Starting phenix.real_space_refine on Wed May 28 23:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y0e_38802/05_2025/8y0e_38802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y0e_38802/05_2025/8y0e_38802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y0e_38802/05_2025/8y0e_38802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y0e_38802/05_2025/8y0e_38802.map" model { file = "/net/cci-nas-00/data/ceres_data/8y0e_38802/05_2025/8y0e_38802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y0e_38802/05_2025/8y0e_38802.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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 6 6.06 5 Mg 1 5.21 5 S 179 5.16 5 C 19901 2.51 5 N 5354 2.21 5 O 5807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31248 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 11157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11157 Classifications: {'peptide': 1400} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1334} Chain breaks: 4 Chain: "B" Number of atoms: 9493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 9493 Classifications: {'peptide': 1200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1147} Chain breaks: 3 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2907 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 839 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1906 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 553 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Chain: "I" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1901 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 222} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 95.400 60.075 68.309 1.00 97.58 S ATOM 471 SG CYS A 62 93.812 58.719 65.148 1.00 75.82 S ATOM 531 SG CYS A 69 92.346 61.693 67.069 1.00 84.07 S ATOM 775 SG CYS A 99 78.618 41.605 107.720 1.00129.34 S ATOM 797 SG CYS A 102 79.399 38.271 105.929 1.00139.73 S ATOM 1049 SG CYS A 134 76.480 38.446 108.210 1.00144.43 S ATOM 1074 SG CYS A 137 79.919 38.552 109.679 1.00155.72 S ATOM 20169 SG CYS B1180 86.484 45.264 67.686 1.00 70.34 S ATOM 20194 SG CYS B1183 85.391 45.493 71.375 1.00 87.89 S ATOM 20310 SG CYS B1198 88.697 46.622 70.443 1.00 94.60 S ATOM 20332 SG CYS B1201 87.737 42.782 69.966 1.00106.68 S ATOM 28002 SG CYS G 4 51.741 83.779 137.711 1.00 97.55 S ATOM 28022 SG CYS G 7 55.219 84.115 136.203 1.00112.57 S ATOM 28156 SG CYS G 24 53.128 81.269 135.037 1.00121.84 S ATOM 28168 SG CYS G 26 54.352 81.257 138.592 1.00119.42 S ATOM 28538 SG CYS G 73 23.693 115.468 107.751 1.00117.16 S ATOM 28559 SG CYS G 76 25.026 118.924 108.350 1.00106.76 S ATOM 28716 SG CYS G 96 27.369 116.214 107.077 1.00 87.22 S ATOM 28733 SG CYS G 98 25.884 115.995 110.662 1.00 90.51 S ATOM 28838 SG CYS H 7 59.987 117.853 46.595 1.00 51.17 S ATOM 28862 SG CYS H 10 58.771 118.013 42.977 1.00 71.38 S ATOM 29203 SG CYS H 65 56.268 117.960 45.713 1.00 54.72 S ATOM 29209 SG CYS H 66 58.357 121.051 44.975 1.00 60.52 S Time building chain proxies: 18.78, per 1000 atoms: 0.60 Number of scatterers: 31248 At special positions: 0 Unit cell: (138.58, 152.52, 169.74, 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 6 29.99 S 179 16.00 Mg 1 11.99 O 5807 8.00 N 5354 7.00 C 19901 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: 9.09 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 4 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " Number of angles added : 33 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7414 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 44 sheets defined 43.8% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 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 98 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.590A pdb=" N ARG A 111 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.388A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 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: 3.670A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.721A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.587A pdb=" N THR A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix removed outlier: 3.594A pdb=" N GLY A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.654A pdb=" N LEU A 393 " --> pdb=" O ILE A 390 " (cutoff:3.500A) 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: 4.265A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.190A pdb=" N ILE A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.924A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.863A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (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: 3.804A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 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: 3.868A 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: 3.861A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 4.066A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (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 978 through 983 Processing helix chain 'A' and resid 988 through 995 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 1032 Processing helix chain 'A' and resid 1040 through 1059 removed outlier: 3.655A pdb=" N GLU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Proline residue: A1052 - end of helix removed outlier: 3.678A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.605A pdb=" N ALA A1110 " --> pdb=" O ASN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.576A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.905A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1159 " --> pdb=" O MET A1155 " (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 1257 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.832A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 removed outlier: 3.535A pdb=" N MET A1416 " --> pdb=" O ALA A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.841A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 4.173A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Proline residue: B 56 - end of helix Processing helix chain 'B' and resid 76 through 81 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 278 Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 300 through 315 Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.603A pdb=" N ILE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 352 removed outlier: 3.967A pdb=" N SER B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.612A pdb=" N VAL B 357 " --> pdb=" O ASP B 353 " (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 Processing helix chain 'B' and resid 421 through 452 Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.686A pdb=" N LYS B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'B' and resid 603 through 611 Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 696 Processing helix chain 'B' and resid 698 through 705 removed outlier: 3.985A pdb=" N TRP B 701 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 702 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.552A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 785 removed outlier: 3.640A pdb=" N VAL B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.717A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 841 removed outlier: 3.632A pdb=" N TYR B 841 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'B' and resid 1031 through 1037 removed outlier: 4.747A pdb=" N SER B1035 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B1036 " --> pdb=" O SER B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.896A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1162 through 1169 Processing helix chain 'B' and resid 1201 through 1205 removed outlier: 3.583A pdb=" N ALA B1205 " --> pdb=" O ASP B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 259 Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.639A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 359 removed outlier: 3.689A pdb=" N ALA C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.872A 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 80 removed outlier: 3.665A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.765A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.757A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.635A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 195 removed outlier: 3.585A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 185 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 removed outlier: 4.187A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 314 removed outlier: 3.904A pdb=" N PHE F 314 " --> pdb=" O LEU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 323 removed outlier: 3.920A pdb=" N LYS F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.827A pdb=" N MET F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 36 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 'H' and resid 14 through 33 removed outlier: 4.422A pdb=" N ALA H 19 " --> pdb=" O GLY H 15 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 32 " --> pdb=" O TYR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 57 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.573A pdb=" N THR H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.743A 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 'I' and resid 1016 through 1027 removed outlier: 3.923A pdb=" N ILE I1020 " --> pdb=" O ASP I1016 " (cutoff:3.500A) Processing helix chain 'I' and resid 1030 through 1035 removed outlier: 3.710A pdb=" N ILE I1034 " --> pdb=" O SER I1030 " (cutoff:3.500A) Processing helix chain 'I' and resid 1044 through 1051 removed outlier: 3.589A pdb=" N GLU I1050 " --> pdb=" O ALA I1046 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY I1051 " --> pdb=" O ASP I1047 " (cutoff:3.500A) Processing helix chain 'I' and resid 1063 through 1085 removed outlier: 3.983A pdb=" N MET I1067 " --> pdb=" O ASP I1063 " (cutoff:3.500A) Processing helix chain 'I' and resid 1086 through 1089 Processing helix chain 'I' and resid 1093 through 1101 Processing helix chain 'I' and resid 1104 through 1115 removed outlier: 4.097A pdb=" N GLU I1112 " --> pdb=" O LYS I1108 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS I1113 " --> pdb=" O GLU I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1121 through 1133 Processing helix chain 'I' and resid 1133 through 1154 Processing helix chain 'I' and resid 1158 through 1183 Processing helix chain 'I' and resid 1209 through 1214 removed outlier: 3.506A pdb=" N TYR I1213 " --> pdb=" O ASP I1209 " (cutoff:3.500A) Processing helix chain 'I' and resid 1242 through 1247 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.216A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.971A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.433A pdb=" N MET A 27 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLN A 77 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS A 199 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.877A pdb=" N ALA A 80 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N VAL A 197 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.416A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 161 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.663A pdb=" N SER A 325 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.674A 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: 3.650A pdb=" N TYR A 406 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 7.079A 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 522 Processing sheet with id=AB2, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.799A 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 836 through 838 removed outlier: 6.433A 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 1272 removed outlier: 3.885A pdb=" N ASN A1267 " --> pdb=" O ASN A1296 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYR A1291 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A1098 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N GLU A1093 " --> pdb=" O ILE A1314 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N ILE A1314 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N LEU A1095 " --> pdb=" O TYR A1312 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N TYR A1312 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG A1097 " --> pdb=" O ASP A1310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.416A pdb=" N ILE A1221 " --> pdb=" O LEU A1178 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A1178 " --> pdb=" O ILE A1221 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1275 through 1278 Processing sheet with id=AC1, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.602A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 145 through 151 removed outlier: 3.838A pdb=" N GLU B 146 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 138 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLY B 126 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 159 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 128 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 157 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 145 through 151 removed outlier: 3.838A pdb=" N GLU B 146 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 138 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC5, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC6, first strand: chain 'B' and resid 416 through 420 Processing sheet with id=AC7, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.065A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 597 removed outlier: 5.252A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.507A pdb=" N ARG B 671 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.720A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.562A pdb=" N ARG B 823 " --> pdb=" O TYR B 882 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 925 " --> pdb=" O VAL B 965 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD4, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.251A pdb=" N VAL B 867 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA B1009 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 866 " --> pdb=" O ILE B1027 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AD6, first strand: chain 'B' and resid 932 through 933 removed outlier: 3.981A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD8, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 12 removed outlier: 6.210A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS C 216 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS C 186 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 218 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 184 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY C 220 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 67 through 73 removed outlier: 5.162A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 123 through 126 removed outlier: 4.457A pdb=" N GLY C 150 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.500A pdb=" N THR C 277 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS C 325 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU C 318 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 313 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 320 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.497A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 88 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR D 121 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU D 90 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.698A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 2 through 10 removed outlier: 5.906A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 86 through 91 removed outlier: 3.625A pdb=" N ILE F 112 " --> pdb=" O GLY F 102 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N SER F 149 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N SER F 137 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR F 151 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE F 87 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 68 through 69 1376 hydrogen bonds defined for protein. 3801 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: 15.13 Time building geometry restraints manager: 10.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10270 1.34 - 1.46: 6357 1.46 - 1.58: 14935 1.58 - 1.70: 3 1.70 - 1.82: 294 Bond restraints: 31859 Sorted by residual: bond pdb=" CG PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.503 1.346 0.157 3.40e-02 8.65e+02 2.14e+01 bond pdb=" CB PRO B 899 " pdb=" CG PRO B 899 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.10e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.42e+00 bond pdb=" CB PRO F 143 " pdb=" CG PRO F 143 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.53e+00 bond pdb=" CB PRO A1204 " pdb=" CG PRO A1204 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.98e+00 ... (remaining 31854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 42914 3.48 - 6.97: 189 6.97 - 10.45: 16 10.45 - 13.94: 5 13.94 - 17.42: 1 Bond angle restraints: 43125 Sorted by residual: angle pdb=" CA PRO B 899 " pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 112.00 94.58 17.42 1.40e+00 5.10e-01 1.55e+02 angle pdb=" N PRO B 899 " pdb=" CD PRO B 899 " pdb=" CG PRO B 899 " ideal model delta sigma weight residual 103.20 93.64 9.56 1.50e+00 4.44e-01 4.06e+01 angle pdb=" CA PRO F 143 " pdb=" N PRO F 143 " pdb=" CD PRO F 143 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.03e+01 angle pdb=" CA GLU C 274 " pdb=" CB GLU C 274 " pdb=" CG GLU C 274 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" N GLU C 274 " pdb=" CA GLU C 274 " pdb=" C GLU C 274 " ideal model delta sigma weight residual 111.30 104.81 6.49 1.43e+00 4.89e-01 2.06e+01 ... (remaining 43120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16688 17.94 - 35.88: 2035 35.88 - 53.83: 540 53.83 - 71.77: 121 71.77 - 89.71: 38 Dihedral angle restraints: 19422 sinusoidal: 7959 harmonic: 11463 Sorted by residual: dihedral pdb=" CA LYS E 124 " pdb=" C LYS E 124 " pdb=" N VAL E 125 " pdb=" CA VAL E 125 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA B1007 " pdb=" C ALA B1007 " pdb=" N LEU B1008 " pdb=" CA LEU B1008 " ideal model delta harmonic sigma weight residual 180.00 157.43 22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU C 29 " pdb=" C LEU C 29 " pdb=" N PHE C 30 " pdb=" CA PHE C 30 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 19419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3887 0.055 - 0.110: 875 0.110 - 0.165: 127 0.165 - 0.221: 2 0.221 - 0.276: 1 Chirality restraints: 4892 Sorted by residual: chirality pdb=" CA PRO B 899 " pdb=" N PRO B 899 " pdb=" C PRO B 899 " pdb=" CB PRO B 899 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE B 934 " pdb=" CA ILE B 934 " pdb=" CG1 ILE B 934 " pdb=" CG2 ILE B 934 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU C 29 " pdb=" N LEU C 29 " pdb=" C LEU C 29 " pdb=" CB LEU C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 4889 not shown) Planarity restraints: 5558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 898 " 0.110 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO B 899 " -0.258 5.00e-02 4.00e+02 pdb=" CA PRO B 899 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 899 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 31 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C GLN G 31 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN G 31 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY G 32 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 701 " -0.014 2.00e-02 2.50e+03 1.66e-02 6.91e+00 pdb=" CG TRP B 701 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 701 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 701 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 701 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 701 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 701 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 701 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 701 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 701 " -0.000 2.00e-02 2.50e+03 ... (remaining 5555 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 273 2.51 - 3.10: 23490 3.10 - 3.70: 50213 3.70 - 4.30: 72624 4.30 - 4.90: 123033 Nonbonded interactions: 269633 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.907 2.170 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1503 " model vdw 2.040 2.170 nonbonded pdb=" OH TYR A1133 " pdb=" O ASP G 17 " model vdw 2.108 3.040 nonbonded pdb=" OH TYR I1080 " pdb=" O PRO I1116 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR B 728 " pdb=" OE1 GLU B 730 " model vdw 2.152 3.040 ... (remaining 269628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 82.130 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.120 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.006 0.166 31883 Z= 0.230 Angle : 0.666 17.422 43158 Z= 0.346 Chirality : 0.046 0.276 4892 Planarity : 0.005 0.150 5558 Dihedral : 17.246 89.709 12008 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 4.19 % Allowed : 23.54 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3882 helix: 0.83 (0.13), residues: 1474 sheet: -0.43 (0.23), residues: 552 loop : -0.53 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 701 HIS 0.009 0.001 HIS B 527 PHE 0.020 0.002 PHE A 912 TYR 0.032 0.002 TYR B 799 ARG 0.015 0.000 ARG I1049 Details of bonding type rmsd hydrogen bonds : bond 0.18150 ( 1370) hydrogen bonds : angle 7.05711 ( 3801) metal coordination : bond 0.00901 ( 24) metal coordination : angle 3.70132 ( 33) covalent geometry : bond 0.00557 (31859) covalent geometry : angle 0.65882 (43125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 290 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6942 (mmt) REVERT: A 1051 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: C 272 MET cc_start: 0.8129 (mtp) cc_final: 0.7928 (mmm) REVERT: E 124 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6978 (mmmt) REVERT: F 317 GLU cc_start: 0.6177 (mm-30) cc_final: 0.3766 (mp0) REVERT: G 70 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8430 (mmmt) REVERT: G 71 LYS cc_start: 0.8864 (tppp) cc_final: 0.8355 (tptt) outliers start: 146 outliers final: 115 residues processed: 418 average time/residue: 1.0866 time to fit residues: 561.2892 Evaluate side-chains 398 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 280 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1240 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1308 ASN Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 731 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 908 LYS Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1195 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain I residue 1037 ILE Chi-restraints excluded: chain I residue 1151 THR Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1162 VAL Chi-restraints excluded: chain I residue 1173 LEU Chi-restraints excluded: chain I residue 1206 SER Chi-restraints excluded: chain I residue 1208 ASP Chi-restraints excluded: chain I residue 1209 ASP Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 184 optimal weight: 0.1980 chunk 225 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 330 ASN A 388 HIS A 445 GLN A 592 GLN A 646 ASN A 724 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS B 802 ASN C 7 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN D 113 ASN E 63 ASN E 130 GLN F 302 ASN G 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.118934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091031 restraints weight = 61021.715| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.32 r_work: 0.3299 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31883 Z= 0.155 Angle : 0.594 8.255 43158 Z= 0.310 Chirality : 0.045 0.182 4892 Planarity : 0.004 0.047 5558 Dihedral : 7.617 77.833 4454 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.10 % Favored : 94.62 % Rotamer: Outliers : 5.74 % Allowed : 21.05 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3882 helix: 0.99 (0.13), residues: 1496 sheet: -0.50 (0.22), residues: 551 loop : -0.51 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 701 HIS 0.010 0.001 HIS B 527 PHE 0.022 0.001 PHE A 918 TYR 0.023 0.001 TYR B 799 ARG 0.007 0.000 ARG I1049 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 1370) hydrogen bonds : angle 5.56396 ( 3801) metal coordination : bond 0.00647 ( 24) metal coordination : angle 3.77456 ( 33) covalent geometry : bond 0.00350 (31859) covalent geometry : angle 0.58486 (43125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 317 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7400 (t) REVERT: A 232 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.5773 (t80) REVERT: A 1173 ASN cc_start: 0.7282 (t0) cc_final: 0.6929 (t0) REVERT: A 1225 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8163 (pp) REVERT: A 1309 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8983 (mp) REVERT: B 352 SER cc_start: 0.8618 (m) cc_final: 0.8332 (p) REVERT: B 900 ASP cc_start: 0.3688 (OUTLIER) cc_final: 0.3414 (p0) REVERT: B 984 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 1036 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6807 (mtm-85) REVERT: C 274 GLU cc_start: 0.7440 (tm-30) cc_final: 0.6701 (tp30) REVERT: C 301 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8339 (tmm) REVERT: E 124 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6845 (mmmt) REVERT: F 317 GLU cc_start: 0.6302 (mm-30) cc_final: 0.4361 (mp0) outliers start: 200 outliers final: 86 residues processed: 475 average time/residue: 1.1234 time to fit residues: 655.5698 Evaluate side-chains 383 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 288 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1020 ASP Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1195 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1067 MET Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1151 THR Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1208 ASP Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 77 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 310 optimal weight: 0.0770 chunk 368 optimal weight: 0.0050 chunk 194 optimal weight: 0.0980 chunk 274 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 overall best weight: 0.8354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 445 GLN A 592 GLN A1100 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS D 33 GLN D 113 ASN E 63 ASN E 130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.092170 restraints weight = 61335.120| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.37 r_work: 0.3316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31883 Z= 0.129 Angle : 0.560 8.276 43158 Z= 0.290 Chirality : 0.044 0.160 4892 Planarity : 0.004 0.047 5558 Dihedral : 6.504 59.957 4359 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.84 % Favored : 94.87 % Rotamer: Outliers : 5.34 % Allowed : 22.05 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3882 helix: 1.05 (0.13), residues: 1507 sheet: -0.59 (0.22), residues: 553 loop : -0.50 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 701 HIS 0.007 0.001 HIS B 527 PHE 0.021 0.001 PHE A 918 TYR 0.040 0.001 TYR B 799 ARG 0.007 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 1370) hydrogen bonds : angle 5.24833 ( 3801) metal coordination : bond 0.00640 ( 24) metal coordination : angle 3.54065 ( 33) covalent geometry : bond 0.00288 (31859) covalent geometry : angle 0.55202 (43125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 326 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7393 (t) REVERT: A 1274 MET cc_start: 0.7943 (mmm) cc_final: 0.7681 (mmm) REVERT: A 1286 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8325 (ttm-80) REVERT: A 1309 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8954 (mp) REVERT: B 329 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7643 (ptt90) REVERT: B 352 SER cc_start: 0.8577 (m) cc_final: 0.8285 (p) REVERT: B 432 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8030 (mp) REVERT: B 900 ASP cc_start: 0.3603 (OUTLIER) cc_final: 0.3344 (p0) REVERT: B 1036 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6789 (mtm-85) REVERT: C 274 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: C 301 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8358 (tmm) REVERT: E 68 SER cc_start: 0.9213 (t) cc_final: 0.8966 (p) REVERT: E 124 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6719 (mmmt) REVERT: F 317 GLU cc_start: 0.6359 (mm-30) cc_final: 0.4619 (mp0) REVERT: G 28 GLU cc_start: 0.7983 (tt0) cc_final: 0.7667 (tt0) REVERT: G 68 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: G 71 LYS cc_start: 0.8913 (tppp) cc_final: 0.8376 (tptt) REVERT: I 1249 GLN cc_start: 0.3801 (OUTLIER) cc_final: 0.3223 (tt0) outliers start: 186 outliers final: 87 residues processed: 468 average time/residue: 1.1215 time to fit residues: 653.4151 Evaluate side-chains 396 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 297 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1067 MET Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1223 ILE Chi-restraints excluded: chain I residue 1228 ASP Chi-restraints excluded: chain I residue 1249 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 29 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 149 optimal weight: 0.0170 chunk 115 optimal weight: 0.0870 chunk 123 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 330 ASN A 445 GLN A 592 GLN A1100 ASN A1161 ASN A1381 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS D 33 GLN D 49 ASN E 63 ASN E 130 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091611 restraints weight = 61545.605| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.35 r_work: 0.3305 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31883 Z= 0.149 Angle : 0.565 8.770 43158 Z= 0.290 Chirality : 0.044 0.176 4892 Planarity : 0.004 0.047 5558 Dihedral : 6.109 58.791 4333 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.07 % Favored : 94.62 % Rotamer: Outliers : 5.74 % Allowed : 22.39 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3882 helix: 1.06 (0.13), residues: 1508 sheet: -0.59 (0.22), residues: 562 loop : -0.49 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 701 HIS 0.008 0.001 HIS B 527 PHE 0.020 0.001 PHE A 918 TYR 0.029 0.001 TYR B 799 ARG 0.013 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 1370) hydrogen bonds : angle 5.12664 ( 3801) metal coordination : bond 0.00713 ( 24) metal coordination : angle 3.43828 ( 33) covalent geometry : bond 0.00346 (31859) covalent geometry : angle 0.55761 (43125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 312 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: A 69 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7430 (t) REVERT: A 117 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7589 (mtp180) REVERT: A 123 GLU cc_start: 0.8687 (tt0) cc_final: 0.8368 (tt0) REVERT: A 232 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6181 (m-80) REVERT: A 1274 MET cc_start: 0.7882 (mmm) cc_final: 0.7595 (mmm) REVERT: A 1288 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: A 1309 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 61 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7742 (mm-40) REVERT: B 329 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7821 (ptp90) REVERT: B 352 SER cc_start: 0.8585 (m) cc_final: 0.8272 (p) REVERT: B 637 MET cc_start: 0.8229 (mmm) cc_final: 0.8013 (mmm) REVERT: B 900 ASP cc_start: 0.3698 (OUTLIER) cc_final: 0.3425 (p0) REVERT: B 968 VAL cc_start: 0.5304 (OUTLIER) cc_final: 0.5065 (m) REVERT: B 984 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8307 (mp) REVERT: B 1036 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6736 (mtm-85) REVERT: C 301 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8401 (tmm) REVERT: D 113 ASN cc_start: 0.8120 (m110) cc_final: 0.7799 (p0) REVERT: E 125 VAL cc_start: 0.5796 (OUTLIER) cc_final: 0.5389 (m) REVERT: F 317 GLU cc_start: 0.6328 (mm-30) cc_final: 0.4494 (mp0) REVERT: G 28 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: G 68 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: H 1 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7798 (mtt) REVERT: I 1157 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: I 1249 GLN cc_start: 0.3727 (OUTLIER) cc_final: 0.3189 (tt0) outliers start: 200 outliers final: 101 residues processed: 467 average time/residue: 1.1578 time to fit residues: 670.0958 Evaluate side-chains 411 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 291 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1161 MET Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1067 MET Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1157 GLU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1208 ASP Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1223 ILE Chi-restraints excluded: chain I residue 1228 ASP Chi-restraints excluded: chain I residue 1249 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 185 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 190 optimal weight: 0.0970 chunk 255 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A 637 GLN A1100 ASN A1161 ASN B 18 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS D 33 GLN D 113 ASN E 63 ASN E 130 GLN I1249 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.093941 restraints weight = 61197.082| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.30 r_work: 0.3338 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31883 Z= 0.115 Angle : 0.549 8.631 43158 Z= 0.282 Chirality : 0.043 0.168 4892 Planarity : 0.004 0.046 5558 Dihedral : 5.807 57.984 4326 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.77 % Favored : 94.95 % Rotamer: Outliers : 5.23 % Allowed : 23.34 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3882 helix: 1.13 (0.13), residues: 1513 sheet: -0.52 (0.23), residues: 556 loop : -0.41 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 701 HIS 0.008 0.001 HIS B 527 PHE 0.021 0.001 PHE C 30 TYR 0.025 0.001 TYR B 799 ARG 0.010 0.000 ARG I1049 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1370) hydrogen bonds : angle 4.94946 ( 3801) metal coordination : bond 0.00548 ( 24) metal coordination : angle 3.23016 ( 33) covalent geometry : bond 0.00258 (31859) covalent geometry : angle 0.54189 (43125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 332 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 69 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 117 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7576 (mtp180) REVERT: A 123 GLU cc_start: 0.8696 (tt0) cc_final: 0.8382 (tt0) REVERT: A 232 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: A 1173 ASN cc_start: 0.7027 (t0) cc_final: 0.6628 (t0) REVERT: A 1274 MET cc_start: 0.7821 (mmm) cc_final: 0.7526 (mmm) REVERT: A 1288 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: A 1306 ASP cc_start: 0.8462 (t0) cc_final: 0.8252 (t0) REVERT: A 1309 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8891 (mp) REVERT: B 61 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7754 (mm-40) REVERT: B 329 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7863 (ptp90) REVERT: B 352 SER cc_start: 0.8610 (m) cc_final: 0.8286 (p) REVERT: B 900 ASP cc_start: 0.3750 (OUTLIER) cc_final: 0.3506 (p0) REVERT: B 968 VAL cc_start: 0.5388 (OUTLIER) cc_final: 0.5187 (m) REVERT: B 984 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 996 MET cc_start: 0.8797 (mtp) cc_final: 0.8582 (mtp) REVERT: C 272 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7898 (mmm) REVERT: C 274 GLU cc_start: 0.7672 (tt0) cc_final: 0.6954 (tp30) REVERT: C 301 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8287 (tmm) REVERT: D 113 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7727 (p0) REVERT: E 125 VAL cc_start: 0.5377 (OUTLIER) cc_final: 0.5025 (m) REVERT: F 317 GLU cc_start: 0.6282 (mm-30) cc_final: 0.4328 (mp0) REVERT: G 28 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: G 71 LYS cc_start: 0.8943 (tppp) cc_final: 0.8429 (tptt) REVERT: H 1 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7706 (mtt) REVERT: I 1157 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: I 1249 GLN cc_start: 0.3697 (OUTLIER) cc_final: 0.3131 (tt0) outliers start: 182 outliers final: 87 residues processed: 476 average time/residue: 1.1749 time to fit residues: 688.2194 Evaluate side-chains 409 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 303 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1067 MET Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1157 GLU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1193 ILE Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1223 ILE Chi-restraints excluded: chain I residue 1249 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 229 optimal weight: 4.9990 chunk 350 optimal weight: 0.6980 chunk 311 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 chunk 365 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 212 optimal weight: 0.4980 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 24 GLN A 261 GLN A 592 GLN A 959 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 HIS B 704 HIS B 861 GLN C 251 GLN D 113 ASN E 63 ASN E 130 GLN ** I1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.119532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091416 restraints weight = 61724.332| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.34 r_work: 0.3297 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31883 Z= 0.188 Angle : 0.594 9.933 43158 Z= 0.304 Chirality : 0.045 0.171 4892 Planarity : 0.004 0.061 5558 Dihedral : 5.954 89.499 4320 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.31 % Favored : 94.41 % Rotamer: Outliers : 5.40 % Allowed : 23.69 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3882 helix: 1.07 (0.13), residues: 1513 sheet: -0.55 (0.23), residues: 542 loop : -0.42 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 701 HIS 0.008 0.001 HIS B 527 PHE 0.019 0.002 PHE A 918 TYR 0.027 0.002 TYR F 69 ARG 0.012 0.000 ARG I1049 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1370) hydrogen bonds : angle 5.03387 ( 3801) metal coordination : bond 0.00792 ( 24) metal coordination : angle 3.43188 ( 33) covalent geometry : bond 0.00443 (31859) covalent geometry : angle 0.58664 (43125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 310 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7540 (t) REVERT: A 117 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7602 (mtp180) REVERT: A 123 GLU cc_start: 0.8728 (tt0) cc_final: 0.8392 (tt0) REVERT: A 232 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: A 253 PRO cc_start: 0.8952 (Cg_exo) cc_final: 0.8746 (Cg_endo) REVERT: A 1144 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7051 (tpt) REVERT: A 1173 ASN cc_start: 0.7247 (t0) cc_final: 0.7036 (t0) REVERT: A 1233 ARG cc_start: 0.8078 (ptt-90) cc_final: 0.7345 (tmm160) REVERT: A 1274 MET cc_start: 0.7983 (mmm) cc_final: 0.7572 (mmm) REVERT: A 1288 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: A 1306 ASP cc_start: 0.8535 (t0) cc_final: 0.8281 (t0) REVERT: B 352 SER cc_start: 0.8592 (m) cc_final: 0.8280 (p) REVERT: B 637 MET cc_start: 0.8147 (mmt) cc_final: 0.7925 (mmm) REVERT: B 900 ASP cc_start: 0.3701 (OUTLIER) cc_final: 0.3451 (p0) REVERT: B 984 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 996 MET cc_start: 0.8873 (mtp) cc_final: 0.8662 (mtp) REVERT: C 274 GLU cc_start: 0.7615 (tt0) cc_final: 0.6934 (tp30) REVERT: C 301 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8293 (tmm) REVERT: D 49 ASN cc_start: 0.8454 (t0) cc_final: 0.8105 (m110) REVERT: E 125 VAL cc_start: 0.5587 (OUTLIER) cc_final: 0.5236 (m) REVERT: G 28 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: I 1157 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: I 1192 MET cc_start: 0.6021 (pp-130) cc_final: 0.5753 (ppp) REVERT: I 1238 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6721 (mt) outliers start: 188 outliers final: 104 residues processed: 457 average time/residue: 1.0390 time to fit residues: 589.9680 Evaluate side-chains 409 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 293 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1195 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1151 THR Chi-restraints excluded: chain I residue 1157 GLU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1208 ASP Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 241 optimal weight: 0.3980 chunk 255 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 337 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS B 861 GLN D 33 GLN D 113 ASN E 63 ASN E 130 GLN ** I1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093070 restraints weight = 61370.857| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.37 r_work: 0.3326 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31883 Z= 0.126 Angle : 0.569 10.633 43158 Z= 0.291 Chirality : 0.044 0.169 4892 Planarity : 0.004 0.045 5558 Dihedral : 5.692 70.657 4316 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.97 % Favored : 94.74 % Rotamer: Outliers : 4.71 % Allowed : 24.17 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3882 helix: 1.13 (0.13), residues: 1513 sheet: -0.54 (0.22), residues: 558 loop : -0.39 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 701 HIS 0.008 0.001 HIS B 527 PHE 0.020 0.001 PHE C 30 TYR 0.058 0.001 TYR B 799 ARG 0.016 0.000 ARG B1036 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1370) hydrogen bonds : angle 4.92768 ( 3801) metal coordination : bond 0.00587 ( 24) metal coordination : angle 3.24754 ( 33) covalent geometry : bond 0.00290 (31859) covalent geometry : angle 0.56242 (43125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 319 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7495 (t) REVERT: A 117 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7152 (mtp180) REVERT: A 123 GLU cc_start: 0.8719 (tt0) cc_final: 0.8401 (tt0) REVERT: A 232 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6135 (m-80) REVERT: A 1173 ASN cc_start: 0.7157 (t0) cc_final: 0.6929 (t0) REVERT: A 1233 ARG cc_start: 0.8036 (ptt-90) cc_final: 0.7347 (tmm160) REVERT: A 1274 MET cc_start: 0.7920 (mmm) cc_final: 0.7519 (mmm) REVERT: A 1288 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: A 1306 ASP cc_start: 0.8544 (t0) cc_final: 0.8311 (t0) REVERT: B 61 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: B 352 SER cc_start: 0.8587 (m) cc_final: 0.8279 (p) REVERT: B 464 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 584 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8190 (tp) REVERT: B 900 ASP cc_start: 0.3665 (OUTLIER) cc_final: 0.3421 (p0) REVERT: B 984 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8190 (mp) REVERT: C 274 GLU cc_start: 0.7650 (tt0) cc_final: 0.6914 (tp30) REVERT: C 301 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8289 (tmm) REVERT: D 49 ASN cc_start: 0.8433 (t0) cc_final: 0.8137 (m110) REVERT: E 125 VAL cc_start: 0.5419 (OUTLIER) cc_final: 0.5088 (m) REVERT: G 28 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: G 31 GLN cc_start: 0.7311 (tm-30) cc_final: 0.7068 (tp-100) REVERT: G 70 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8557 (tptm) REVERT: G 71 LYS cc_start: 0.8925 (tppp) cc_final: 0.8409 (tptt) REVERT: I 1157 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: I 1238 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6671 (mt) outliers start: 164 outliers final: 98 residues processed: 450 average time/residue: 1.1155 time to fit residues: 623.2053 Evaluate side-chains 408 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 296 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 912 ASN Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1157 GLU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1208 ASP Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1223 ILE Chi-restraints excluded: chain I residue 1238 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 275 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 261 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS E 63 ASN E 130 GLN ** I1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090406 restraints weight = 61732.210| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.29 r_work: 0.3295 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31883 Z= 0.213 Angle : 0.632 11.989 43158 Z= 0.322 Chirality : 0.046 0.192 4892 Planarity : 0.004 0.060 5558 Dihedral : 5.908 85.881 4314 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.33 % Favored : 94.38 % Rotamer: Outliers : 4.51 % Allowed : 24.49 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3882 helix: 0.99 (0.13), residues: 1513 sheet: -0.61 (0.23), residues: 536 loop : -0.46 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 701 HIS 0.009 0.001 HIS B 527 PHE 0.020 0.002 PHE A 417 TYR 0.042 0.002 TYR B 799 ARG 0.007 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1370) hydrogen bonds : angle 5.07522 ( 3801) metal coordination : bond 0.00880 ( 24) metal coordination : angle 3.79029 ( 33) covalent geometry : bond 0.00504 (31859) covalent geometry : angle 0.62354 (43125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 299 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7656 (t) REVERT: A 117 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7231 (mtp180) REVERT: A 123 GLU cc_start: 0.8748 (tt0) cc_final: 0.8440 (tt0) REVERT: A 226 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6505 (tp) REVERT: A 232 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: A 1173 ASN cc_start: 0.7228 (t0) cc_final: 0.6988 (t0) REVERT: A 1233 ARG cc_start: 0.8045 (ptt-90) cc_final: 0.7359 (tmm160) REVERT: A 1274 MET cc_start: 0.8009 (mmm) cc_final: 0.7586 (mmm) REVERT: A 1288 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: A 1306 ASP cc_start: 0.8589 (t0) cc_final: 0.8384 (t0) REVERT: B 61 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7834 (mm-40) REVERT: B 352 SER cc_start: 0.8615 (m) cc_final: 0.8312 (p) REVERT: B 464 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: B 900 ASP cc_start: 0.3718 (OUTLIER) cc_final: 0.3448 (p0) REVERT: B 984 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8254 (mp) REVERT: C 274 GLU cc_start: 0.7635 (tt0) cc_final: 0.6996 (tp30) REVERT: C 301 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8331 (tmm) REVERT: D 49 ASN cc_start: 0.8482 (t0) cc_final: 0.8211 (m110) REVERT: E 125 VAL cc_start: 0.5648 (OUTLIER) cc_final: 0.5274 (m) REVERT: G 28 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: G 70 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8574 (tppt) REVERT: G 71 LYS cc_start: 0.8913 (tppp) cc_final: 0.8403 (tptt) REVERT: G 79 ASP cc_start: 0.7871 (t0) cc_final: 0.7589 (t0) REVERT: I 1157 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7374 (pp20) REVERT: I 1238 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6799 (mt) outliers start: 157 outliers final: 98 residues processed: 426 average time/residue: 1.1184 time to fit residues: 588.5498 Evaluate side-chains 400 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 288 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1195 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1151 THR Chi-restraints excluded: chain I residue 1157 GLU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1208 ASP Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1238 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 178 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 369 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 379 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS D 33 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 130 GLN ** I1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.092145 restraints weight = 60988.571| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.30 r_work: 0.3319 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31883 Z= 0.127 Angle : 0.598 12.103 43158 Z= 0.304 Chirality : 0.044 0.175 4892 Planarity : 0.004 0.074 5558 Dihedral : 5.770 90.257 4313 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.82 % Rotamer: Outliers : 3.67 % Allowed : 25.41 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3882 helix: 1.09 (0.13), residues: 1512 sheet: -0.54 (0.22), residues: 561 loop : -0.40 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 701 HIS 0.009 0.001 HIS B 527 PHE 0.024 0.001 PHE C 30 TYR 0.044 0.001 TYR B 799 ARG 0.007 0.000 ARG I1049 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1370) hydrogen bonds : angle 4.92761 ( 3801) metal coordination : bond 0.00628 ( 24) metal coordination : angle 3.37985 ( 33) covalent geometry : bond 0.00292 (31859) covalent geometry : angle 0.59091 (43125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 312 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7526 (t) REVERT: A 117 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: A 123 GLU cc_start: 0.8760 (tt0) cc_final: 0.8424 (tt0) REVERT: A 226 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6368 (tp) REVERT: A 232 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: A 301 ARG cc_start: 0.8548 (tpm170) cc_final: 0.8249 (tpm170) REVERT: A 1173 ASN cc_start: 0.7285 (t0) cc_final: 0.7010 (t0) REVERT: A 1233 ARG cc_start: 0.8046 (ptt-90) cc_final: 0.7347 (tmm160) REVERT: A 1245 LYS cc_start: 0.8195 (tppp) cc_final: 0.7608 (ttmm) REVERT: A 1274 MET cc_start: 0.7998 (mmm) cc_final: 0.7585 (mmm) REVERT: A 1288 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 1306 ASP cc_start: 0.8561 (t0) cc_final: 0.8357 (t0) REVERT: B 61 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: B 352 SER cc_start: 0.8620 (m) cc_final: 0.8309 (p) REVERT: B 900 ASP cc_start: 0.3605 (OUTLIER) cc_final: 0.3335 (p0) REVERT: B 984 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 274 GLU cc_start: 0.7725 (tt0) cc_final: 0.7066 (tp30) REVERT: C 301 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8337 (tmm) REVERT: D 49 ASN cc_start: 0.8473 (t0) cc_final: 0.8209 (m110) REVERT: E 125 VAL cc_start: 0.5451 (OUTLIER) cc_final: 0.5103 (m) REVERT: F 73 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8201 (ttt90) REVERT: G 28 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: G 49 MET cc_start: 0.7398 (tpp) cc_final: 0.6900 (ttp) REVERT: G 70 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8570 (tppt) REVERT: G 71 LYS cc_start: 0.8867 (tppp) cc_final: 0.8351 (tptt) REVERT: G 79 ASP cc_start: 0.7782 (t0) cc_final: 0.7515 (t0) REVERT: I 1238 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6649 (mt) outliers start: 128 outliers final: 93 residues processed: 418 average time/residue: 1.1631 time to fit residues: 600.6287 Evaluate side-chains 403 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 298 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 260 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 239 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 592 GLN A1100 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS C 353 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 130 GLN ** I1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095446 restraints weight = 60860.538| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.32 r_work: 0.3340 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31883 Z= 0.122 Angle : 0.598 12.197 43158 Z= 0.303 Chirality : 0.044 0.175 4892 Planarity : 0.004 0.097 5558 Dihedral : 5.585 81.132 4311 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.00 % Favored : 94.74 % Rotamer: Outliers : 3.10 % Allowed : 26.13 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3882 helix: 1.15 (0.13), residues: 1507 sheet: -0.50 (0.23), residues: 550 loop : -0.35 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 701 HIS 0.009 0.001 HIS D 193 PHE 0.025 0.001 PHE C 30 TYR 0.042 0.001 TYR B 799 ARG 0.014 0.000 ARG B1036 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 1370) hydrogen bonds : angle 4.88387 ( 3801) metal coordination : bond 0.00557 ( 24) metal coordination : angle 3.16224 ( 33) covalent geometry : bond 0.00277 (31859) covalent geometry : angle 0.59197 (43125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 333 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 117 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7241 (mtp180) REVERT: A 123 GLU cc_start: 0.8735 (tt0) cc_final: 0.8411 (tt0) REVERT: A 226 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6379 (tp) REVERT: A 232 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: A 301 ARG cc_start: 0.8520 (tpm170) cc_final: 0.8294 (tpm170) REVERT: A 685 LEU cc_start: 0.8753 (tt) cc_final: 0.8432 (mp) REVERT: A 1008 THR cc_start: 0.8773 (m) cc_final: 0.8565 (t) REVERT: A 1059 ASP cc_start: 0.7772 (t70) cc_final: 0.7411 (t70) REVERT: A 1173 ASN cc_start: 0.7234 (t0) cc_final: 0.6973 (t0) REVERT: A 1233 ARG cc_start: 0.8017 (ptt-90) cc_final: 0.7349 (tmm160) REVERT: A 1245 LYS cc_start: 0.8143 (tppp) cc_final: 0.7633 (ttmm) REVERT: A 1274 MET cc_start: 0.7951 (mmm) cc_final: 0.7581 (mmm) REVERT: A 1288 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: A 1323 MET cc_start: 0.8429 (tpt) cc_final: 0.8214 (tpt) REVERT: B 61 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7767 (mm-40) REVERT: B 352 SER cc_start: 0.8588 (m) cc_final: 0.8275 (p) REVERT: B 900 ASP cc_start: 0.3831 (OUTLIER) cc_final: 0.3594 (p0) REVERT: B 984 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (mp) REVERT: C 274 GLU cc_start: 0.7686 (tt0) cc_final: 0.7029 (tp30) REVERT: C 301 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8265 (tmm) REVERT: D 49 ASN cc_start: 0.8419 (t0) cc_final: 0.8174 (m110) REVERT: E 125 VAL cc_start: 0.5608 (OUTLIER) cc_final: 0.5329 (m) REVERT: F 73 ARG cc_start: 0.8550 (ttt90) cc_final: 0.8226 (ttt90) REVERT: G 28 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: G 49 MET cc_start: 0.7330 (tpp) cc_final: 0.6910 (ttp) REVERT: G 70 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8734 (tptm) REVERT: G 71 LYS cc_start: 0.8892 (tppp) cc_final: 0.8365 (tptt) REVERT: I 1172 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: I 1238 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6469 (mt) outliers start: 108 outliers final: 83 residues processed: 421 average time/residue: 1.1540 time to fit residues: 596.0193 Evaluate side-chains 402 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 306 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 1029 ILE Chi-restraints excluded: chain I residue 1138 LEU Chi-restraints excluded: chain I residue 1161 VAL Chi-restraints excluded: chain I residue 1172 GLU Chi-restraints excluded: chain I residue 1222 ASP Chi-restraints excluded: chain I residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 145 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 344 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 345 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN A 592 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** I1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.120784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093968 restraints weight = 61293.754| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.40 r_work: 0.3342 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31883 Z= 0.125 Angle : 0.604 12.198 43158 Z= 0.306 Chirality : 0.044 0.269 4892 Planarity : 0.004 0.085 5558 Dihedral : 5.536 90.216 4308 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.10 % Favored : 94.64 % Rotamer: Outliers : 3.10 % Allowed : 26.53 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3882 helix: 1.16 (0.13), residues: 1506 sheet: -0.45 (0.23), residues: 548 loop : -0.34 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 701 HIS 0.008 0.001 HIS B 527 PHE 0.025 0.001 PHE C 30 TYR 0.040 0.001 TYR B 799 ARG 0.012 0.000 ARG I1049 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1370) hydrogen bonds : angle 4.84655 ( 3801) metal coordination : bond 0.00565 ( 24) metal coordination : angle 3.03049 ( 33) covalent geometry : bond 0.00288 (31859) covalent geometry : angle 0.59822 (43125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23288.73 seconds wall clock time: 402 minutes 2.16 seconds (24122.16 seconds total)