cc_final: 0.7516 (tt0) REVERT: A 866 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: A 900 ARG cc_start: 0.7878 (tpt90) cc_final: 0.7605 (mmp-170) REVERT: A 955 LYS cc_start: 0.8072 (ptmt) cc_final: 0.7563 (mttp) REVERT: A 1229 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6277 (pp20) REVERT: A 1266 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7290 (mmmt) REVERT: A 1296 ASN cc_start: 0.7979 (t0) cc_final: 0.7649 (t0) REVERT: A 1371 LYS cc_start: 0.8479 (tptm) cc_final: 0.8221 (tptp) REVERT: A 1375 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7894 (m-40) REVERT: A 1433 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: E 104 ASP cc_start: 0.8681 (m-30) cc_final: 0.8408 (m-30) REVERT: B 97 GLU cc_start: 0.8309 (mt-10) cc_final: 0.6849 (tm-30) REVERT: B 98 ARG cc_start: 0.8438 (mtt90) cc_final: 0.7822 (mtt90) REVERT: B 109 LYS cc_start: 0.6790 (mmmt) cc_final: 0.6035 (mppt) REVERT: B 241 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: B 333 ILE cc_start: 0.7733 (mt) cc_final: 0.7420 (mp) REVERT: B 369 ASP cc_start: 0.8212 (m-30) cc_final: 0.7976 (m-30) REVERT: B 480 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6921 (mtm-85) REVERT: B 507 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8082 (pt0) REVERT: B 703 LYS cc_start: 0.8462 (pptt) cc_final: 0.8248 (pptt) REVERT: B 918 ASP cc_start: 0.7673 (t0) cc_final: 0.7269 (t70) REVERT: B 953 ARG cc_start: 0.7364 (mtt180) cc_final: 0.6995 (mtt-85) REVERT: B 987 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: C 7 ASN cc_start: 0.8066 (t0) cc_final: 0.7798 (t0) REVERT: C 11 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8164 (pttt) REVERT: D 15 GLU cc_start: 0.8147 (tp30) cc_final: 0.7945 (tp30) REVERT: D 146 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: J 216 SER cc_start: 0.6627 (m) cc_final: 0.6357 (p) REVERT: J 677 LEU cc_start: 0.6286 (tp) cc_final: 0.6031 (tp) REVERT: J 706 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6437 (mtt180) REVERT: J 731 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5882 (mm-30) REVERT: J 741 TYR cc_start: 0.5300 (OUTLIER) cc_final: 0.4722 (t80) REVERT: J 851 ASP cc_start: 0.8137 (p0) cc_final: 0.7775 (p0) REVERT: J 934 GLU cc_start: 0.7903 (tt0) cc_final: 0.7638 (tt0) REVERT: J 1177 ILE cc_start: 0.8119 (mm) cc_final: 0.7906 (mt) REVERT: J 1203 GLU cc_start: 0.7201 (pt0) cc_final: 0.6584 (mp0) REVERT: J 1240 LEU cc_start: 0.8629 (mt) cc_final: 0.8362 (mm) REVERT: F 30 GLU cc_start: 0.8140 (tp30) cc_final: 0.7809 (tp30) REVERT: F 94 LYS cc_start: 0.7086 (ttpt) cc_final: 0.6574 (tmtt) REVERT: F 158 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6082 (mtmm) REVERT: F 197 PHE cc_start: 0.6797 (t80) cc_final: 0.6011 (t80) REVERT: F 231 MET cc_start: 0.4826 (ttt) cc_final: 0.4515 (ttm) REVERT: F 256 PHE cc_start: 0.4881 (m-80) cc_final: 0.4288 (m-10) REVERT: F 328 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6529 (pp-130) REVERT: F 329 LEU cc_start: 0.7589 (mp) cc_final: 0.7208 (mp) outliers start: 94 outliers final: 35 residues processed: 589 average time/residue: 0.6854 time to fit residues: 484.3946 Evaluate side-chains 559 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 507 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1229 GLU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 736 ILE Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 328 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 417 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 412 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 853 GLN ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 ASN B 321 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS C 118 ASN C 315 HIS ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 812 GLN F 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116781 restraints weight = 40866.891| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.77 r_work: 0.3176 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36784 Z= 0.196 Angle : 0.577 17.143 49779 Z= 0.303 Chirality : 0.047 0.207 5617 Planarity : 0.005 0.057 6396 Dihedral : 4.839 49.001 4907 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.57 % Allowed : 10.92 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.12), residues: 4469 helix: 0.72 (0.12), residues: 1735 sheet: -0.29 (0.20), residues: 610 loop : -0.33 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 842 TYR 0.018 0.002 TYR B 350 PHE 0.030 0.002 PHE A 918 TRP 0.016 0.002 TRP A 466 HIS 0.010 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00474 (36753) covalent geometry : angle 0.56945 (49743) hydrogen bonds : bond 0.04904 ( 1574) hydrogen bonds : angle 5.15589 ( 4383) metal coordination : bond 0.00545 ( 31) metal coordination : angle 3.52029 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 526 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7795 (pttp) REVERT: A 67 LYS cc_start: 0.8188 (mppt) cc_final: 0.7911 (mppt) REVERT: A 101 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.7770 (m-40) REVERT: A 128 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: A 171 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7034 (ttp-170) REVERT: A 678 GLU cc_start: 0.7949 (tt0) cc_final: 0.7628 (tt0) REVERT: A 955 LYS cc_start: 0.8004 (ptmt) cc_final: 0.7487 (mttp) REVERT: A 1057 MET cc_start: 0.9013 (tpt) cc_final: 0.8807 (tpt) REVERT: A 1229 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6229 (pp20) REVERT: A 1266 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7297 (mmmt) REVERT: A 1296 ASN cc_start: 0.8004 (t0) cc_final: 0.7667 (t0) REVERT: A 1371 LYS cc_start: 0.8428 (tptm) cc_final: 0.8138 (tptp) REVERT: A 1375 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: A 1433 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: E 104 ASP cc_start: 0.8653 (m-30) cc_final: 0.8381 (m-30) REVERT: B 97 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 109 LYS cc_start: 0.6731 (mmmt) cc_final: 0.5944 (mppt) REVERT: B 241 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 333 ILE cc_start: 0.7720 (mt) cc_final: 0.7418 (mp) REVERT: B 369 ASP cc_start: 0.8171 (m-30) cc_final: 0.7902 (m-30) REVERT: B 703 LYS cc_start: 0.8507 (pptt) cc_final: 0.8151 (pptt) REVERT: B 918 ASP cc_start: 0.7648 (t0) cc_final: 0.7226 (t70) REVERT: B 928 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8372 (mtpp) REVERT: B 953 ARG cc_start: 0.7362 (mtt180) cc_final: 0.7090 (mtt-85) REVERT: C 345 GLN cc_start: 0.8303 (tt0) cc_final: 0.8089 (tt0) REVERT: D 146 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: J 216 SER cc_start: 0.6600 (m) cc_final: 0.6375 (p) REVERT: J 677 LEU cc_start: 0.6306 (tp) cc_final: 0.6083 (tp) REVERT: J 706 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5986 (mtm110) REVERT: J 731 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5979 (mm-30) REVERT: J 741 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.4731 (t80) REVERT: J 812 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6901 (mp10) REVERT: J 851 ASP cc_start: 0.8128 (p0) cc_final: 0.7766 (p0) REVERT: J 934 GLU cc_start: 0.7887 (tt0) cc_final: 0.7611 (tt0) REVERT: J 974 TYR cc_start: 0.7987 (t80) cc_final: 0.7478 (t80) REVERT: J 980 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: J 986 MET cc_start: 0.6310 (mtm) cc_final: 0.6024 (mmt) REVERT: J 1156 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.5596 (mtmm) REVERT: J 1203 GLU cc_start: 0.7049 (pt0) cc_final: 0.6453 (mp0) REVERT: J 1240 LEU cc_start: 0.8607 (mt) cc_final: 0.8321 (mm) REVERT: F 30 GLU cc_start: 0.8134 (tp30) cc_final: 0.7785 (tp30) REVERT: F 94 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6620 (tmtt) REVERT: F 158 LYS cc_start: 0.6870 (mmtt) cc_final: 0.6084 (mtmm) REVERT: F 161 PHE cc_start: 0.7900 (p90) cc_final: 0.7509 (p90) REVERT: F 197 PHE cc_start: 0.6737 (t80) cc_final: 0.5853 (t80) REVERT: F 208 TYR cc_start: 0.5480 (t80) cc_final: 0.5025 (t80) REVERT: F 231 MET cc_start: 0.4870 (ttt) cc_final: 0.4558 (ttm) REVERT: F 256 PHE cc_start: 0.4802 (m-80) cc_final: 0.4494 (m-10) REVERT: F 328 MET cc_start: 0.7008 (tmm) cc_final: 0.6551 (pp-130) REVERT: F 329 LEU cc_start: 0.7673 (mp) cc_final: 0.7279 (mp) outliers start: 103 outliers final: 48 residues processed: 575 average time/residue: 0.6699 time to fit residues: 462.2737 Evaluate side-chains 565 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 503 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1229 GLU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 980 GLN Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain J residue 1156 LYS Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 326 optimal weight: 0.6980 chunk 337 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 431 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 289 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A1018 GLN A1106 ASN A1256 ASN B 321 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN B1090 ASN C 118 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118984 restraints weight = 40618.098| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.85 r_work: 0.3212 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36784 Z= 0.126 Angle : 0.515 17.439 49779 Z= 0.270 Chirality : 0.044 0.185 5617 Planarity : 0.004 0.051 6396 Dihedral : 4.550 42.914 4907 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.19 % Allowed : 12.61 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.13), residues: 4469 helix: 1.03 (0.13), residues: 1737 sheet: -0.19 (0.21), residues: 600 loop : -0.22 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 480 TYR 0.015 0.001 TYR B 350 PHE 0.026 0.001 PHE A 918 TRP 0.015 0.001 TRP A 466 HIS 0.007 0.001 HIS B 972 Details of bonding type rmsd covalent geometry : bond 0.00290 (36753) covalent geometry : angle 0.50881 (49743) hydrogen bonds : bond 0.04061 ( 1574) hydrogen bonds : angle 4.89922 ( 4383) metal coordination : bond 0.00384 ( 31) metal coordination : angle 2.93932 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 548 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8289 (ptmt) cc_final: 0.7790 (pttp) REVERT: A 67 LYS cc_start: 0.8185 (mppt) cc_final: 0.7921 (mppt) REVERT: A 171 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7038 (ttp-170) REVERT: A 378 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7410 (mtp180) REVERT: A 678 GLU cc_start: 0.7919 (tt0) cc_final: 0.7510 (tt0) REVERT: A 688 ASP cc_start: 0.7964 (t70) cc_final: 0.7607 (t0) REVERT: A 955 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7514 (mttp) REVERT: A 1266 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7321 (mmmt) REVERT: A 1296 ASN cc_start: 0.7934 (t0) cc_final: 0.7639 (t0) REVERT: A 1371 LYS cc_start: 0.8399 (tptm) cc_final: 0.8065 (tptp) REVERT: A 1375 ASN cc_start: 0.8174 (m-40) cc_final: 0.7706 (m-40) REVERT: A 1433 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: E 104 ASP cc_start: 0.8610 (m-30) cc_final: 0.8349 (m-30) REVERT: B 133 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: B 241 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 321 GLN cc_start: 0.7757 (tp40) cc_final: 0.7311 (mm-40) REVERT: B 333 ILE cc_start: 0.7669 (mt) cc_final: 0.7380 (mp) REVERT: B 369 ASP cc_start: 0.8171 (m-30) cc_final: 0.7913 (m-30) REVERT: B 480 ARG cc_start: 0.7086 (mtm-85) cc_final: 0.6570 (mtm110) REVERT: B 703 LYS cc_start: 0.8443 (pptt) cc_final: 0.8084 (pptt) REVERT: B 918 ASP cc_start: 0.7625 (t0) cc_final: 0.7203 (t70) REVERT: B 953 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7124 (mtt-85) REVERT: C 34 GLU cc_start: 0.7968 (pm20) cc_final: 0.7278 (pm20) REVERT: D 1 MET cc_start: 0.6107 (ptp) cc_final: 0.5697 (ptp) REVERT: H 52 LYS cc_start: 0.8751 (tttm) cc_final: 0.8442 (tttp) REVERT: J 100 ARG cc_start: 0.6751 (ttt180) cc_final: 0.5480 (tpt170) REVERT: J 126 GLU cc_start: 0.6688 (pm20) cc_final: 0.6017 (pm20) REVERT: J 677 LEU cc_start: 0.6292 (tp) cc_final: 0.6074 (tp) REVERT: J 706 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6006 (mtm110) REVERT: J 731 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5685 (mm-30) REVERT: J 741 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.4741 (t80) REVERT: J 851 ASP cc_start: 0.8170 (p0) cc_final: 0.7779 (p0) REVERT: J 934 GLU cc_start: 0.7874 (tt0) cc_final: 0.7629 (tt0) REVERT: J 974 TYR cc_start: 0.7970 (t80) cc_final: 0.7561 (t80) REVERT: J 980 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: J 986 MET cc_start: 0.6251 (mtm) cc_final: 0.5997 (mmt) REVERT: J 1067 MET cc_start: 0.7777 (mpp) cc_final: 0.7515 (mpm) REVERT: J 1203 GLU cc_start: 0.7063 (pt0) cc_final: 0.6455 (mp0) REVERT: F 30 GLU cc_start: 0.8068 (tp30) cc_final: 0.7648 (tp30) REVERT: F 94 LYS cc_start: 0.7135 (ttpt) cc_final: 0.6616 (tmtp) REVERT: F 197 PHE cc_start: 0.6709 (t80) cc_final: 0.5917 (t80) REVERT: F 208 TYR cc_start: 0.5420 (t80) cc_final: 0.5040 (t80) REVERT: F 231 MET cc_start: 0.4974 (ttt) cc_final: 0.4654 (ttm) REVERT: F 328 MET cc_start: 0.7090 (tmm) cc_final: 0.6609 (pp-130) REVERT: F 329 LEU cc_start: 0.7675 (mp) cc_final: 0.7268 (mp) outliers start: 88 outliers final: 42 residues processed: 595 average time/residue: 0.6593 time to fit residues: 471.9867 Evaluate side-chains 572 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 520 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 980 GLN Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 353 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 429 optimal weight: 9.9990 chunk 388 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 0.0470 chunk 295 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 362 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A1256 ASN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN C 353 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 812 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.158408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116907 restraints weight = 40696.385| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.73 r_work: 0.3173 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36784 Z= 0.182 Angle : 0.552 17.118 49779 Z= 0.289 Chirality : 0.046 0.203 5617 Planarity : 0.004 0.050 6396 Dihedral : 4.614 39.907 4907 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.12 % Allowed : 12.99 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.13), residues: 4469 helix: 1.02 (0.12), residues: 1737 sheet: -0.19 (0.20), residues: 608 loop : -0.23 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 842 TYR 0.016 0.001 TYR B 350 PHE 0.028 0.002 PHE A 918 TRP 0.014 0.001 TRP A 466 HIS 0.007 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00442 (36753) covalent geometry : angle 0.54462 (49743) hydrogen bonds : bond 0.04407 ( 1574) hydrogen bonds : angle 4.92586 ( 4383) metal coordination : bond 0.00539 ( 31) metal coordination : angle 3.37625 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 518 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8360 (ptmt) cc_final: 0.7874 (pttp) REVERT: A 67 LYS cc_start: 0.8216 (mppt) cc_final: 0.7926 (mppt) REVERT: A 128 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: A 171 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7100 (ttp-170) REVERT: A 678 GLU cc_start: 0.7917 (tt0) cc_final: 0.7536 (tt0) REVERT: A 688 ASP cc_start: 0.7966 (t70) cc_final: 0.7601 (t0) REVERT: A 765 GLN cc_start: 0.8563 (mm110) cc_final: 0.8288 (mp10) REVERT: A 955 LYS cc_start: 0.7999 (ptmt) cc_final: 0.7494 (mttp) REVERT: A 1057 MET cc_start: 0.9067 (tpt) cc_final: 0.8844 (tpt) REVERT: A 1266 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7368 (mmmt) REVERT: A 1296 ASN cc_start: 0.8032 (t0) cc_final: 0.7731 (t0) REVERT: A 1371 LYS cc_start: 0.8560 (tptm) cc_final: 0.8203 (tptp) REVERT: A 1375 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7756 (m-40) REVERT: A 1433 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: E 104 ASP cc_start: 0.8691 (m-30) cc_final: 0.8439 (m-30) REVERT: B 97 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: B 231 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8266 (mt-10) REVERT: B 241 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: B 321 GLN cc_start: 0.7815 (tp40) cc_final: 0.7398 (mm-40) REVERT: B 333 ILE cc_start: 0.7761 (mt) cc_final: 0.7463 (mp) REVERT: B 369 ASP cc_start: 0.8229 (m-30) cc_final: 0.7973 (m-30) REVERT: B 378 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8636 (mt0) REVERT: B 480 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6533 (mtm110) REVERT: B 700 ASP cc_start: 0.6560 (p0) cc_final: 0.6246 (p0) REVERT: B 703 LYS cc_start: 0.8494 (pptt) cc_final: 0.8114 (pttp) REVERT: B 918 ASP cc_start: 0.7619 (t0) cc_final: 0.7181 (t70) REVERT: B 953 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7088 (mtt-85) REVERT: C 7 ASN cc_start: 0.8014 (t0) cc_final: 0.7713 (t0) REVERT: C 11 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8120 (pttt) REVERT: C 285 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8237 (t0) REVERT: D 46 GLU cc_start: 0.7604 (tp30) cc_final: 0.7285 (tp30) REVERT: G 1 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.5514 (pmm) REVERT: J 87 ASP cc_start: 0.6542 (m-30) cc_final: 0.6314 (m-30) REVERT: J 706 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6014 (mtm110) REVERT: J 712 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: J 741 TYR cc_start: 0.5416 (OUTLIER) cc_final: 0.4752 (t80) REVERT: J 780 ARG cc_start: 0.7774 (tpm170) cc_final: 0.7570 (tpm170) REVERT: J 851 ASP cc_start: 0.8207 (p0) cc_final: 0.7843 (p0) REVERT: J 934 GLU cc_start: 0.7924 (tt0) cc_final: 0.7663 (tt0) REVERT: J 974 TYR cc_start: 0.7962 (t80) cc_final: 0.7525 (t80) REVERT: J 980 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: J 1154 GLU cc_start: 0.6662 (pt0) cc_final: 0.6260 (mt-10) REVERT: F 30 GLU cc_start: 0.8157 (tp30) cc_final: 0.7749 (tp30) REVERT: F 94 LYS cc_start: 0.7127 (ttpt) cc_final: 0.6657 (tmtt) REVERT: F 197 PHE cc_start: 0.6730 (t80) cc_final: 0.5812 (t80) REVERT: F 208 TYR cc_start: 0.5432 (t80) cc_final: 0.5029 (t80) REVERT: F 296 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7861 (tt) REVERT: F 328 MET cc_start: 0.7082 (tmm) cc_final: 0.6587 (pp-130) REVERT: F 329 LEU cc_start: 0.7756 (mt) cc_final: 0.7349 (mp) outliers start: 125 outliers final: 66 residues processed: 585 average time/residue: 0.6388 time to fit residues: 451.7549 Evaluate side-chains 587 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 504 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 712 GLU Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 980 GLN Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 118 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 425 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 383 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 426 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN A1256 ASN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN C 118 ASN C 353 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 812 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118073 restraints weight = 40573.102| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.76 r_work: 0.3199 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36784 Z= 0.154 Angle : 0.529 17.239 49779 Z= 0.277 Chirality : 0.045 0.201 5617 Planarity : 0.004 0.050 6396 Dihedral : 4.482 28.776 4904 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.44 % Allowed : 14.18 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 4469 helix: 1.10 (0.12), residues: 1735 sheet: -0.18 (0.21), residues: 600 loop : -0.18 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 145 TYR 0.015 0.001 TYR B 350 PHE 0.028 0.001 PHE A 918 TRP 0.014 0.001 TRP A1154 HIS 0.007 0.001 HIS B 972 Details of bonding type rmsd covalent geometry : bond 0.00368 (36753) covalent geometry : angle 0.52243 (49743) hydrogen bonds : bond 0.04144 ( 1574) hydrogen bonds : angle 4.86261 ( 4383) metal coordination : bond 0.00465 ( 31) metal coordination : angle 3.18758 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 515 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7657 (pptt) REVERT: A 67 LYS cc_start: 0.8172 (mppt) cc_final: 0.7881 (mppt) REVERT: A 171 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6964 (ttp-170) REVERT: A 678 GLU cc_start: 0.7914 (tt0) cc_final: 0.7522 (tt0) REVERT: A 688 ASP cc_start: 0.7954 (t70) cc_final: 0.7582 (t0) REVERT: A 866 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: A 867 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8427 (m) REVERT: A 955 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7520 (mttp) REVERT: A 1266 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7340 (mmmt) REVERT: A 1296 ASN cc_start: 0.8022 (t0) cc_final: 0.7729 (t0) REVERT: A 1371 LYS cc_start: 0.8545 (tptm) cc_final: 0.8201 (tptp) REVERT: A 1375 ASN cc_start: 0.8206 (m-40) cc_final: 0.7722 (m-40) REVERT: A 1433 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: E 104 ASP cc_start: 0.8644 (m-30) cc_final: 0.8388 (m-30) REVERT: B 97 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: B 98 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8119 (mtt90) REVERT: B 231 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: B 241 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: B 321 GLN cc_start: 0.7752 (tp40) cc_final: 0.7318 (mm-40) REVERT: B 333 ILE cc_start: 0.7711 (mt) cc_final: 0.7417 (mp) REVERT: B 369 ASP cc_start: 0.8201 (m-30) cc_final: 0.7940 (m-30) REVERT: B 378 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8615 (mt0) REVERT: B 700 ASP cc_start: 0.6504 (p0) cc_final: 0.6089 (p0) REVERT: B 703 LYS cc_start: 0.8515 (pptt) cc_final: 0.8035 (ptmm) REVERT: B 918 ASP cc_start: 0.7585 (t0) cc_final: 0.7180 (t70) REVERT: B 953 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7168 (mtt-85) REVERT: C 11 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8095 (pttt) REVERT: C 233 GLN cc_start: 0.7914 (tt0) cc_final: 0.7573 (tt0) REVERT: D 46 GLU cc_start: 0.7630 (tp30) cc_final: 0.7277 (tp30) REVERT: D 146 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: G 1 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.5513 (pmm) REVERT: J 126 GLU cc_start: 0.6746 (pm20) cc_final: 0.4971 (mm-30) REVERT: J 193 LYS cc_start: 0.6648 (mmtt) cc_final: 0.6431 (tttm) REVERT: J 226 MET cc_start: 0.7040 (ttm) cc_final: 0.6781 (ttt) REVERT: J 706 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.5999 (mtm110) REVERT: J 741 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.4866 (t80) REVERT: J 851 ASP cc_start: 0.8187 (p0) cc_final: 0.7810 (p0) REVERT: J 934 GLU cc_start: 0.7890 (tt0) cc_final: 0.7641 (tt0) REVERT: J 974 TYR cc_start: 0.7928 (t80) cc_final: 0.7587 (t80) REVERT: J 980 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: J 1152 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7180 (mp) REVERT: J 1154 GLU cc_start: 0.6567 (pt0) cc_final: 0.6248 (mt-10) REVERT: F 94 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6650 (tmtt) REVERT: F 197 PHE cc_start: 0.6711 (t80) cc_final: 0.5891 (t80) REVERT: F 208 TYR cc_start: 0.5460 (t80) cc_final: 0.5024 (t80) REVERT: F 296 LEU cc_start: 0.8082 (mp) cc_final: 0.7878 (tt) outliers start: 98 outliers final: 60 residues processed: 567 average time/residue: 0.7084 time to fit residues: 484.0861 Evaluate side-chains 587 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 511 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1245 LYS Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 875 GLU Chi-restraints excluded: chain J residue 980 GLN Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain J residue 1152 LEU Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 61 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 chunk 335 optimal weight: 0.0070 chunk 163 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 189 optimal weight: 0.0030 chunk 282 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN A 388 HIS A1256 ASN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1240 GLN C 118 ASN C 353 ASN G 75 ASN J 812 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121368 restraints weight = 40877.287| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.70 r_work: 0.3259 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 36784 Z= 0.100 Angle : 0.487 17.557 49779 Z= 0.255 Chirality : 0.043 0.224 5617 Planarity : 0.004 0.051 6396 Dihedral : 4.185 28.747 4904 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.94 % Allowed : 15.08 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.13), residues: 4469 helix: 1.33 (0.13), residues: 1733 sheet: -0.04 (0.21), residues: 595 loop : -0.09 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 235 TYR 0.015 0.001 TYR C 310 PHE 0.025 0.001 PHE B 454 TRP 0.015 0.001 TRP A1154 HIS 0.005 0.001 HIS B 972 Details of bonding type rmsd covalent geometry : bond 0.00215 (36753) covalent geometry : angle 0.48241 (49743) hydrogen bonds : bond 0.03452 ( 1574) hydrogen bonds : angle 4.67615 ( 4383) metal coordination : bond 0.00364 ( 31) metal coordination : angle 2.58904 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 562 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7631 (pptt) REVERT: A 67 LYS cc_start: 0.8133 (mppt) cc_final: 0.7848 (mppt) REVERT: A 171 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7047 (ttp-170) REVERT: A 678 GLU cc_start: 0.7820 (tt0) cc_final: 0.7452 (tt0) REVERT: A 688 ASP cc_start: 0.7948 (t70) cc_final: 0.7554 (t0) REVERT: A 867 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8132 (m) REVERT: A 955 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7477 (mttp) REVERT: A 1093 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8054 (tt0) REVERT: A 1202 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6640 (ttmt) REVERT: A 1266 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7299 (mmmt) REVERT: A 1296 ASN cc_start: 0.7907 (t0) cc_final: 0.7649 (t0) REVERT: A 1371 LYS cc_start: 0.8485 (tptm) cc_final: 0.8090 (tptp) REVERT: A 1375 ASN cc_start: 0.8069 (m-40) cc_final: 0.7665 (m-40) REVERT: E 104 ASP cc_start: 0.8542 (m-30) cc_final: 0.8298 (m-30) REVERT: B 98 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.7991 (mtt90) REVERT: B 231 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: B 241 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: B 302 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8123 (t0) REVERT: B 321 GLN cc_start: 0.7704 (tp40) cc_final: 0.7320 (mm-40) REVERT: B 333 ILE cc_start: 0.7653 (mt) cc_final: 0.7379 (mp) REVERT: B 369 ASP cc_start: 0.8118 (m-30) cc_final: 0.7806 (m-30) REVERT: B 480 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6570 (mtt90) REVERT: B 700 ASP cc_start: 0.6479 (p0) cc_final: 0.6241 (p0) REVERT: B 703 LYS cc_start: 0.8498 (pptt) cc_final: 0.8078 (ptmm) REVERT: B 918 ASP cc_start: 0.7526 (t0) cc_final: 0.7154 (t70) REVERT: B 953 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7139 (mtt-85) REVERT: C 34 GLU cc_start: 0.7994 (pm20) cc_final: 0.7632 (pm20) REVERT: C 211 THR cc_start: 0.9028 (m) cc_final: 0.8779 (p) REVERT: C 233 GLN cc_start: 0.7855 (tt0) cc_final: 0.7489 (tt0) REVERT: C 255 LYS cc_start: 0.6863 (mtpp) cc_final: 0.6544 (tttm) REVERT: C 285 ASP cc_start: 0.8361 (t0) cc_final: 0.8159 (t0) REVERT: D 1 MET cc_start: 0.6004 (ptp) cc_final: 0.5658 (ptp) REVERT: D 46 GLU cc_start: 0.7640 (tp30) cc_final: 0.7266 (tp30) REVERT: D 145 GLU cc_start: 0.7742 (mp0) cc_final: 0.7527 (mp0) REVERT: D 146 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: H 52 LYS cc_start: 0.8737 (tttm) cc_final: 0.8455 (tttp) REVERT: J 126 GLU cc_start: 0.6726 (pm20) cc_final: 0.4922 (mm-30) REVERT: J 193 LYS cc_start: 0.6657 (mmtt) cc_final: 0.6449 (tttm) REVERT: J 706 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5849 (mtm110) REVERT: J 731 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5574 (mm-30) REVERT: J 851 ASP cc_start: 0.8186 (p0) cc_final: 0.7771 (p0) REVERT: J 934 GLU cc_start: 0.7812 (tt0) cc_final: 0.7537 (tt0) REVERT: J 1067 MET cc_start: 0.7771 (mpp) cc_final: 0.7526 (mpm) REVERT: F 94 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6718 (tmtp) REVERT: F 197 PHE cc_start: 0.6681 (t80) cc_final: 0.5898 (t80) REVERT: F 208 TYR cc_start: 0.5471 (t80) cc_final: 0.5048 (t80) REVERT: F 231 MET cc_start: 0.5246 (ttt) cc_final: 0.5009 (ttm) REVERT: F 296 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7887 (tt) REVERT: F 328 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.6066 (pp-130) REVERT: F 329 LEU cc_start: 0.7419 (mp) cc_final: 0.7111 (mp) outliers start: 78 outliers final: 41 residues processed: 604 average time/residue: 0.7219 time to fit residues: 526.2116 Evaluate side-chains 572 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 520 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 328 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 206 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 407 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 389 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 391 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 431 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 33 ASN A1256 ASN B 328 ASN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN B1240 GLN C 19 ASN C 353 ASN G 75 ASN J 812 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119993 restraints weight = 40659.938| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.68 r_work: 0.3233 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36784 Z= 0.125 Angle : 0.505 17.225 49779 Z= 0.263 Chirality : 0.044 0.214 5617 Planarity : 0.004 0.050 6396 Dihedral : 4.207 28.367 4902 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.82 % Allowed : 15.73 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.13), residues: 4469 helix: 1.34 (0.13), residues: 1735 sheet: -0.04 (0.21), residues: 597 loop : -0.06 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 235 TYR 0.018 0.001 TYR J 974 PHE 0.027 0.001 PHE B 454 TRP 0.015 0.001 TRP A1174 HIS 0.007 0.001 HIS B 972 Details of bonding type rmsd covalent geometry : bond 0.00293 (36753) covalent geometry : angle 0.49935 (49743) hydrogen bonds : bond 0.03711 ( 1574) hydrogen bonds : angle 4.67823 ( 4383) metal coordination : bond 0.00374 ( 31) metal coordination : angle 2.81310 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 528 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8339 (ptmt) cc_final: 0.7677 (pptt) REVERT: A 67 LYS cc_start: 0.8086 (mppt) cc_final: 0.7854 (mppt) REVERT: A 128 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: A 171 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7060 (ttp-170) REVERT: A 667 GLN cc_start: 0.8167 (tt0) cc_final: 0.7832 (mt0) REVERT: A 678 GLU cc_start: 0.7833 (tt0) cc_final: 0.7464 (tt0) REVERT: A 688 ASP cc_start: 0.7956 (t70) cc_final: 0.7569 (t0) REVERT: A 867 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 955 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7457 (mttp) REVERT: A 1093 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8101 (tt0) REVERT: A 1202 LYS cc_start: 0.7001 (ttmt) cc_final: 0.6661 (ttmt) REVERT: A 1266 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7323 (mmmt) REVERT: A 1296 ASN cc_start: 0.7952 (t0) cc_final: 0.7727 (t0) REVERT: A 1371 LYS cc_start: 0.8520 (tptm) cc_final: 0.8143 (tptp) REVERT: A 1375 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7702 (m-40) REVERT: E 104 ASP cc_start: 0.8585 (m-30) cc_final: 0.8334 (m-30) REVERT: B 98 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8013 (mtt90) REVERT: B 231 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: B 241 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 302 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8144 (t0) REVERT: B 321 GLN cc_start: 0.7788 (tp40) cc_final: 0.7347 (mm-40) REVERT: B 333 ILE cc_start: 0.7669 (mt) cc_final: 0.7374 (mp) REVERT: B 369 ASP cc_start: 0.8160 (m-30) cc_final: 0.7836 (m-30) REVERT: B 480 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.6567 (mtt90) REVERT: B 700 ASP cc_start: 0.6562 (p0) cc_final: 0.6342 (p0) REVERT: B 703 LYS cc_start: 0.8512 (pptt) cc_final: 0.8072 (ptmm) REVERT: B 918 ASP cc_start: 0.7496 (t0) cc_final: 0.7120 (t70) REVERT: B 953 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7067 (mtt-85) REVERT: C 34 GLU cc_start: 0.8003 (pm20) cc_final: 0.7627 (pm20) REVERT: C 211 THR cc_start: 0.9024 (m) cc_final: 0.8751 (p) REVERT: C 233 GLN cc_start: 0.7867 (tt0) cc_final: 0.7506 (tt0) REVERT: C 255 LYS cc_start: 0.6884 (mtpp) cc_final: 0.6565 (tttm) REVERT: C 285 ASP cc_start: 0.8391 (t0) cc_final: 0.8173 (t0) REVERT: D 46 GLU cc_start: 0.7632 (tp30) cc_final: 0.7236 (tp30) REVERT: D 47 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7491 (m) REVERT: D 146 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: J 706 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5783 (mtm110) REVERT: J 731 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5480 (mt-10) REVERT: J 851 ASP cc_start: 0.8207 (p0) cc_final: 0.7794 (p0) REVERT: J 934 GLU cc_start: 0.7851 (tt0) cc_final: 0.7563 (tt0) REVERT: J 1067 MET cc_start: 0.7797 (mpp) cc_final: 0.7533 (mpm) REVERT: F 94 LYS cc_start: 0.7135 (ttpt) cc_final: 0.6682 (tmtt) REVERT: F 197 PHE cc_start: 0.6702 (t80) cc_final: 0.5878 (t80) REVERT: F 208 TYR cc_start: 0.5473 (t80) cc_final: 0.5099 (t80) REVERT: F 231 MET cc_start: 0.5182 (ttt) cc_final: 0.4781 (ttm) REVERT: F 292 MET cc_start: 0.7252 (tmm) cc_final: 0.7052 (tmt) REVERT: F 296 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7766 (tt) REVERT: F 328 MET cc_start: 0.6350 (tmm) cc_final: 0.6059 (pp-130) REVERT: F 329 LEU cc_start: 0.7420 (mp) cc_final: 0.7081 (mp) outliers start: 73 outliers final: 44 residues processed: 562 average time/residue: 0.7123 time to fit residues: 484.9688 Evaluate side-chains 572 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 515 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1139 LYS Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 706 ARG Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 1106 GLU Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7642 > 50: distance: 61 - 82: 5.105 distance: 73 - 97: 11.389 distance: 77 - 82: 6.039 distance: 78 - 105: 7.084 distance: 82 - 83: 7.965 distance: 83 - 84: 5.129 distance: 83 - 86: 11.413 distance: 84 - 85: 4.253 distance: 84 - 90: 21.088 distance: 86 - 87: 12.440 distance: 87 - 88: 15.148 distance: 87 - 89: 12.955 distance: 90 - 91: 13.039 distance: 91 - 92: 10.676 distance: 91 - 94: 18.422 distance: 92 - 93: 10.574 distance: 92 - 97: 17.109 distance: 94 - 95: 12.092 distance: 94 - 96: 26.271 distance: 97 - 98: 9.277 distance: 98 - 99: 15.630 distance: 98 - 101: 14.727 distance: 99 - 100: 26.517 distance: 99 - 105: 12.044 distance: 101 - 102: 12.035 distance: 101 - 103: 12.742 distance: 102 - 104: 20.506 distance: 105 - 106: 11.221 distance: 106 - 107: 17.984 distance: 106 - 109: 10.017 distance: 107 - 108: 21.025 distance: 107 - 113: 36.567 distance: 109 - 110: 17.258 distance: 110 - 111: 23.595 distance: 111 - 112: 30.270 distance: 113 - 114: 20.723 distance: 114 - 115: 23.704 distance: 114 - 117: 25.487 distance: 115 - 116: 22.238 distance: 115 - 121: 4.874 distance: 117 - 118: 19.669 distance: 118 - 119: 16.319 distance: 118 - 120: 36.780 distance: 121 - 122: 15.165 distance: 122 - 123: 10.299 distance: 122 - 125: 11.940 distance: 123 - 124: 12.979 distance: 123 - 128: 48.845 distance: 125 - 126: 9.387 distance: 125 - 127: 31.910 distance: 128 - 129: 13.332 distance: 129 - 130: 30.037 distance: 129 - 132: 22.388 distance: 130 - 131: 20.696 distance: 130 - 139: 8.288 distance: 132 - 133: 13.856 distance: 133 - 134: 37.158 distance: 133 - 135: 17.698 distance: 134 - 136: 5.732 distance: 135 - 137: 30.188 distance: 136 - 138: 17.258 distance: 137 - 138: 39.502 distance: 139 - 140: 25.843 distance: 139 - 145: 14.464 distance: 140 - 141: 9.116 distance: 140 - 143: 29.867 distance: 141 - 142: 19.358 distance: 141 - 146: 18.549 distance: 143 - 144: 15.771 distance: 144 - 145: 23.047 distance: 146 - 147: 11.712 distance: 146 - 152: 15.662 distance: 147 - 148: 25.813 distance: 147 - 150: 22.119 distance: 148 - 149: 23.856 distance: 148 - 153: 32.236 distance: 150 - 151: 21.204 distance: 151 - 152: 28.154 distance: 153 - 154: 8.588 distance: 154 - 155: 10.381 distance: 154 - 157: 9.165 distance: 155 - 156: 5.823 distance: 155 - 160: 14.754 distance: 157 - 158: 12.630 distance: 157 - 159: 20.531