Starting phenix.real_space_refine on Mon Aug 10 07:53:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k2g_61994/08_2026/9k2g_61994.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k2g_61994/08_2026/9k2g_61994.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/9k2g_61994/08_2026/9k2g_61994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k2g_61994/08_2026/9k2g_61994.map" model { file = "/net/cci-nas-00/data/ceres_data/9k2g_61994/08_2026/9k2g_61994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k2g_61994/08_2026/9k2g_61994.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.114 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 115 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 27840 2.51 5 N 7755 2.21 5 O 8599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44605 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8741 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "V" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 246 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "X" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1051 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Y" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1040 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Z" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 7} Link IDs: {'rna3p': 9} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, '3AT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 63.333 114.003 77.664 1.00103.58 S ATOM 565 SG CYS A 72 63.767 117.248 79.681 1.00106.71 S ATOM 613 SG CYS A 79 66.846 115.317 78.416 1.00104.11 S ATOM 854 SG CYS A 109 68.010 85.014 116.098 1.00114.77 S ATOM 876 SG CYS A 112 65.434 87.352 117.716 1.00118.64 S ATOM 1245 SG CYS A 156 68.125 85.821 119.847 1.00130.18 S ATOM 1271 SG CYS A 159 65.374 83.661 118.553 1.00130.36 S ATOM 19142 SG CYS B1080 62.999 118.918 95.997 1.00102.14 S ATOM 19161 SG CYS B1083 64.330 115.346 95.907 1.00101.99 S ATOM 19227 SG CYS B1092 61.868 116.475 93.330 1.00 97.16 S ATOM 19255 SG CYS B1095 60.705 115.976 96.917 1.00100.21 S ATOM 28165 SG CYS I 5 118.551 45.826 103.008 1.00130.73 S ATOM 28182 SG CYS I 8 115.458 46.659 100.771 1.00130.05 S ATOM 28312 SG CYS I 25 115.563 48.136 104.170 1.00130.27 S ATOM 28333 SG CYS I 28 115.498 44.338 103.859 1.00128.16 S ATOM 28605 SG CYS J 7 126.915 127.235 46.490 1.00 75.41 S ATOM 28629 SG CYS J 10 128.356 130.695 45.743 1.00 75.83 S ATOM 28893 SG CYS J 44 130.223 128.112 47.917 1.00 81.33 S ATOM 28899 SG CYS J 45 129.882 127.812 44.072 1.00 82.39 S ATOM 29942 SG CYS L 19 95.496 103.206 30.003 1.00103.46 S ATOM 29961 SG CYS L 22 96.232 101.126 26.884 1.00109.30 S ATOM 30078 SG CYS L 36 92.625 102.515 27.810 1.00117.09 S ATOM 30104 SG CYS L 39 94.008 99.504 29.304 1.00117.30 S ATOM 41050 SG CYS P 290 48.037 93.942 96.362 1.00103.33 S ATOM 41097 SG CYS P 296 49.795 99.405 99.562 1.00104.54 S ATOM 41032 SG CYS P 287 45.239 96.154 102.102 1.00106.27 S ATOM 41174 SG CYS P 307 44.203 98.478 96.345 1.00108.29 S Time building chain proxies: 8.63, per 1000 atoms: 0.19 Number of scatterers: 44605 At special positions: 0 Unit cell: (183.954, 181.288, 163.959, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 285 16.00 P 115 15.00 Mg 1 11.99 O 8599 8.00 N 7755 7.00 C 27840 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 296 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 33 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10006 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 57 sheets defined 43.3% alpha, 17.7% beta 33 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 5.93 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.562A pdb=" N GLY A 61 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 removed outlier: 4.522A pdb=" N ARG A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.808A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 212 Proline residue: A 209 - end of helix removed outlier: 4.399A pdb=" N GLY A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.732A pdb=" N MET A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.704A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.968A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 572 No H-bonds generated for 'chain 'A' and resid 571 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 4.062A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.858A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.758A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 Processing helix chain 'A' and resid 743 through 771 Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 827 through 831 Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.917A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.527A pdb=" N LYS A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 959 Processing helix chain 'A' and resid 962 through 988 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1188 through 1196 Processing helix chain 'A' and resid 1231 through 1238 Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.728A pdb=" N THR A1246 " --> pdb=" O GLY A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.755A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.888A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1322 Processing helix chain 'A' and resid 1323 through 1335 Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.632A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.045A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.808A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.629A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 275 Proline residue: B 267 - end of helix removed outlier: 3.542A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.656A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 422 removed outlier: 4.026A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 removed outlier: 3.718A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.500A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.732A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.928A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.524A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.822A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.588A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.522A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.748A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.719A pdb=" N PHE C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.551A pdb=" N LYS C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 295' Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.731A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 40 through 56 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.283A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.833A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.757A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.709A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 140 through 159 Processing helix chain 'M' and resid 182 through 192 Processing helix chain 'M' and resid 192 through 203 removed outlier: 3.942A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.818A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 269 through 276 Processing helix chain 'M' and resid 277 through 290 Processing helix chain 'M' and resid 293 through 302 Processing helix chain 'M' and resid 306 through 317 removed outlier: 3.602A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 333 Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.556A pdb=" N LEU M 349 " --> pdb=" O PRO M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 Processing helix chain 'M' and resid 378 through 388 Processing helix chain 'M' and resid 405 through 412 removed outlier: 3.858A pdb=" N ILE M 409 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 Processing helix chain 'N' and resid 147 through 151 removed outlier: 4.233A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 259 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 388 through 396 removed outlier: 3.744A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 19 through 32 removed outlier: 3.921A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.548A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 85 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 118 through 133 removed outlier: 4.079A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET O 133 " --> pdb=" O LEU O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 3.940A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 Processing helix chain 'O' and resid 260 through 278 removed outlier: 4.547A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 401 Processing helix chain 'O' and resid 416 through 418 No H-bonds generated for 'chain 'O' and resid 416 through 418' Processing helix chain 'O' and resid 427 through 457 Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.847A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.601A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 3.918A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 29 Processing helix chain 'P' and resid 34 through 42 Processing helix chain 'P' and resid 46 through 60 Processing helix chain 'P' and resid 88 through 103 removed outlier: 5.576A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 119 through 133 Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.550A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 281 through 284 Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.756A pdb=" N LEU P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 296 Processing helix chain 'P' and resid 307 through 316 Processing helix chain 'Q' and resid 51 through 69 removed outlier: 3.697A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.558A pdb=" N MET Q 110 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET Q 111 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 107 through 111' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.870A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.870A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA G 57 " --> pdb=" O HIS A1364 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 7.122A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B1123 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.548A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N ILE A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.325A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.643A pdb=" N SER A 268 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 6.074A pdb=" N VAL A 380 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 481 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL A 382 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER A 370 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.967A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.510A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.930A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1210 through 1216 Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 3.891A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1114 through 1121 removed outlier: 3.723A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 4.834A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.733A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.378A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 189 through 193 Processing sheet with id=AC2, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 603 through 604 removed outlier: 3.509A pdb=" N LYS B 603 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 550 removed outlier: 5.491A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.665A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.665A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.167A pdb=" N LEU B 755 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 909 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 929 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.571A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 826 through 828 removed outlier: 6.755A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.022A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.235A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.552A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.232A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.605A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.524A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.638A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE3, first strand: chain 'E' and resid 58 through 62 removed outlier: 5.645A pdb=" N THR E 59 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL E 74 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 61 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE5, first strand: chain 'G' and resid 105 through 108 removed outlier: 3.637A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.823A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 12 through 16 Processing sheet with id=AE8, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 17 removed outlier: 8.524A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY N 324 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL M 15 " --> pdb=" O VAL N 326 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS N 328 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE M 13 " --> pdb=" O LYS N 328 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU N 330 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN M 11 " --> pdb=" O LEU N 330 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.836A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU M 57 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA M 47 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU M 59 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 291 through 292 Processing sheet with id=AF3, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AF4, first strand: chain 'O' and resid 34 through 35 Processing sheet with id=AF5, first strand: chain 'O' and resid 116 through 117 Processing sheet with id=AF6, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AF7, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AF8, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AF9, first strand: chain 'P' and resid 63 through 68 Processing sheet with id=AG1, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG2, first strand: chain 'P' and resid 211 through 212 Processing sheet with id=AG3, first strand: chain 'V' and resid 15 through 17 removed outlier: 6.533A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1937 hydrogen bonds defined for protein. 5451 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 14.38 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 18616 1.42 - 1.64: 26580 1.64 - 1.85: 452 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 45660 Sorted by residual: bond pdb=" O3' DG X 2 " pdb=" P DC X 3 " ideal model delta sigma weight residual 1.607 1.415 0.192 1.20e-02 6.94e+03 2.57e+02 bond pdb=" O3' DT X 22 " pdb=" P DA X 23 " ideal model delta sigma weight residual 1.607 1.415 0.192 1.20e-02 6.94e+03 2.55e+02 bond pdb=" C2' DG Y 2 " pdb=" C1' DG Y 2 " ideal model delta sigma weight residual 1.518 1.361 0.157 1.00e-02 1.00e+04 2.45e+02 bond pdb=" O3' DG Y -3 " pdb=" P DC Y -2 " ideal model delta sigma weight residual 1.607 1.423 0.184 1.20e-02 6.94e+03 2.35e+02 bond pdb=" C4' DA X -13 " pdb=" O4' DA X -13 " ideal model delta sigma weight residual 1.446 1.294 0.152 1.00e-02 1.00e+04 2.31e+02 ... (remaining 45655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.58: 62029 5.58 - 11.16: 87 11.16 - 16.73: 21 16.73 - 22.31: 4 22.31 - 27.89: 3 Bond angle restraints: 62144 Sorted by residual: angle pdb=" C3' DT Y 7 " pdb=" O3' DT Y 7 " pdb=" P DC Y 8 " ideal model delta sigma weight residual 119.70 99.11 20.59 1.20e+00 6.94e-01 2.94e+02 angle pdb=" C3' DC Y 0 " pdb=" O3' DC Y 0 " pdb=" P DG Y 1 " ideal model delta sigma weight residual 119.70 105.06 14.64 1.20e+00 6.94e-01 1.49e+02 angle pdb=" C3' DA Y -20 " pdb=" C2' DA Y -20 " pdb=" C1' DA Y -20 " ideal model delta sigma weight residual 102.50 88.78 13.72 1.20e+00 6.94e-01 1.31e+02 angle pdb=" O3' DT Y 7 " pdb=" P DC Y 8 " pdb=" O5' DC Y 8 " ideal model delta sigma weight residual 104.00 83.36 20.64 1.90e+00 2.77e-01 1.18e+02 angle pdb=" O4' DG Y 2 " pdb=" C1' DG Y 2 " pdb=" C2' DG Y 2 " ideal model delta sigma weight residual 105.90 97.87 8.03 8.00e-01 1.56e+00 1.01e+02 ... (remaining 62139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 26958 35.43 - 70.87: 837 70.87 - 106.30: 36 106.30 - 141.73: 1 141.73 - 177.17: 9 Dihedral angle restraints: 27841 sinusoidal: 12360 harmonic: 15481 Sorted by residual: dihedral pdb=" CA TYR A1187 " pdb=" C TYR A1187 " pdb=" N VAL A1188 " pdb=" CA VAL A1188 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" O1A 3AT B1202 " pdb=" O3A 3AT B1202 " pdb=" PA 3AT B1202 " pdb=" PB 3AT B1202 " ideal model delta sinusoidal sigma weight residual 157.19 -19.98 177.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' 3AT B1202 " pdb=" O3A 3AT B1202 " pdb=" PA 3AT B1202 " pdb=" PB 3AT B1202 " ideal model delta sinusoidal sigma weight residual 270.98 94.23 176.75 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 27838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 6978 0.252 - 0.504: 15 0.504 - 0.756: 4 0.756 - 1.008: 1 1.008 - 1.259: 1 Chirality restraints: 6999 Sorted by residual: chirality pdb=" C3' DC Y -2 " pdb=" C4' DC Y -2 " pdb=" O3' DC Y -2 " pdb=" C2' DC Y -2 " both_signs ideal model delta sigma weight residual False -2.73 -1.47 -1.26 2.00e-01 2.50e+01 3.97e+01 chirality pdb=" C3' DT X 20 " pdb=" C4' DT X 20 " pdb=" O3' DT X 20 " pdb=" C2' DT X 20 " both_signs ideal model delta sigma weight residual False -2.73 -1.97 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" C3' DA Y -20 " pdb=" C4' DA Y -20 " pdb=" O3' DA Y -20 " pdb=" C2' DA Y -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.04 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 6996 not shown) Planarity restraints: 7608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA Y -20 " -0.037 2.00e-02 2.50e+03 3.42e-02 3.21e+01 pdb=" N9 DA Y -20 " 0.044 2.00e-02 2.50e+03 pdb=" C8 DA Y -20 " -0.043 2.00e-02 2.50e+03 pdb=" N7 DA Y -20 " 0.051 2.00e-02 2.50e+03 pdb=" C5 DA Y -20 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA Y -20 " -0.027 2.00e-02 2.50e+03 pdb=" N6 DA Y -20 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA Y -20 " -0.044 2.00e-02 2.50e+03 pdb=" C2 DA Y -20 " 0.050 2.00e-02 2.50e+03 pdb=" N3 DA Y -20 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA Y -20 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG X -12 " 0.077 2.00e-02 2.50e+03 2.89e-02 2.50e+01 pdb=" N9 DG X -12 " -0.036 2.00e-02 2.50e+03 pdb=" C8 DG X -12 " -0.026 2.00e-02 2.50e+03 pdb=" N7 DG X -12 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG X -12 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG X -12 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG X -12 " 0.028 2.00e-02 2.50e+03 pdb=" N1 DG X -12 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DG X -12 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG X -12 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG X -12 " -0.022 2.00e-02 2.50e+03 pdb=" C4 DG X -12 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC X 24 " 0.063 2.00e-02 2.50e+03 2.87e-02 1.85e+01 pdb=" N1 DC X 24 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DC X 24 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC X 24 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DC X 24 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DC X 24 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC X 24 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DC X 24 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC X 24 " -0.032 2.00e-02 2.50e+03 ... (remaining 7605 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 56 2.33 - 2.97: 20933 2.97 - 3.61: 67102 3.61 - 4.26: 104201 4.26 - 4.90: 172309 Nonbonded interactions: 364601 Sorted by model distance: nonbonded pdb=" NH2 ARG B 682 " pdb=" O1G 3AT B1202 " model vdw 1.684 2.496 nonbonded pdb=" O LYS B 211 " pdb=" O5' DG X 11 " model vdw 1.915 3.040 nonbonded pdb=" OD1 ASP A 501 " pdb="MG MG A1403 " model vdw 2.095 2.170 nonbonded pdb=" NH1 ARG A 366 " pdb=" OD1 ASN A 506 " model vdw 2.129 3.120 nonbonded pdb=" N3 DC X -2 " pdb=" N2 DG Y 2 " model vdw 2.133 2.560 ... (remaining 364596 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: 3.120 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: 0.060 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 60.880 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 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 0.638 45690 Z= 0.509 Angle : 0.745 27.888 62189 Z= 0.441 Chirality : 0.053 1.259 6999 Planarity : 0.004 0.039 7608 Dihedral : 15.555 177.168 17835 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.49 % Allowed : 2.26 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 5269 helix: 1.73 (0.12), residues: 2056 sheet: -0.52 (0.19), residues: 689 loop : -0.53 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 339 TYR 0.011 0.001 TYR B1003 PHE 0.012 0.001 PHE E 75 TRP 0.013 0.001 TRP P 313 HIS 0.004 0.001 HIS B1014 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.40 (45660) covalent geometry : angle 0.72562 / 0.44 (62144) hydrogen bonds : bond 0.15349 / 10.42 ( 1986) hydrogen bonds : angle 6.11760 / 4.31 ( 5601) metal coordination : bond 0.00463 / 0.26 ( 28) metal coordination : angle 6.37986 / 3.43 ( 45) Misc. bond : bond 0.48289 / 25.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1267 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.8409 (t80) cc_final: 0.7844 (t80) REVERT: A 14 LYS cc_start: 0.7676 (tttt) cc_final: 0.7074 (ttpt) REVERT: A 17 HIS cc_start: 0.6885 (p-80) cc_final: 0.6665 (p90) REVERT: A 60 MET cc_start: 0.7757 (mtm) cc_final: 0.7437 (mtp) REVERT: A 111 THR cc_start: 0.7977 (m) cc_final: 0.7699 (p) REVERT: A 119 GLN cc_start: 0.7312 (tp-100) cc_final: 0.6730 (tp-100) REVERT: A 233 GLU cc_start: 0.8023 (tt0) cc_final: 0.7050 (tp30) REVERT: A 261 CYS cc_start: 0.8099 (m) cc_final: 0.7604 (p) REVERT: A 280 THR cc_start: 0.6953 (m) cc_final: 0.6748 (m) REVERT: A 311 ASP cc_start: 0.8066 (t0) cc_final: 0.7806 (t0) REVERT: A 362 ASP cc_start: 0.7657 (p0) cc_final: 0.7391 (p0) REVERT: A 384 VAL cc_start: 0.8045 (t) cc_final: 0.7738 (p) REVERT: A 406 LYS cc_start: 0.7508 (ttpt) cc_final: 0.7053 (mmtt) REVERT: A 448 ASP cc_start: 0.7308 (m-30) cc_final: 0.6947 (m-30) REVERT: A 512 THR cc_start: 0.8167 (m) cc_final: 0.7785 (p) REVERT: A 637 TYR cc_start: 0.6338 (t80) cc_final: 0.6040 (t80) REVERT: A 680 MET cc_start: 0.8322 (mtp) cc_final: 0.7682 (mtt) REVERT: A 685 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6878 (mtp85) REVERT: A 693 ASN cc_start: 0.7352 (m-40) cc_final: 0.6929 (m110) REVERT: A 729 GLU cc_start: 0.7659 (tp30) cc_final: 0.7089 (pt0) REVERT: A 738 GLN cc_start: 0.8084 (tt0) cc_final: 0.7848 (tt0) REVERT: A 917 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6018 (mm-30) REVERT: A 979 LYS cc_start: 0.6459 (mptt) cc_final: 0.6234 (ttpt) REVERT: A 1020 ASP cc_start: 0.7173 (t70) cc_final: 0.6835 (m-30) REVERT: A 1141 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7642 (mmm160) REVERT: A 1228 GLU cc_start: 0.6658 (tt0) cc_final: 0.5786 (tm-30) REVERT: A 1253 GLU cc_start: 0.6346 (mm-30) cc_final: 0.6126 (mt-10) REVERT: A 1275 MET cc_start: 0.7098 (tpp) cc_final: 0.6810 (mmp) REVERT: A 1294 MET cc_start: 0.8078 (mtp) cc_final: 0.7658 (mtm) REVERT: A 1299 GLU cc_start: 0.7418 (tt0) cc_final: 0.7173 (tt0) REVERT: A 1345 GLU cc_start: 0.7118 (pm20) cc_final: 0.6847 (mp0) REVERT: B 64 LYS cc_start: 0.6842 (ttmt) cc_final: 0.6452 (ttpt) REVERT: B 184 LEU cc_start: 0.8497 (mt) cc_final: 0.8292 (mm) REVERT: B 190 ILE cc_start: 0.8234 (mt) cc_final: 0.7940 (pp) REVERT: B 222 ARG cc_start: 0.6532 (ptp90) cc_final: 0.5598 (ptp-110) REVERT: B 243 MET cc_start: 0.8225 (mtm) cc_final: 0.8025 (mtp) REVERT: B 279 THR cc_start: 0.8898 (p) cc_final: 0.8688 (t) REVERT: B 363 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6281 (mm-30) REVERT: B 470 SER cc_start: 0.6496 (t) cc_final: 0.6276 (p) REVERT: B 472 GLN cc_start: 0.7281 (mp10) cc_final: 0.6876 (mp10) REVERT: B 567 TYR cc_start: 0.8289 (m-80) cc_final: 0.8084 (m-80) REVERT: B 572 VAL cc_start: 0.8562 (t) cc_final: 0.8346 (m) REVERT: B 601 LYS cc_start: 0.7614 (mttp) cc_final: 0.7076 (mtpt) REVERT: B 609 LYS cc_start: 0.8297 (tmmt) cc_final: 0.7935 (tmmm) REVERT: B 611 MET cc_start: 0.8640 (mmm) cc_final: 0.8406 (mmp) REVERT: B 726 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6275 (mt-10) REVERT: B 805 ARG cc_start: 0.6995 (ttp-110) cc_final: 0.6628 (mtp-110) REVERT: B 960 TYR cc_start: 0.7936 (m-80) cc_final: 0.7318 (m-80) REVERT: B 1101 VAL cc_start: 0.7913 (t) cc_final: 0.7505 (p) REVERT: C 8 GLU cc_start: 0.6326 (tp30) cc_final: 0.6113 (mm-30) REVERT: C 22 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: C 62 GLU cc_start: 0.7485 (tt0) cc_final: 0.7206 (tt0) REVERT: C 87 MET cc_start: 0.9091 (mmm) cc_final: 0.8742 (mmp) REVERT: C 123 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7165 (mm-30) REVERT: C 139 GLN cc_start: 0.7393 (mt0) cc_final: 0.6851 (mm110) REVERT: C 143 GLN cc_start: 0.7355 (tt0) cc_final: 0.6995 (tm130) REVERT: C 277 ASN cc_start: 0.7688 (t0) cc_final: 0.7475 (t0) REVERT: C 280 LEU cc_start: 0.8256 (mt) cc_final: 0.7925 (mp) REVERT: C 291 GLU cc_start: 0.7581 (tp30) cc_final: 0.7285 (tp30) REVERT: D 4 LYS cc_start: 0.6596 (mmpt) cc_final: 0.6022 (mttt) REVERT: D 24 LYS cc_start: 0.8799 (tttt) cc_final: 0.8345 (tptt) REVERT: D 52 TYR cc_start: 0.7868 (t80) cc_final: 0.7482 (t80) REVERT: D 65 ILE cc_start: 0.9063 (mt) cc_final: 0.8578 (tp) REVERT: D 83 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8288 (ptpp) REVERT: E 67 ASP cc_start: 0.8238 (t0) cc_final: 0.7489 (p0) REVERT: E 70 ASP cc_start: 0.6621 (t0) cc_final: 0.5675 (p0) REVERT: E 91 CYS cc_start: 0.9377 (t) cc_final: 0.8943 (p) REVERT: E 127 LEU cc_start: 0.7675 (mp) cc_final: 0.7308 (mm) REVERT: E 139 ILE cc_start: 0.8040 (mt) cc_final: 0.7584 (tt) REVERT: E 147 GLU cc_start: 0.7405 (tt0) cc_final: 0.6762 (tm-30) REVERT: F 54 THR cc_start: 0.8320 (p) cc_final: 0.8002 (t) REVERT: F 56 TYR cc_start: 0.8349 (m-80) cc_final: 0.8042 (m-80) REVERT: F 84 GLU cc_start: 0.7262 (mp0) cc_final: 0.6381 (mp0) REVERT: F 95 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7826 (mtpp) REVERT: G 7 MET cc_start: 0.6496 (mtp) cc_final: 0.5958 (mtt) REVERT: G 19 GLU cc_start: 0.7977 (pm20) cc_final: 0.7742 (pm20) REVERT: G 28 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7191 (mt-10) REVERT: G 29 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7520 (tp30) REVERT: G 41 ASN cc_start: 0.7962 (m-40) cc_final: 0.7679 (m-40) REVERT: G 47 CYS cc_start: 0.8436 (p) cc_final: 0.7977 (p) REVERT: G 58 TYR cc_start: 0.8461 (m-80) cc_final: 0.7859 (m-10) REVERT: G 104 PHE cc_start: 0.6454 (t80) cc_final: 0.5934 (t80) REVERT: G 110 PRO cc_start: 0.6343 (Cg_exo) cc_final: 0.6058 (Cg_endo) REVERT: G 146 GLU cc_start: 0.5429 (mp0) cc_final: 0.5208 (mp0) REVERT: G 154 ASP cc_start: 0.7124 (p0) cc_final: 0.6780 (p0) REVERT: H 89 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7708 (mt-10) REVERT: H 138 ASP cc_start: 0.7731 (t0) cc_final: 0.7503 (t0) REVERT: K 36 ASP cc_start: 0.5051 (t0) cc_final: 0.4702 (t0) REVERT: K 38 HIS cc_start: 0.6094 (m170) cc_final: 0.5742 (m-70) REVERT: K 115 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7230 (mt-10) REVERT: K 118 ILE cc_start: 0.7790 (mm) cc_final: 0.7384 (mp) REVERT: L 50 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7582 (mmmt) REVERT: M 66 ASN cc_start: 0.7175 (p0) cc_final: 0.6911 (p0) REVERT: M 70 CYS cc_start: 0.8033 (t) cc_final: 0.7806 (t) REVERT: M 105 SER cc_start: 0.6536 (t) cc_final: 0.6215 (p) REVERT: M 144 LYS cc_start: 0.8588 (mttt) cc_final: 0.8386 (ttpt) REVERT: M 233 VAL cc_start: 0.4000 (t) cc_final: 0.3758 (p) REVERT: N 272 PRO cc_start: 0.7427 (Cg_endo) cc_final: 0.7096 (Cg_exo) REVERT: N 328 LYS cc_start: 0.7257 (mtpp) cc_final: 0.7057 (tppp) REVERT: O 19 GLU cc_start: 0.7297 (tp30) cc_final: 0.7091 (tp30) REVERT: O 317 ASP cc_start: 0.7576 (m-30) cc_final: 0.7346 (m-30) REVERT: O 501 THR cc_start: 0.8909 (p) cc_final: 0.8452 (p) REVERT: P 267 MET cc_start: 0.8233 (mmt) cc_final: 0.8033 (tpt) REVERT: Q 49 LYS cc_start: 0.6571 (mtpp) cc_final: 0.6354 (tptp) outliers start: 23 outliers final: 18 residues processed: 1288 average time/residue: 0.7547 time to fit residues: 1196.7863 Evaluate side-chains 791 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 773 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1379 PHE Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 285 THR Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 134 LYS Chi-restraints excluded: chain Q residue 60 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 0.0270 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 163 ASN A 314 GLN A 599 GLN A 739 GLN A 791 ASN A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1336 GLN B 215 ASN B 517 ASN B 552 HIS D 13 ASN E 71 GLN E 189 GLN G 31 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN M 11 GLN M 197 GLN M 209 HIS M 362 GLN N 338 GLN O 59 GLN O 61 ASN O 371 GLN O 407 GLN P 117 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.220127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135467 restraints weight = 54824.870| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.66 r_work: 0.3347 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 45690 Z= 0.224 Angle : 0.755 12.827 62189 Z= 0.383 Chirality : 0.050 0.349 6999 Planarity : 0.005 0.055 7608 Dihedral : 16.803 177.834 7160 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.90 % Allowed : 13.58 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.12), residues: 5269 helix: 1.34 (0.11), residues: 2064 sheet: -0.53 (0.20), residues: 658 loop : -0.66 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1245 TYR 0.024 0.002 TYR E 90 PHE 0.025 0.002 PHE D 69 TRP 0.036 0.002 TRP Q 103 HIS 0.015 0.002 HIS P 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (45660) covalent geometry : angle 0.74105 / 0.38 (62144) hydrogen bonds : bond 0.05006 / 3.29 ( 1986) hydrogen bonds : angle 4.96816 / 3.56 ( 5601) metal coordination : bond 0.00929 / 0.47 ( 28) metal coordination : angle 5.42384 / 3.18 ( 45) Misc. bond : bond 0.01387 / 0.68 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 823 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.7815 (p-80) cc_final: 0.7495 (p-80) REVERT: A 115 ILE cc_start: 0.7408 (tt) cc_final: 0.7080 (tt) REVERT: A 116 MET cc_start: 0.7082 (mtm) cc_final: 0.6629 (mtm) REVERT: A 119 GLN cc_start: 0.7595 (tp-100) cc_final: 0.6957 (tp-100) REVERT: A 243 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: A 261 CYS cc_start: 0.8524 (m) cc_final: 0.8183 (p) REVERT: A 305 MET cc_start: 0.7982 (ptp) cc_final: 0.7627 (ptm) REVERT: A 311 ASP cc_start: 0.8503 (t0) cc_final: 0.8212 (t0) REVERT: A 349 GLN cc_start: 0.8543 (mp10) cc_final: 0.8333 (mp10) REVERT: A 406 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8222 (mmtt) REVERT: A 430 ARG cc_start: 0.8403 (mtp85) cc_final: 0.7917 (mmm-85) REVERT: A 448 ASP cc_start: 0.8460 (m-30) cc_final: 0.8235 (m-30) REVERT: A 646 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8962 (mmp) REVERT: A 693 ASN cc_start: 0.8794 (m-40) cc_final: 0.8257 (m-40) REVERT: A 729 GLU cc_start: 0.8025 (tp30) cc_final: 0.7338 (pt0) REVERT: A 738 GLN cc_start: 0.8199 (tt0) cc_final: 0.7957 (tt0) REVERT: A 873 ARG cc_start: 0.8841 (ttt90) cc_final: 0.8537 (ttt90) REVERT: A 912 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8666 (mmm) REVERT: A 920 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: A 979 LYS cc_start: 0.7677 (mptt) cc_final: 0.7169 (ttpt) REVERT: A 1020 ASP cc_start: 0.8647 (t70) cc_final: 0.8318 (m-30) REVERT: A 1039 GLN cc_start: 0.8886 (mt0) cc_final: 0.8458 (mt0) REVERT: A 1129 LEU cc_start: 0.8012 (tp) cc_final: 0.7653 (tm) REVERT: A 1141 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7909 (mtp85) REVERT: A 1174 CYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6555 (m) REVERT: A 1228 GLU cc_start: 0.7262 (tt0) cc_final: 0.6640 (tm-30) REVERT: A 1245 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8170 (mtt90) REVERT: A 1275 MET cc_start: 0.8237 (tpp) cc_final: 0.7964 (mmt) REVERT: A 1326 ASP cc_start: 0.7568 (m-30) cc_final: 0.7312 (m-30) REVERT: B 35 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7898 (mtmt) REVERT: B 215 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8142 (m-40) REVERT: B 222 ARG cc_start: 0.7023 (ptp90) cc_final: 0.6268 (ptp-110) REVERT: B 243 MET cc_start: 0.8318 (mtm) cc_final: 0.8068 (mtp) REVERT: B 363 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8453 (mt-10) REVERT: B 408 GLN cc_start: 0.7079 (tt0) cc_final: 0.6494 (tp-100) REVERT: B 413 ASN cc_start: 0.8097 (m-40) cc_final: 0.7713 (m110) REVERT: B 459 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5692 (t80) REVERT: B 461 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5347 (pttp) REVERT: B 470 SER cc_start: 0.7901 (t) cc_final: 0.7582 (p) REVERT: B 506 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.6641 (mpt) REVERT: B 533 TYR cc_start: 0.8461 (m-10) cc_final: 0.8098 (m-80) REVERT: B 553 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7193 (mmtt) REVERT: B 600 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7287 (mtpt) REVERT: B 601 LYS cc_start: 0.8159 (mttp) cc_final: 0.7927 (mtpt) REVERT: B 609 LYS cc_start: 0.8429 (tmmt) cc_final: 0.8071 (tmmt) REVERT: B 611 MET cc_start: 0.8801 (mmm) cc_final: 0.8230 (mmp) REVERT: B 627 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 628 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8290 (t) REVERT: B 719 MET cc_start: 0.8980 (mmm) cc_final: 0.8699 (mmm) REVERT: B 726 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 776 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8518 (ptmm) REVERT: B 791 MET cc_start: 0.7855 (mpp) cc_final: 0.7431 (mpt) REVERT: B 805 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7855 (mtp-110) REVERT: B 870 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8579 (ttp) REVERT: B 929 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8414 (ptp) REVERT: B 970 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7276 (mttp) REVERT: B 1075 PHE cc_start: 0.8818 (t80) cc_final: 0.8606 (t80) REVERT: C 22 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8518 (mtm-85) REVERT: C 28 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8198 (p0) REVERT: C 87 MET cc_start: 0.9456 (mmm) cc_final: 0.9157 (mmp) REVERT: C 143 GLN cc_start: 0.8221 (tt0) cc_final: 0.7909 (tm130) REVERT: C 180 ASN cc_start: 0.8386 (t0) cc_final: 0.8135 (t0) REVERT: C 253 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 263 GLU cc_start: 0.8297 (pt0) cc_final: 0.7799 (pp20) REVERT: C 277 ASN cc_start: 0.8124 (t0) cc_final: 0.7906 (t0) REVERT: C 280 LEU cc_start: 0.9007 (mt) cc_final: 0.8791 (mp) REVERT: C 291 GLU cc_start: 0.8056 (tp30) cc_final: 0.7832 (tp30) REVERT: D 4 LYS cc_start: 0.7416 (mmpt) cc_final: 0.6977 (mttt) REVERT: D 23 LEU cc_start: 0.8410 (mt) cc_final: 0.7937 (mt) REVERT: D 59 ARG cc_start: 0.8885 (mpp80) cc_final: 0.8619 (mpp80) REVERT: D 73 LEU cc_start: 0.8961 (mp) cc_final: 0.8388 (tm) REVERT: E 3 ASP cc_start: 0.7493 (m-30) cc_final: 0.6567 (t0) REVERT: E 90 TYR cc_start: 0.8126 (m-10) cc_final: 0.7606 (m-80) REVERT: E 91 CYS cc_start: 0.9386 (t) cc_final: 0.9055 (p) REVERT: E 127 LEU cc_start: 0.8299 (mp) cc_final: 0.7915 (mm) REVERT: E 147 GLU cc_start: 0.8299 (tt0) cc_final: 0.7818 (tm-30) REVERT: F 54 THR cc_start: 0.8981 (p) cc_final: 0.8473 (t) REVERT: F 56 TYR cc_start: 0.9216 (m-80) cc_final: 0.8883 (m-80) REVERT: F 62 ARG cc_start: 0.8733 (ttp-110) cc_final: 0.8514 (ttm-80) REVERT: G 7 MET cc_start: 0.7751 (mtp) cc_final: 0.7350 (mtt) REVERT: G 37 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7836 (mppt) REVERT: G 59 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8854 (t) REVERT: G 80 PHE cc_start: 0.8274 (p90) cc_final: 0.7500 (p90) REVERT: G 104 PHE cc_start: 0.6166 (t80) cc_final: 0.5851 (t80) REVERT: G 154 ASP cc_start: 0.7123 (p0) cc_final: 0.6799 (p0) REVERT: H 18 GLU cc_start: 0.8229 (mp0) cc_final: 0.7928 (mp0) REVERT: H 89 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8318 (mt-10) REVERT: H 138 ASP cc_start: 0.8101 (t0) cc_final: 0.7881 (t0) REVERT: K 38 HIS cc_start: 0.7549 (m170) cc_final: 0.7128 (m90) REVERT: K 115 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8301 (mt-10) REVERT: M 13 ILE cc_start: 0.5762 (mt) cc_final: 0.5317 (mt) REVERT: M 42 ILE cc_start: 0.8691 (mt) cc_final: 0.8415 (mt) REVERT: M 70 CYS cc_start: 0.8378 (t) cc_final: 0.8003 (t) REVERT: M 105 SER cc_start: 0.6705 (t) cc_final: 0.6244 (p) REVERT: M 113 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7306 (ttp80) REVERT: M 132 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7923 (pp) REVERT: M 144 LYS cc_start: 0.8615 (mttt) cc_final: 0.8290 (ttpt) REVERT: M 188 ARG cc_start: 0.9302 (ptt180) cc_final: 0.8532 (ptm-80) REVERT: M 286 MET cc_start: 0.9280 (mmm) cc_final: 0.8637 (mmm) REVERT: N 142 LYS cc_start: 0.5967 (tttm) cc_final: 0.5739 (tptt) REVERT: N 328 LYS cc_start: 0.7449 (mtpp) cc_final: 0.7128 (tppp) REVERT: O 19 GLU cc_start: 0.7462 (tp30) cc_final: 0.7203 (tp30) REVERT: O 43 THR cc_start: 0.8214 (m) cc_final: 0.7828 (p) REVERT: O 260 ASP cc_start: 0.7703 (p0) cc_final: 0.7501 (p0) REVERT: O 273 MET cc_start: 0.9030 (tmm) cc_final: 0.8560 (tmm) REVERT: O 317 ASP cc_start: 0.7727 (m-30) cc_final: 0.7345 (m-30) REVERT: O 338 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.5035 (mt) REVERT: O 371 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6338 (mm110) REVERT: P 217 TRP cc_start: 0.9411 (t60) cc_final: 0.8954 (t60) REVERT: Q 33 LYS cc_start: 0.6887 (ttpp) cc_final: 0.6687 (ttpp) REVERT: Q 49 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6676 (tptp) REVERT: Q 54 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6374 (mm-30) REVERT: Q 80 GLU cc_start: 0.8504 (pm20) cc_final: 0.7185 (mp0) REVERT: Q 85 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6906 (pt0) REVERT: Q 92 MET cc_start: 0.5973 (ppp) cc_final: 0.5508 (pmm) outliers start: 183 outliers final: 68 residues processed: 929 average time/residue: 0.7245 time to fit residues: 837.8460 Evaluate side-chains 775 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 685 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain O residue 371 GLN Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 286 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 431 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 326 optimal weight: 1.9990 chunk 470 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 327 optimal weight: 0.1980 chunk 124 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 157 HIS A 158 HIS A 425 HIS A 662 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN A1213 HIS ** A1278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN B 280 GLN C 139 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 189 GLN E 210 GLN M 362 GLN O 155 HIS O 371 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.218601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132070 restraints weight = 54259.954| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.66 r_work: 0.3311 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45690 Z= 0.175 Angle : 0.676 13.772 62189 Z= 0.343 Chirality : 0.046 0.315 6999 Planarity : 0.005 0.051 7608 Dihedral : 16.521 176.530 7136 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.87 % Allowed : 15.86 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.11), residues: 5269 helix: 1.29 (0.11), residues: 2066 sheet: -0.61 (0.20), residues: 632 loop : -0.70 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 272 TYR 0.033 0.002 TYR P 219 PHE 0.020 0.002 PHE C 336 TRP 0.021 0.001 TRP O 235 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (45660) covalent geometry : angle 0.66243 / 0.34 (62144) hydrogen bonds : bond 0.04458 / 2.93 ( 1986) hydrogen bonds : angle 4.82358 / 3.47 ( 5601) metal coordination : bond 0.00738 / 0.42 ( 28) metal coordination : angle 5.02086 / 3.06 ( 45) Misc. bond : bond 0.00560 / 0.28 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 729 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.7467 (tt) cc_final: 0.7080 (tt) REVERT: A 116 MET cc_start: 0.7492 (mtm) cc_final: 0.7083 (mtm) REVERT: A 119 GLN cc_start: 0.7479 (tp-100) cc_final: 0.6859 (tp-100) REVERT: A 307 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7307 (mpt) REVERT: A 311 ASP cc_start: 0.8436 (t0) cc_final: 0.8149 (t0) REVERT: A 349 GLN cc_start: 0.8560 (mp10) cc_final: 0.8351 (mp10) REVERT: A 406 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8173 (mmtt) REVERT: A 430 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8102 (mmt90) REVERT: A 448 ASP cc_start: 0.8557 (m-30) cc_final: 0.8287 (m-30) REVERT: A 646 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8974 (mmp) REVERT: A 693 ASN cc_start: 0.8793 (m-40) cc_final: 0.8271 (m-40) REVERT: A 729 GLU cc_start: 0.8004 (tp30) cc_final: 0.7305 (pt0) REVERT: A 738 GLN cc_start: 0.8210 (tt0) cc_final: 0.7953 (tt0) REVERT: A 873 ARG cc_start: 0.8776 (ttt90) cc_final: 0.8410 (ttt90) REVERT: A 912 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8773 (mmm) REVERT: A 920 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: A 979 LYS cc_start: 0.7602 (mptt) cc_final: 0.7082 (ttpt) REVERT: A 1020 ASP cc_start: 0.8635 (t70) cc_final: 0.8077 (m-30) REVERT: A 1039 GLN cc_start: 0.8830 (mt0) cc_final: 0.8402 (mt0) REVERT: A 1141 ARG cc_start: 0.8247 (mtt90) cc_final: 0.7867 (mtp85) REVERT: A 1150 ARG cc_start: 0.8841 (tmt170) cc_final: 0.8621 (tmt170) REVERT: A 1167 VAL cc_start: 0.8849 (m) cc_final: 0.8566 (t) REVERT: A 1174 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6514 (m) REVERT: A 1194 GLU cc_start: 0.7863 (pt0) cc_final: 0.7449 (pm20) REVERT: A 1202 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: A 1228 GLU cc_start: 0.7544 (tt0) cc_final: 0.6577 (tm-30) REVERT: A 1245 ARG cc_start: 0.8444 (ttm110) cc_final: 0.8149 (mtt90) REVERT: A 1275 MET cc_start: 0.8293 (tpp) cc_final: 0.7886 (mmt) REVERT: A 1326 ASP cc_start: 0.7636 (m-30) cc_final: 0.7371 (m-30) REVERT: B 35 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7953 (mtmm) REVERT: B 222 ARG cc_start: 0.7042 (ptp90) cc_final: 0.6227 (ptp-110) REVERT: B 243 MET cc_start: 0.8293 (mtm) cc_final: 0.8080 (mtp) REVERT: B 254 MET cc_start: 0.7727 (mtp) cc_final: 0.7466 (mtp) REVERT: B 282 GLN cc_start: 0.8267 (mt0) cc_final: 0.7898 (mt0) REVERT: B 311 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8316 (tm-30) REVERT: B 363 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8472 (mt-10) REVERT: B 408 GLN cc_start: 0.7016 (tt0) cc_final: 0.6414 (tp-100) REVERT: B 413 ASN cc_start: 0.8010 (m-40) cc_final: 0.7600 (m110) REVERT: B 459 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5623 (t80) REVERT: B 470 SER cc_start: 0.7660 (t) cc_final: 0.7365 (p) REVERT: B 533 TYR cc_start: 0.8569 (m-10) cc_final: 0.8346 (m-80) REVERT: B 553 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7090 (mmtt) REVERT: B 601 LYS cc_start: 0.8375 (mttp) cc_final: 0.8135 (mtpt) REVERT: B 609 LYS cc_start: 0.8378 (tmmt) cc_final: 0.7991 (tmmt) REVERT: B 611 MET cc_start: 0.8702 (mmm) cc_final: 0.8248 (mmp) REVERT: B 627 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 628 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 653 ASP cc_start: 0.7995 (t0) cc_final: 0.7707 (t0) REVERT: B 719 MET cc_start: 0.8988 (mmm) cc_final: 0.8697 (mmm) REVERT: B 776 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8477 (ptmm) REVERT: B 791 MET cc_start: 0.7666 (mpp) cc_final: 0.7253 (mpt) REVERT: B 805 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.7953 (mtp-110) REVERT: B 870 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8689 (ttp) REVERT: B 906 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 929 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7975 (tmt) REVERT: B 1075 PHE cc_start: 0.8862 (t80) cc_final: 0.8630 (t80) REVERT: C 28 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8170 (p0) REVERT: C 83 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: C 87 MET cc_start: 0.9452 (mmm) cc_final: 0.9197 (mmp) REVERT: C 137 THR cc_start: 0.8884 (t) cc_final: 0.8660 (m) REVERT: C 141 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.8097 (tpt-90) REVERT: C 143 GLN cc_start: 0.8516 (tt0) cc_final: 0.8167 (tm130) REVERT: C 277 ASN cc_start: 0.8114 (t0) cc_final: 0.7904 (t0) REVERT: C 280 LEU cc_start: 0.9059 (mt) cc_final: 0.8842 (mp) REVERT: C 291 GLU cc_start: 0.8137 (tp30) cc_final: 0.7839 (tp30) REVERT: D 4 LYS cc_start: 0.7109 (mmpt) cc_final: 0.6730 (mttt) REVERT: D 59 ARG cc_start: 0.8867 (mpp80) cc_final: 0.8540 (mpp80) REVERT: D 114 GLU cc_start: 0.9247 (mp0) cc_final: 0.8859 (mp0) REVERT: E 127 LEU cc_start: 0.8338 (mp) cc_final: 0.7972 (mm) REVERT: E 147 GLU cc_start: 0.8301 (tt0) cc_final: 0.7757 (tm-30) REVERT: F 56 TYR cc_start: 0.9211 (m-80) cc_final: 0.8829 (m-80) REVERT: F 82 GLU cc_start: 0.8451 (pp20) cc_final: 0.7851 (pp20) REVERT: F 84 GLU cc_start: 0.8298 (mp0) cc_final: 0.7820 (mp0) REVERT: F 98 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8494 (ttmm) REVERT: G 7 MET cc_start: 0.7746 (mtp) cc_final: 0.7301 (mtt) REVERT: G 59 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8759 (t) REVERT: G 73 ARG cc_start: 0.8402 (mpp80) cc_final: 0.8150 (mpp80) REVERT: G 80 PHE cc_start: 0.8184 (p90) cc_final: 0.7679 (p90) REVERT: G 82 ASP cc_start: 0.6818 (m-30) cc_final: 0.6082 (m-30) REVERT: G 104 PHE cc_start: 0.5949 (t80) cc_final: 0.5641 (t80) REVERT: G 154 ASP cc_start: 0.7070 (p0) cc_final: 0.6776 (p0) REVERT: H 89 GLU cc_start: 0.8715 (mt-10) cc_final: 0.7965 (mt-10) REVERT: H 122 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8727 (mm) REVERT: J 19 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8277 (mp0) REVERT: K 38 HIS cc_start: 0.7745 (m170) cc_final: 0.7522 (m90) REVERT: K 53 ASN cc_start: 0.8822 (t0) cc_final: 0.8606 (t0) REVERT: K 115 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8344 (mt-10) REVERT: L 50 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7691 (mmtm) REVERT: M 19 LYS cc_start: 0.7573 (mmmm) cc_final: 0.7328 (mmmm) REVERT: M 42 ILE cc_start: 0.8673 (mt) cc_final: 0.8447 (mt) REVERT: M 70 CYS cc_start: 0.8407 (t) cc_final: 0.8037 (t) REVERT: M 80 ASN cc_start: 0.8949 (m110) cc_final: 0.8294 (p0) REVERT: M 102 PHE cc_start: 0.7502 (m-10) cc_final: 0.7150 (m-10) REVERT: M 105 SER cc_start: 0.7013 (t) cc_final: 0.6496 (p) REVERT: M 132 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7908 (pp) REVERT: M 144 LYS cc_start: 0.8574 (mttt) cc_final: 0.8312 (ttpt) REVERT: M 195 PHE cc_start: 0.9528 (t80) cc_final: 0.8967 (t80) REVERT: M 298 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7246 (mmm) REVERT: O 19 GLU cc_start: 0.7299 (tp30) cc_final: 0.6880 (tp30) REVERT: O 43 THR cc_start: 0.8195 (m) cc_final: 0.7793 (p) REVERT: O 260 ASP cc_start: 0.7170 (p0) cc_final: 0.6774 (p0) REVERT: O 317 ASP cc_start: 0.7750 (m-30) cc_final: 0.7389 (m-30) REVERT: O 338 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5233 (mt) REVERT: O 394 MET cc_start: 0.7079 (mmt) cc_final: 0.6726 (mmp) REVERT: P 217 TRP cc_start: 0.9430 (t60) cc_final: 0.8945 (t-100) REVERT: Q 49 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6674 (tptp) REVERT: Q 68 MET cc_start: 0.6119 (tpp) cc_final: 0.5591 (tpt) REVERT: Q 71 MET cc_start: 0.8131 (tpp) cc_final: 0.7803 (tpp) REVERT: Q 85 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7165 (pt0) REVERT: Q 103 TRP cc_start: 0.7216 (t-100) cc_final: 0.6888 (t-100) outliers start: 182 outliers final: 73 residues processed: 826 average time/residue: 0.7232 time to fit residues: 744.8117 Evaluate side-chains 747 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 655 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1131 LYS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1202 GLN Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain P residue 181 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain Q residue 31 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 523 optimal weight: 100.0000 chunk 236 optimal weight: 0.8980 chunk 352 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 460 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 154 ASN A 157 HIS ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 280 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN H 46 GLN O 371 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 ASN P 181 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.215540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126581 restraints weight = 53742.782| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.51 r_work: 0.3276 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 45690 Z= 0.215 Angle : 0.695 15.015 62189 Z= 0.351 Chirality : 0.047 0.310 6999 Planarity : 0.005 0.057 7608 Dihedral : 16.417 178.571 7130 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.43 % Allowed : 16.62 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.11), residues: 5269 helix: 1.21 (0.11), residues: 2059 sheet: -0.70 (0.19), residues: 666 loop : -0.72 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 149 TYR 0.043 0.002 TYR P 219 PHE 0.023 0.002 PHE C 336 TRP 0.015 0.001 TRP P 217 HIS 0.018 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (45660) covalent geometry : angle 0.68300 / 0.35 (62144) hydrogen bonds : bond 0.04385 / 2.92 ( 1986) hydrogen bonds : angle 4.79325 / 3.45 ( 5601) metal coordination : bond 0.00893 / 0.51 ( 28) metal coordination : angle 4.84870 / 2.97 ( 45) Misc. bond : bond 0.00291 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 679 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8538 (m110) cc_final: 0.8308 (m110) REVERT: A 51 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7383 (mt) REVERT: A 115 ILE cc_start: 0.7668 (tt) cc_final: 0.7261 (tt) REVERT: A 116 MET cc_start: 0.7439 (mtm) cc_final: 0.7095 (mtm) REVERT: A 119 GLN cc_start: 0.7569 (tp-100) cc_final: 0.6944 (tp-100) REVERT: A 307 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7238 (mpt) REVERT: A 311 ASP cc_start: 0.8522 (t0) cc_final: 0.8224 (t0) REVERT: A 349 GLN cc_start: 0.8615 (mp10) cc_final: 0.8372 (mp10) REVERT: A 406 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8144 (mmtt) REVERT: A 430 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8146 (mmt90) REVERT: A 448 ASP cc_start: 0.8593 (m-30) cc_final: 0.8343 (m-30) REVERT: A 505 MET cc_start: 0.9379 (mtp) cc_final: 0.9083 (mtm) REVERT: A 646 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8928 (mmp) REVERT: A 693 ASN cc_start: 0.8902 (m-40) cc_final: 0.8440 (m-40) REVERT: A 729 GLU cc_start: 0.8079 (tp30) cc_final: 0.7356 (pt0) REVERT: A 738 GLN cc_start: 0.8248 (tt0) cc_final: 0.7993 (tt0) REVERT: A 805 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 873 ARG cc_start: 0.8703 (ttt90) cc_final: 0.8299 (ttt90) REVERT: A 920 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8545 (mt-10) REVERT: A 979 LYS cc_start: 0.7599 (mptt) cc_final: 0.6987 (ttpt) REVERT: A 1020 ASP cc_start: 0.8585 (t70) cc_final: 0.8009 (m-30) REVERT: A 1039 GLN cc_start: 0.8809 (mt0) cc_final: 0.8397 (mt0) REVERT: A 1129 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7531 (tm) REVERT: A 1141 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7874 (mtp85) REVERT: A 1167 VAL cc_start: 0.8982 (m) cc_final: 0.8677 (t) REVERT: A 1174 CYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6492 (m) REVERT: A 1228 GLU cc_start: 0.7584 (tt0) cc_final: 0.6561 (tm-30) REVERT: A 1245 ARG cc_start: 0.8667 (ttm110) cc_final: 0.8135 (mpt-90) REVERT: A 1275 MET cc_start: 0.8294 (tpp) cc_final: 0.7882 (mmt) REVERT: A 1313 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: A 1326 ASP cc_start: 0.7691 (m-30) cc_final: 0.7491 (m-30) REVERT: B 136 MET cc_start: 0.8682 (tpt) cc_final: 0.8389 (tpp) REVERT: B 222 ARG cc_start: 0.7236 (ptp90) cc_final: 0.6387 (ptp-110) REVERT: B 243 MET cc_start: 0.8308 (mtm) cc_final: 0.8043 (mtp) REVERT: B 248 ASP cc_start: 0.8046 (m-30) cc_final: 0.7699 (m-30) REVERT: B 282 GLN cc_start: 0.8311 (mt0) cc_final: 0.7917 (mt0) REVERT: B 311 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8413 (tm-30) REVERT: B 363 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8561 (mt-10) REVERT: B 408 GLN cc_start: 0.7012 (tt0) cc_final: 0.6459 (tp-100) REVERT: B 413 ASN cc_start: 0.8035 (m-40) cc_final: 0.7648 (m110) REVERT: B 459 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5670 (t80) REVERT: B 470 SER cc_start: 0.7955 (t) cc_final: 0.7614 (p) REVERT: B 553 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7180 (mmtt) REVERT: B 557 ASN cc_start: 0.8376 (m-40) cc_final: 0.8159 (m-40) REVERT: B 580 ASP cc_start: 0.8100 (m-30) cc_final: 0.7859 (t0) REVERT: B 601 LYS cc_start: 0.8459 (mttp) cc_final: 0.8246 (mtpt) REVERT: B 609 LYS cc_start: 0.8453 (tmmt) cc_final: 0.8031 (tmmt) REVERT: B 611 MET cc_start: 0.8668 (mmm) cc_final: 0.8364 (mmp) REVERT: B 627 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8288 (mm-30) REVERT: B 628 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 697 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9146 (mp) REVERT: B 719 MET cc_start: 0.9026 (mmm) cc_final: 0.8772 (mmm) REVERT: B 726 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 776 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8545 (ptmm) REVERT: B 791 MET cc_start: 0.7766 (mpp) cc_final: 0.7342 (mpt) REVERT: B 805 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.8024 (mtp-110) REVERT: B 906 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 929 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8417 (ptp) REVERT: B 960 TYR cc_start: 0.9066 (m-80) cc_final: 0.8842 (m-80) REVERT: C 28 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8187 (p0) REVERT: C 83 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8408 (mt-10) REVERT: C 87 MET cc_start: 0.9454 (mmm) cc_final: 0.9213 (mmp) REVERT: C 125 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7519 (mtm-85) REVERT: C 141 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8148 (tpt-90) REVERT: C 143 GLN cc_start: 0.8699 (tt0) cc_final: 0.8318 (tm130) REVERT: D 59 ARG cc_start: 0.8806 (mpp80) cc_final: 0.8455 (mpp80) REVERT: D 88 ASN cc_start: 0.8084 (m110) cc_final: 0.7878 (m110) REVERT: E 91 CYS cc_start: 0.9377 (OUTLIER) cc_final: 0.8987 (p) REVERT: E 126 ILE cc_start: 0.8198 (mt) cc_final: 0.7810 (pp) REVERT: E 127 LEU cc_start: 0.8392 (mp) cc_final: 0.8015 (mm) REVERT: E 147 GLU cc_start: 0.8444 (tt0) cc_final: 0.7933 (tm-30) REVERT: F 56 TYR cc_start: 0.9170 (m-80) cc_final: 0.8799 (m-80) REVERT: G 7 MET cc_start: 0.7911 (mtp) cc_final: 0.7479 (mtt) REVERT: G 37 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7938 (mppt) REVERT: G 63 ASP cc_start: 0.6205 (t0) cc_final: 0.5943 (t0) REVERT: G 104 PHE cc_start: 0.6063 (t80) cc_final: 0.5717 (t80) REVERT: G 154 ASP cc_start: 0.7074 (p0) cc_final: 0.6786 (p0) REVERT: H 89 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 122 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8943 (mm) REVERT: H 124 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8244 (ttm170) REVERT: I 4 PHE cc_start: 0.8178 (m-80) cc_final: 0.7919 (m-80) REVERT: I 22 ARG cc_start: 0.5614 (ptt180) cc_final: 0.5218 (ptt180) REVERT: K 53 ASN cc_start: 0.8810 (t0) cc_final: 0.8606 (t0) REVERT: K 102 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8575 (tp30) REVERT: M 42 ILE cc_start: 0.8540 (mt) cc_final: 0.8320 (mt) REVERT: M 70 CYS cc_start: 0.8519 (t) cc_final: 0.8066 (t) REVERT: M 102 PHE cc_start: 0.7399 (m-10) cc_final: 0.7038 (m-10) REVERT: M 105 SER cc_start: 0.7248 (t) cc_final: 0.6796 (p) REVERT: M 132 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8007 (pp) REVERT: M 144 LYS cc_start: 0.8594 (mttt) cc_final: 0.8298 (ttpt) REVERT: O 19 GLU cc_start: 0.7251 (tp30) cc_final: 0.6793 (tp30) REVERT: O 43 THR cc_start: 0.8166 (m) cc_final: 0.7762 (p) REVERT: O 260 ASP cc_start: 0.7169 (p0) cc_final: 0.6899 (p0) REVERT: O 317 ASP cc_start: 0.7766 (m-30) cc_final: 0.7438 (m-30) REVERT: O 338 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5243 (mt) REVERT: O 456 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8512 (pp20) REVERT: P 151 MET cc_start: 0.2262 (OUTLIER) cc_final: 0.0859 (mmp) REVERT: P 217 TRP cc_start: 0.9415 (t60) cc_final: 0.8922 (t-100) REVERT: P 267 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7066 (tpt) REVERT: Q 49 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6750 (tptp) REVERT: Q 68 MET cc_start: 0.6279 (tpp) cc_final: 0.5666 (tpt) REVERT: Q 71 MET cc_start: 0.8231 (tpp) cc_final: 0.7961 (tpp) REVERT: Q 85 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7147 (pt0) outliers start: 208 outliers final: 106 residues processed: 803 average time/residue: 0.7146 time to fit residues: 712.1747 Evaluate side-chains 759 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 628 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1131 LYS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 421 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 159 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 411 optimal weight: 50.0000 chunk 286 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 487 optimal weight: 50.0000 chunk 456 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 485 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 154 ASN A 157 HIS A 794 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN B 280 GLN C 268 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN O 155 HIS O 371 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 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 = 0.4451 r_free = 0.4451 target = 0.212092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122588 restraints weight = 53133.424| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.48 r_work: 0.3194 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 45690 Z= 0.274 Angle : 0.745 14.803 62189 Z= 0.376 Chirality : 0.048 0.307 6999 Planarity : 0.005 0.063 7608 Dihedral : 16.362 179.263 7130 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.73 % Allowed : 17.58 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.11), residues: 5269 helix: 1.05 (0.11), residues: 2058 sheet: -0.81 (0.19), residues: 681 loop : -0.88 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 47 TYR 0.040 0.002 TYR P 219 PHE 0.026 0.002 PHE G 80 TRP 0.020 0.002 TRP O 235 HIS 0.033 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.27 (45660) covalent geometry : angle 0.73068 / 0.38 (62144) hydrogen bonds : bond 0.04617 / 3.08 ( 1986) hydrogen bonds : angle 4.90918 / 3.54 ( 5601) metal coordination : bond 0.01136 / 0.65 ( 28) metal coordination : angle 5.37114 / 3.35 ( 45) Misc. bond : bond 0.00219 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 676 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8559 (m110) cc_final: 0.8333 (m110) REVERT: A 75 ASN cc_start: 0.8042 (m-40) cc_final: 0.7740 (p0) REVERT: A 80 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 115 ILE cc_start: 0.8049 (tt) cc_final: 0.7644 (tt) REVERT: A 116 MET cc_start: 0.7681 (mtm) cc_final: 0.7353 (mtm) REVERT: A 119 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7256 (tm-30) REVERT: A 154 ASN cc_start: 0.8750 (m-40) cc_final: 0.8457 (t0) REVERT: A 311 ASP cc_start: 0.8556 (t0) cc_final: 0.8231 (t0) REVERT: A 349 GLN cc_start: 0.8686 (mp10) cc_final: 0.8469 (mp10) REVERT: A 406 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8063 (mmtt) REVERT: A 430 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8080 (mmt90) REVERT: A 507 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8968 (tp) REVERT: A 536 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8241 (mm-30) REVERT: A 646 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9119 (mmp) REVERT: A 693 ASN cc_start: 0.8943 (m-40) cc_final: 0.8402 (m-40) REVERT: A 722 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7223 (ttmm) REVERT: A 729 GLU cc_start: 0.8328 (tp30) cc_final: 0.7564 (pt0) REVERT: A 738 GLN cc_start: 0.8349 (tt0) cc_final: 0.8086 (tt0) REVERT: A 760 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7568 (ttt-90) REVERT: A 920 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: A 979 LYS cc_start: 0.7615 (mptt) cc_final: 0.7057 (mtpt) REVERT: A 990 ASN cc_start: 0.8505 (t0) cc_final: 0.8301 (t0) REVERT: A 1020 ASP cc_start: 0.8619 (t70) cc_final: 0.7949 (m-30) REVERT: A 1039 GLN cc_start: 0.8823 (mt0) cc_final: 0.8394 (mt0) REVERT: A 1096 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7960 (t70) REVERT: A 1118 GLU cc_start: 0.7888 (pt0) cc_final: 0.7169 (pt0) REVERT: A 1129 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7632 (tm) REVERT: A 1141 ARG cc_start: 0.8278 (mtt90) cc_final: 0.7864 (mmm160) REVERT: A 1157 LYS cc_start: 0.8073 (tppp) cc_final: 0.7276 (tppp) REVERT: A 1174 CYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6572 (m) REVERT: A 1194 GLU cc_start: 0.7950 (pt0) cc_final: 0.7574 (pm20) REVERT: A 1202 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: A 1228 GLU cc_start: 0.7592 (tt0) cc_final: 0.6618 (tm-30) REVERT: A 1275 MET cc_start: 0.8408 (tpp) cc_final: 0.8032 (mmp) REVERT: B 64 LYS cc_start: 0.6590 (ttmt) cc_final: 0.6373 (ttmm) REVERT: B 133 ILE cc_start: 0.8446 (pt) cc_final: 0.7998 (pt) REVERT: B 136 MET cc_start: 0.8668 (tpt) cc_final: 0.8332 (tpp) REVERT: B 222 ARG cc_start: 0.7382 (ptp90) cc_final: 0.6011 (ptp-110) REVERT: B 243 MET cc_start: 0.8375 (mtm) cc_final: 0.8095 (mtp) REVERT: B 253 GLN cc_start: 0.8519 (mt0) cc_final: 0.8249 (mt0) REVERT: B 271 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7370 (tt0) REVERT: B 282 GLN cc_start: 0.8375 (mt0) cc_final: 0.7807 (mt0) REVERT: B 292 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6537 (mtp-110) REVERT: B 311 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8325 (tm-30) REVERT: B 344 LEU cc_start: 0.9269 (mm) cc_final: 0.9066 (mm) REVERT: B 408 GLN cc_start: 0.7268 (tt0) cc_final: 0.6754 (tp-100) REVERT: B 434 GLN cc_start: 0.8492 (mt0) cc_final: 0.8211 (mt0) REVERT: B 459 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.5970 (t80) REVERT: B 461 LYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5695 (pttp) REVERT: B 470 SER cc_start: 0.7916 (t) cc_final: 0.7531 (p) REVERT: B 553 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7379 (mmtt) REVERT: B 570 GLU cc_start: 0.8841 (pt0) cc_final: 0.8571 (pt0) REVERT: B 580 ASP cc_start: 0.8206 (m-30) cc_final: 0.7793 (t0) REVERT: B 609 LYS cc_start: 0.8548 (tmmt) cc_final: 0.8044 (tmmt) REVERT: B 611 MET cc_start: 0.8709 (mmm) cc_final: 0.8427 (mmp) REVERT: B 627 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8380 (mm-30) REVERT: B 628 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8879 (p) REVERT: B 652 LYS cc_start: 0.8933 (pmtt) cc_final: 0.8695 (pttp) REVERT: B 697 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9098 (mp) REVERT: B 776 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8639 (ptmm) REVERT: B 791 MET cc_start: 0.7927 (mpp) cc_final: 0.7441 (mpt) REVERT: B 805 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8031 (mtp-110) REVERT: B 870 MET cc_start: 0.9131 (ttp) cc_final: 0.8874 (ttp) REVERT: B 906 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8745 (p) REVERT: B 929 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8453 (ptp) REVERT: C 28 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8247 (p0) REVERT: C 87 MET cc_start: 0.9467 (mmm) cc_final: 0.9240 (mmp) REVERT: C 125 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: C 148 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7128 (mtp180) REVERT: C 195 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8711 (p0) REVERT: C 286 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: D 59 ARG cc_start: 0.8751 (mpp80) cc_final: 0.8407 (mpp80) REVERT: D 73 LEU cc_start: 0.8880 (mp) cc_final: 0.8416 (tm) REVERT: D 100 MET cc_start: 0.6180 (ptp) cc_final: 0.5951 (ptm) REVERT: E 126 ILE cc_start: 0.8152 (mt) cc_final: 0.7859 (pp) REVERT: E 147 GLU cc_start: 0.8415 (tt0) cc_final: 0.7944 (tm-30) REVERT: E 186 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8196 (ttpp) REVERT: F 54 THR cc_start: 0.8917 (p) cc_final: 0.8542 (t) REVERT: F 56 TYR cc_start: 0.9171 (m-80) cc_final: 0.8812 (m-80) REVERT: F 82 GLU cc_start: 0.8213 (pm20) cc_final: 0.7966 (pm20) REVERT: G 7 MET cc_start: 0.8175 (mtp) cc_final: 0.7633 (mtt) REVERT: G 63 ASP cc_start: 0.6428 (t0) cc_final: 0.6162 (t0) REVERT: G 82 ASP cc_start: 0.7837 (t0) cc_final: 0.7210 (m-30) REVERT: G 104 PHE cc_start: 0.5955 (t80) cc_final: 0.5670 (t80) REVERT: G 154 ASP cc_start: 0.7101 (p0) cc_final: 0.6881 (p0) REVERT: H 37 MET cc_start: 0.8422 (mmm) cc_final: 0.7856 (mmt) REVERT: H 122 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8965 (mm) REVERT: H 124 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8278 (ttm170) REVERT: I 4 PHE cc_start: 0.8397 (m-80) cc_final: 0.8158 (m-80) REVERT: I 15 GLU cc_start: 0.6410 (tp30) cc_final: 0.5907 (tm-30) REVERT: K 47 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8634 (mm-30) REVERT: K 59 ILE cc_start: 0.8426 (tt) cc_final: 0.7722 (mt) REVERT: K 64 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8558 (mt-10) REVERT: K 102 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8644 (tp30) REVERT: K 119 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7980 (ttpp) REVERT: L 50 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7690 (mmtm) REVERT: M 42 ILE cc_start: 0.8639 (mt) cc_final: 0.8422 (mt) REVERT: M 70 CYS cc_start: 0.8547 (t) cc_final: 0.8191 (t) REVERT: M 80 ASN cc_start: 0.9180 (m110) cc_final: 0.8727 (p0) REVERT: M 99 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6694 (ptmm) REVERT: M 102 PHE cc_start: 0.7559 (m-10) cc_final: 0.7145 (m-10) REVERT: M 105 SER cc_start: 0.7725 (t) cc_final: 0.7184 (p) REVERT: M 132 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8015 (pp) REVERT: M 144 LYS cc_start: 0.8518 (mttt) cc_final: 0.8229 (ttpt) REVERT: M 247 MET cc_start: 0.6746 (tpp) cc_final: 0.6530 (tpp) REVERT: M 286 MET cc_start: 0.9383 (mmm) cc_final: 0.8847 (mmm) REVERT: M 298 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7546 (mmm) REVERT: N 350 MET cc_start: 0.8573 (tpp) cc_final: 0.7969 (tpt) REVERT: N 357 LEU cc_start: 0.6185 (tt) cc_final: 0.5906 (tp) REVERT: O 19 GLU cc_start: 0.7126 (tp30) cc_final: 0.6649 (tp30) REVERT: O 43 THR cc_start: 0.8143 (m) cc_final: 0.7762 (p) REVERT: O 260 ASP cc_start: 0.7350 (p0) cc_final: 0.6790 (p0) REVERT: O 338 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5740 (mt) REVERT: P 151 MET cc_start: 0.1823 (OUTLIER) cc_final: 0.0471 (mmp) REVERT: P 217 TRP cc_start: 0.9360 (t60) cc_final: 0.8878 (t-100) REVERT: P 232 MET cc_start: 0.8014 (mmm) cc_final: 0.7650 (mmm) REVERT: Q 49 LYS cc_start: 0.7393 (mtpp) cc_final: 0.6849 (tptp) REVERT: Q 68 MET cc_start: 0.6430 (tpp) cc_final: 0.5839 (tpt) REVERT: Q 71 MET cc_start: 0.8193 (tpp) cc_final: 0.7928 (tpp) REVERT: Q 85 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7236 (pt0) REVERT: Q 103 TRP cc_start: 0.7073 (t-100) cc_final: 0.6827 (t-100) outliers start: 222 outliers final: 108 residues processed: 820 average time/residue: 0.6824 time to fit residues: 699.3289 Evaluate side-chains 770 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 631 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1202 GLN Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain G residue 45 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 523 optimal weight: 90.0000 chunk 464 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 338 optimal weight: 0.5980 chunk 232 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 485 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 492 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN B 557 ASN C 96 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 371 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.213875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126780 restraints weight = 53165.580| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.62 r_work: 0.3208 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 45690 Z= 0.158 Angle : 0.665 13.210 62189 Z= 0.336 Chirality : 0.045 0.304 6999 Planarity : 0.005 0.060 7608 Dihedral : 16.250 179.893 7125 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.49 % Allowed : 19.73 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.11), residues: 5269 helix: 1.19 (0.12), residues: 2062 sheet: -0.70 (0.19), residues: 676 loop : -0.79 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 172 TYR 0.057 0.002 TYR B 533 PHE 0.024 0.002 PHE O 452 TRP 0.017 0.001 TRP O 235 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (45660) covalent geometry : angle 0.65077 / 0.34 (62144) hydrogen bonds : bond 0.04034 / 2.66 ( 1986) hydrogen bonds : angle 4.76939 / 3.43 ( 5601) metal coordination : bond 0.00744 / 0.42 ( 28) metal coordination : angle 5.21517 / 3.12 ( 45) Misc. bond : bond 0.00154 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 679 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8520 (m110) cc_final: 0.8298 (m110) REVERT: A 65 LYS cc_start: 0.9126 (tppp) cc_final: 0.8902 (tptt) REVERT: A 75 ASN cc_start: 0.8055 (m-40) cc_final: 0.7725 (p0) REVERT: A 115 ILE cc_start: 0.8159 (tt) cc_final: 0.7756 (tt) REVERT: A 116 MET cc_start: 0.7674 (mtm) cc_final: 0.7449 (mtm) REVERT: A 119 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7228 (tm-30) REVERT: A 154 ASN cc_start: 0.8497 (m-40) cc_final: 0.8168 (t0) REVERT: A 215 GLN cc_start: 0.7689 (mm-40) cc_final: 0.6409 (mm-40) REVERT: A 225 ASN cc_start: 0.8241 (t0) cc_final: 0.7509 (m110) REVERT: A 307 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7545 (mpt) REVERT: A 311 ASP cc_start: 0.8659 (t0) cc_final: 0.8424 (m-30) REVERT: A 349 GLN cc_start: 0.8707 (mp10) cc_final: 0.8477 (mp10) REVERT: A 406 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8176 (mmtt) REVERT: A 430 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8235 (mmt90) REVERT: A 693 ASN cc_start: 0.8840 (m-40) cc_final: 0.8334 (m-40) REVERT: A 722 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7345 (ttmm) REVERT: A 726 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: A 729 GLU cc_start: 0.8297 (tp30) cc_final: 0.7492 (pt0) REVERT: A 738 GLN cc_start: 0.8385 (tt0) cc_final: 0.8115 (tt0) REVERT: A 760 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7634 (ttt-90) REVERT: A 871 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8680 (ttp) REVERT: A 920 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: A 979 LYS cc_start: 0.7757 (mptt) cc_final: 0.7198 (mtpt) REVERT: A 1020 ASP cc_start: 0.8724 (t70) cc_final: 0.8111 (m-30) REVERT: A 1039 GLN cc_start: 0.8862 (mt0) cc_final: 0.8429 (mt0) REVERT: A 1096 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7931 (t70) REVERT: A 1129 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7665 (tm) REVERT: A 1141 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7908 (mmm160) REVERT: A 1174 CYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6638 (m) REVERT: A 1194 GLU cc_start: 0.8080 (pt0) cc_final: 0.7641 (pm20) REVERT: A 1202 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 1228 GLU cc_start: 0.7611 (tt0) cc_final: 0.6772 (tm-30) REVERT: A 1275 MET cc_start: 0.8509 (tpp) cc_final: 0.8147 (mmt) REVERT: A 1313 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: B 136 MET cc_start: 0.8704 (tpt) cc_final: 0.8376 (tpp) REVERT: B 243 MET cc_start: 0.8407 (mtm) cc_final: 0.8112 (mtp) REVERT: B 253 GLN cc_start: 0.8341 (mt0) cc_final: 0.8024 (mt0) REVERT: B 282 GLN cc_start: 0.8371 (mt0) cc_final: 0.7955 (mt0) REVERT: B 311 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8417 (pp20) REVERT: B 344 LEU cc_start: 0.9293 (mm) cc_final: 0.9062 (mm) REVERT: B 408 GLN cc_start: 0.7237 (tt0) cc_final: 0.6559 (tp40) REVERT: B 413 ASN cc_start: 0.8234 (m-40) cc_final: 0.7939 (m110) REVERT: B 431 MET cc_start: 0.7071 (ttp) cc_final: 0.6862 (tmm) REVERT: B 452 MET cc_start: 0.8655 (mmp) cc_final: 0.8440 (mmm) REVERT: B 459 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6021 (t80) REVERT: B 470 SER cc_start: 0.8038 (t) cc_final: 0.7710 (p) REVERT: B 533 TYR cc_start: 0.8286 (m-80) cc_final: 0.8054 (m-80) REVERT: B 553 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7439 (mmtt) REVERT: B 557 ASN cc_start: 0.8506 (m-40) cc_final: 0.8254 (m-40) REVERT: B 570 GLU cc_start: 0.8869 (pt0) cc_final: 0.8613 (pt0) REVERT: B 580 ASP cc_start: 0.8168 (m-30) cc_final: 0.7820 (t0) REVERT: B 609 LYS cc_start: 0.8548 (tmmt) cc_final: 0.8279 (tppp) REVERT: B 611 MET cc_start: 0.8862 (mmm) cc_final: 0.8546 (mmp) REVERT: B 627 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8457 (mm-30) REVERT: B 628 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8893 (p) REVERT: B 652 LYS cc_start: 0.8999 (pmtt) cc_final: 0.8744 (pttp) REVERT: B 697 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9079 (mp) REVERT: B 791 MET cc_start: 0.7864 (mpp) cc_final: 0.7432 (mpt) REVERT: B 805 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8134 (mtp-110) REVERT: B 906 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 929 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8391 (ptp) REVERT: C 28 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8318 (p0) REVERT: C 83 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: C 87 MET cc_start: 0.9463 (mmm) cc_final: 0.9223 (mmp) REVERT: C 135 ILE cc_start: 0.8739 (tp) cc_final: 0.8378 (pt) REVERT: C 195 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8698 (p0) REVERT: D 59 ARG cc_start: 0.8684 (mpp80) cc_final: 0.8429 (mpp80) REVERT: D 73 LEU cc_start: 0.8840 (mp) cc_final: 0.8445 (tm) REVERT: D 100 MET cc_start: 0.5921 (ptp) cc_final: 0.5574 (ptm) REVERT: E 91 CYS cc_start: 0.9415 (t) cc_final: 0.8940 (p) REVERT: E 94 MET cc_start: 0.6399 (mmp) cc_final: 0.5881 (tpp) REVERT: E 126 ILE cc_start: 0.8164 (mt) cc_final: 0.7816 (pp) REVERT: E 147 GLU cc_start: 0.8468 (tt0) cc_final: 0.8022 (tm-30) REVERT: F 54 THR cc_start: 0.8952 (p) cc_final: 0.8571 (t) REVERT: F 56 TYR cc_start: 0.9219 (m-80) cc_final: 0.8873 (m-80) REVERT: G 7 MET cc_start: 0.8166 (mtp) cc_final: 0.7662 (mtt) REVERT: G 63 ASP cc_start: 0.6253 (t0) cc_final: 0.6007 (t0) REVERT: G 82 ASP cc_start: 0.7884 (t0) cc_final: 0.7208 (m-30) REVERT: H 37 MET cc_start: 0.8412 (mmm) cc_final: 0.7880 (mmt) REVERT: H 122 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8953 (mm) REVERT: H 124 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8297 (ttm170) REVERT: H 136 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: I 4 PHE cc_start: 0.8425 (m-80) cc_final: 0.8217 (m-80) REVERT: I 15 GLU cc_start: 0.6960 (tp30) cc_final: 0.6080 (tm-30) REVERT: J 19 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: J 36 ASP cc_start: 0.8821 (m-30) cc_final: 0.8467 (m-30) REVERT: K 59 ILE cc_start: 0.8419 (tt) cc_final: 0.7731 (mt) REVERT: K 64 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8658 (mt-10) REVERT: K 98 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8529 (ttp-170) REVERT: K 102 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8700 (tp30) REVERT: K 119 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8097 (ttpp) REVERT: L 27 GLU cc_start: 0.7657 (tt0) cc_final: 0.7357 (tp30) REVERT: L 28 ILE cc_start: 0.7877 (pt) cc_final: 0.7558 (pt) REVERT: L 50 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7628 (mmtm) REVERT: M 30 TYR cc_start: 0.7532 (m-80) cc_final: 0.7198 (m-80) REVERT: M 42 ILE cc_start: 0.8528 (mt) cc_final: 0.8208 (mt) REVERT: M 70 CYS cc_start: 0.8590 (t) cc_final: 0.8234 (t) REVERT: M 99 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6618 (ptmm) REVERT: M 102 PHE cc_start: 0.7602 (m-10) cc_final: 0.7166 (m-10) REVERT: M 105 SER cc_start: 0.7488 (t) cc_final: 0.6907 (p) REVERT: M 132 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (pp) REVERT: M 144 LYS cc_start: 0.8558 (mttt) cc_final: 0.8210 (tttt) REVERT: M 195 PHE cc_start: 0.9619 (t80) cc_final: 0.9358 (t80) REVERT: M 247 MET cc_start: 0.7041 (tpp) cc_final: 0.6743 (tpp) REVERT: M 286 MET cc_start: 0.9400 (mmm) cc_final: 0.8825 (mmm) REVERT: N 347 ASP cc_start: 0.6802 (p0) cc_final: 0.6526 (m-30) REVERT: N 350 MET cc_start: 0.8382 (tpp) cc_final: 0.7824 (tpt) REVERT: O 19 GLU cc_start: 0.7120 (tp30) cc_final: 0.6677 (tp30) REVERT: O 43 THR cc_start: 0.8111 (m) cc_final: 0.7737 (p) REVERT: O 76 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7189 (mp0) REVERT: O 260 ASP cc_start: 0.6844 (p0) cc_final: 0.6160 (p0) REVERT: O 317 ASP cc_start: 0.7766 (m-30) cc_final: 0.7487 (m-30) REVERT: O 385 MET cc_start: 0.8037 (ttt) cc_final: 0.7650 (tmm) REVERT: O 490 MET cc_start: 0.2526 (pmm) cc_final: 0.2105 (pmm) REVERT: O 523 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7205 (mm) REVERT: P 151 MET cc_start: 0.1988 (OUTLIER) cc_final: 0.0734 (mmp) REVERT: P 205 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7107 (mm-40) REVERT: P 217 TRP cc_start: 0.9359 (t60) cc_final: 0.8872 (t-100) REVERT: P 232 MET cc_start: 0.7931 (mmm) cc_final: 0.7636 (mmm) REVERT: Q 49 LYS cc_start: 0.7380 (mtpp) cc_final: 0.6859 (tptp) REVERT: Q 68 MET cc_start: 0.6469 (tpp) cc_final: 0.5885 (tpt) REVERT: Q 71 MET cc_start: 0.8208 (tpp) cc_final: 0.7947 (tpp) REVERT: Q 85 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7236 (pt0) REVERT: Q 92 MET cc_start: 0.5801 (ppp) cc_final: 0.5193 (pmm) REVERT: Q 103 TRP cc_start: 0.6823 (OUTLIER) cc_final: 0.6555 (t-100) outliers start: 164 outliers final: 81 residues processed: 784 average time/residue: 0.5915 time to fit residues: 578.0422 Evaluate side-chains 743 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 633 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1202 GLN Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 510 ASP Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 282 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 478 optimal weight: 10.0000 chunk 423 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 402 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 157 HIS ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN B 327 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 371 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.214133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126680 restraints weight = 52913.298| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.54 r_work: 0.3236 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45690 Z= 0.149 Angle : 0.662 13.211 62189 Z= 0.334 Chirality : 0.045 0.300 6999 Planarity : 0.005 0.102 7608 Dihedral : 16.196 179.216 7125 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.58 % Allowed : 20.35 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.11), residues: 5269 helix: 1.25 (0.12), residues: 2063 sheet: -0.65 (0.19), residues: 662 loop : -0.77 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 189 TYR 0.049 0.002 TYR B 533 PHE 0.027 0.001 PHE O 452 TRP 0.023 0.001 TRP G 200 HIS 0.013 0.001 HIS I 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (45660) covalent geometry : angle 0.64739 / 0.33 (62144) hydrogen bonds : bond 0.03921 / 2.58 ( 1986) hydrogen bonds : angle 4.70234 / 3.38 ( 5601) metal coordination : bond 0.00662 / 0.40 ( 28) metal coordination : angle 5.10872 / 3.01 ( 45) Misc. bond : bond 0.00078 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 659 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8536 (m110) cc_final: 0.8295 (m110) REVERT: A 75 ASN cc_start: 0.8022 (m-40) cc_final: 0.7722 (p0) REVERT: A 119 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7268 (tm-30) REVERT: A 154 ASN cc_start: 0.8472 (m-40) cc_final: 0.8157 (t0) REVERT: A 215 GLN cc_start: 0.7835 (mm-40) cc_final: 0.6603 (mm-40) REVERT: A 217 ASN cc_start: 0.7604 (t0) cc_final: 0.7243 (p0) REVERT: A 225 ASN cc_start: 0.8233 (t0) cc_final: 0.7466 (m110) REVERT: A 307 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7551 (mpt) REVERT: A 349 GLN cc_start: 0.8694 (mp10) cc_final: 0.8463 (mp10) REVERT: A 406 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8185 (mmtt) REVERT: A 430 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8272 (mmt90) REVERT: A 693 ASN cc_start: 0.8825 (m-40) cc_final: 0.8301 (m-40) REVERT: A 722 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7445 (ttmm) REVERT: A 729 GLU cc_start: 0.8260 (tp30) cc_final: 0.7443 (pt0) REVERT: A 738 GLN cc_start: 0.8382 (tt0) cc_final: 0.8125 (tt0) REVERT: A 760 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7556 (ttt-90) REVERT: A 871 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8665 (ttp) REVERT: A 920 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: A 979 LYS cc_start: 0.7747 (mptt) cc_final: 0.7190 (mtpt) REVERT: A 1020 ASP cc_start: 0.8699 (t70) cc_final: 0.8148 (m-30) REVERT: A 1039 GLN cc_start: 0.8866 (mt0) cc_final: 0.8428 (mt0) REVERT: A 1129 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7675 (tm) REVERT: A 1141 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7922 (mmm160) REVERT: A 1174 CYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6634 (m) REVERT: A 1191 PHE cc_start: 0.7749 (t80) cc_final: 0.7424 (t80) REVERT: A 1194 GLU cc_start: 0.8091 (pt0) cc_final: 0.7677 (pm20) REVERT: A 1202 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: A 1228 GLU cc_start: 0.7602 (tt0) cc_final: 0.6758 (tm-30) REVERT: A 1275 MET cc_start: 0.8503 (tpp) cc_final: 0.8166 (mmt) REVERT: A 1313 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: B 136 MET cc_start: 0.8669 (tpt) cc_final: 0.8314 (tpp) REVERT: B 243 MET cc_start: 0.8359 (mtm) cc_final: 0.8025 (mtp) REVERT: B 253 GLN cc_start: 0.8323 (mt0) cc_final: 0.8009 (mt0) REVERT: B 271 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7315 (tt0) REVERT: B 280 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: B 282 GLN cc_start: 0.8404 (mt0) cc_final: 0.7938 (mt0) REVERT: B 344 LEU cc_start: 0.9280 (mm) cc_final: 0.9051 (mm) REVERT: B 363 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8701 (mt-10) REVERT: B 408 GLN cc_start: 0.7355 (tt0) cc_final: 0.6686 (tp40) REVERT: B 459 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5988 (t80) REVERT: B 470 SER cc_start: 0.8100 (t) cc_final: 0.7790 (p) REVERT: B 526 LEU cc_start: 0.8121 (pt) cc_final: 0.7729 (mm) REVERT: B 533 TYR cc_start: 0.8173 (m-80) cc_final: 0.7944 (m-80) REVERT: B 553 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7515 (mmtt) REVERT: B 570 GLU cc_start: 0.8821 (pt0) cc_final: 0.8582 (pt0) REVERT: B 580 ASP cc_start: 0.8147 (m-30) cc_final: 0.7825 (t0) REVERT: B 609 LYS cc_start: 0.8544 (tmmt) cc_final: 0.8300 (tppp) REVERT: B 611 MET cc_start: 0.8875 (mmm) cc_final: 0.8571 (mmp) REVERT: B 628 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8904 (p) REVERT: B 652 LYS cc_start: 0.8998 (pmtt) cc_final: 0.8745 (pttp) REVERT: B 697 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9012 (mp) REVERT: B 791 MET cc_start: 0.7822 (mpp) cc_final: 0.7435 (mpt) REVERT: B 805 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8137 (mtp-110) REVERT: B 906 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8670 (p) REVERT: C 28 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8250 (p0) REVERT: C 83 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: C 87 MET cc_start: 0.9446 (mmm) cc_final: 0.9217 (mmp) REVERT: C 125 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7544 (mtm-85) REVERT: C 135 ILE cc_start: 0.8769 (tp) cc_final: 0.8389 (pt) REVERT: C 139 GLN cc_start: 0.9033 (mt0) cc_final: 0.8770 (mt0) REVERT: C 141 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8314 (tpt-90) REVERT: C 143 GLN cc_start: 0.8510 (mt0) cc_final: 0.8292 (mt0) REVERT: C 195 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8652 (p0) REVERT: C 212 MET cc_start: 0.9214 (mtm) cc_final: 0.8955 (mtm) REVERT: D 59 ARG cc_start: 0.8685 (mpp80) cc_final: 0.8408 (mpp80) REVERT: D 73 LEU cc_start: 0.8806 (mp) cc_final: 0.8439 (tm) REVERT: D 100 MET cc_start: 0.5944 (ptp) cc_final: 0.5709 (ptm) REVERT: E 18 MET cc_start: 0.9071 (mtm) cc_final: 0.8740 (mtm) REVERT: E 91 CYS cc_start: 0.9353 (t) cc_final: 0.8908 (p) REVERT: E 94 MET cc_start: 0.6463 (mmp) cc_final: 0.5806 (tpp) REVERT: E 121 MET cc_start: 0.8022 (ppp) cc_final: 0.7808 (ppp) REVERT: E 125 TYR cc_start: 0.6025 (m-80) cc_final: 0.5658 (m-10) REVERT: E 126 ILE cc_start: 0.8341 (mt) cc_final: 0.7953 (pp) REVERT: F 51 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.4834 (mmm160) REVERT: F 54 THR cc_start: 0.8958 (p) cc_final: 0.8571 (t) REVERT: F 56 TYR cc_start: 0.9211 (m-80) cc_final: 0.8875 (m-80) REVERT: G 7 MET cc_start: 0.8176 (mtp) cc_final: 0.7892 (mtm) REVERT: G 80 PHE cc_start: 0.7878 (p90) cc_final: 0.7524 (p90) REVERT: G 82 ASP cc_start: 0.7853 (t0) cc_final: 0.7090 (m-30) REVERT: G 104 PHE cc_start: 0.5446 (t80) cc_final: 0.5076 (t80) REVERT: H 37 MET cc_start: 0.8391 (mmm) cc_final: 0.7857 (mmt) REVERT: H 122 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8953 (mm) REVERT: H 124 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8286 (ttm170) REVERT: H 136 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: I 15 GLU cc_start: 0.6904 (tp30) cc_final: 0.6274 (tm-30) REVERT: J 19 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: J 36 ASP cc_start: 0.8886 (m-30) cc_final: 0.8503 (m-30) REVERT: J 47 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8788 (ttt-90) REVERT: K 59 ILE cc_start: 0.8406 (tt) cc_final: 0.7810 (mt) REVERT: K 64 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8619 (mt-10) REVERT: K 98 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8517 (ttp-170) REVERT: K 119 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8108 (ttpp) REVERT: L 28 ILE cc_start: 0.7917 (pt) cc_final: 0.7640 (pt) REVERT: L 50 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7573 (mmtm) REVERT: M 30 TYR cc_start: 0.7593 (m-80) cc_final: 0.7351 (m-80) REVERT: M 42 ILE cc_start: 0.8526 (mt) cc_final: 0.8207 (mt) REVERT: M 70 CYS cc_start: 0.8597 (t) cc_final: 0.8243 (t) REVERT: M 80 ASN cc_start: 0.9233 (m110) cc_final: 0.8796 (p0) REVERT: M 99 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6614 (ptmm) REVERT: M 102 PHE cc_start: 0.7508 (m-10) cc_final: 0.7083 (m-10) REVERT: M 105 SER cc_start: 0.7512 (t) cc_final: 0.6925 (p) REVERT: M 132 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8000 (pp) REVERT: M 144 LYS cc_start: 0.8523 (mttt) cc_final: 0.8162 (tttt) REVERT: M 247 MET cc_start: 0.7199 (tpp) cc_final: 0.6900 (tpp) REVERT: M 286 MET cc_start: 0.9416 (mmm) cc_final: 0.8949 (mmm) REVERT: N 350 MET cc_start: 0.8335 (tpp) cc_final: 0.7706 (tpt) REVERT: O 19 GLU cc_start: 0.7056 (tp30) cc_final: 0.6616 (tp30) REVERT: O 43 THR cc_start: 0.8087 (m) cc_final: 0.7711 (p) REVERT: O 76 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7192 (mp0) REVERT: O 259 MET cc_start: 0.4949 (mtp) cc_final: 0.3935 (ptp) REVERT: O 317 ASP cc_start: 0.7726 (m-30) cc_final: 0.7464 (m-30) REVERT: O 344 SER cc_start: 0.8593 (m) cc_final: 0.8101 (p) REVERT: O 385 MET cc_start: 0.8044 (ttt) cc_final: 0.7669 (tmm) REVERT: O 490 MET cc_start: 0.2265 (pmm) cc_final: 0.1866 (pmm) REVERT: P 151 MET cc_start: 0.1920 (OUTLIER) cc_final: 0.0546 (mmp) REVERT: P 217 TRP cc_start: 0.9346 (t60) cc_final: 0.8882 (t-100) REVERT: Q 49 LYS cc_start: 0.7402 (mtpp) cc_final: 0.6834 (tptp) REVERT: Q 68 MET cc_start: 0.6149 (tpp) cc_final: 0.5565 (tpt) REVERT: Q 71 MET cc_start: 0.8241 (tpp) cc_final: 0.7968 (tpp) REVERT: Q 85 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7220 (pt0) REVERT: Q 103 TRP cc_start: 0.6753 (OUTLIER) cc_final: 0.6168 (t-100) outliers start: 168 outliers final: 97 residues processed: 764 average time/residue: 0.7141 time to fit residues: 678.1015 Evaluate side-chains 753 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 630 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1202 GLN Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 136 optimal weight: 0.9990 chunk 389 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 374 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 496 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 342 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 358 optimal weight: 0.5980 chunk 263 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN G 67 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 371 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 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 = 0.4471 r_free = 0.4471 target = 0.214257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126592 restraints weight = 53154.612| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.45 r_work: 0.3239 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 45690 Z= 0.147 Angle : 0.663 13.462 62189 Z= 0.334 Chirality : 0.044 0.297 6999 Planarity : 0.005 0.078 7608 Dihedral : 16.139 178.956 7125 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.53 % Allowed : 20.50 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 5269 helix: 1.27 (0.12), residues: 2063 sheet: -0.59 (0.19), residues: 675 loop : -0.73 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 229 TYR 0.045 0.002 TYR B 533 PHE 0.024 0.001 PHE O 452 TRP 0.028 0.001 TRP G 200 HIS 0.028 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (45660) covalent geometry : angle 0.64901 / 0.33 (62144) hydrogen bonds : bond 0.03828 / 2.52 ( 1986) hydrogen bonds : angle 4.66662 / 3.34 ( 5601) metal coordination : bond 0.00654 / 0.39 ( 28) metal coordination : angle 5.03865 / 2.93 ( 45) Misc. bond : bond 0.00314 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 639 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8481 (m110) cc_final: 0.8254 (m110) REVERT: A 75 ASN cc_start: 0.7974 (m-40) cc_final: 0.7617 (p0) REVERT: A 119 GLN cc_start: 0.7606 (tp-100) cc_final: 0.7274 (tm-30) REVERT: A 154 ASN cc_start: 0.8463 (m-40) cc_final: 0.8118 (t0) REVERT: A 215 GLN cc_start: 0.7804 (mm-40) cc_final: 0.6499 (mm-40) REVERT: A 217 ASN cc_start: 0.7660 (t0) cc_final: 0.7251 (p0) REVERT: A 225 ASN cc_start: 0.8175 (t0) cc_final: 0.7346 (m110) REVERT: A 307 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7419 (mpt) REVERT: A 312 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 349 GLN cc_start: 0.8681 (mp10) cc_final: 0.8425 (mp10) REVERT: A 406 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8067 (mmtt) REVERT: A 430 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8227 (mmt90) REVERT: A 507 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8860 (tp) REVERT: A 693 ASN cc_start: 0.8836 (m-40) cc_final: 0.8328 (m-40) REVERT: A 722 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7359 (ttmm) REVERT: A 729 GLU cc_start: 0.8203 (tp30) cc_final: 0.7380 (pt0) REVERT: A 738 GLN cc_start: 0.8407 (tt0) cc_final: 0.8131 (tt0) REVERT: A 761 ASP cc_start: 0.8120 (m-30) cc_final: 0.7893 (m-30) REVERT: A 871 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8612 (ttp) REVERT: A 920 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8508 (mt-10) REVERT: A 979 LYS cc_start: 0.7628 (mptt) cc_final: 0.7067 (mtpt) REVERT: A 1020 ASP cc_start: 0.8633 (t70) cc_final: 0.8001 (m-30) REVERT: A 1039 GLN cc_start: 0.8822 (mt0) cc_final: 0.8364 (mt0) REVERT: A 1129 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7601 (tm) REVERT: A 1141 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7876 (mtp85) REVERT: A 1174 CYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6511 (m) REVERT: A 1191 PHE cc_start: 0.7660 (t80) cc_final: 0.7320 (t80) REVERT: A 1193 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7988 (mtmm) REVERT: A 1194 GLU cc_start: 0.7993 (pt0) cc_final: 0.7564 (pm20) REVERT: A 1228 GLU cc_start: 0.7742 (tt0) cc_final: 0.6804 (tm-30) REVERT: A 1275 MET cc_start: 0.8485 (tpp) cc_final: 0.8118 (mmt) REVERT: A 1313 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: B 243 MET cc_start: 0.8301 (mtm) cc_final: 0.7947 (mtp) REVERT: B 253 GLN cc_start: 0.8237 (mt0) cc_final: 0.7916 (mt0) REVERT: B 262 MET cc_start: 0.8394 (mpp) cc_final: 0.8162 (mtm) REVERT: B 280 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: B 282 GLN cc_start: 0.8415 (mt0) cc_final: 0.7748 (mt0) REVERT: B 312 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7366 (tm) REVERT: B 344 LEU cc_start: 0.9258 (mm) cc_final: 0.9000 (mm) REVERT: B 363 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 408 GLN cc_start: 0.7335 (tt0) cc_final: 0.6612 (tp40) REVERT: B 413 ASN cc_start: 0.8136 (m-40) cc_final: 0.7210 (m110) REVERT: B 431 MET cc_start: 0.7731 (tmm) cc_final: 0.7425 (ttp) REVERT: B 459 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.6029 (t80) REVERT: B 470 SER cc_start: 0.8030 (t) cc_final: 0.7706 (p) REVERT: B 553 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7410 (mmtt) REVERT: B 570 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: B 580 ASP cc_start: 0.8210 (m-30) cc_final: 0.7810 (t0) REVERT: B 609 LYS cc_start: 0.8496 (tmmt) cc_final: 0.8246 (tppp) REVERT: B 611 MET cc_start: 0.8764 (mmm) cc_final: 0.8495 (mmp) REVERT: B 628 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 652 LYS cc_start: 0.8977 (pmtt) cc_final: 0.8727 (pttp) REVERT: B 697 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9009 (mp) REVERT: B 781 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7552 (mtp85) REVERT: B 791 MET cc_start: 0.7740 (mpp) cc_final: 0.7327 (mpt) REVERT: B 805 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8058 (mtp-110) REVERT: B 906 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8707 (p) REVERT: B 929 MET cc_start: 0.8516 (ptp) cc_final: 0.8082 (ttt) REVERT: B 936 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.8843 (t) REVERT: C 28 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8180 (p0) REVERT: C 83 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: C 87 MET cc_start: 0.9455 (mmm) cc_final: 0.9237 (mmp) REVERT: C 90 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: C 125 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7530 (mtm-85) REVERT: C 135 ILE cc_start: 0.8489 (tp) cc_final: 0.8093 (pt) REVERT: C 141 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8294 (tpt-90) REVERT: C 143 GLN cc_start: 0.8590 (mt0) cc_final: 0.8330 (mt0) REVERT: C 195 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (p0) REVERT: D 59 ARG cc_start: 0.8686 (mpp80) cc_final: 0.8386 (mpp80) REVERT: D 73 LEU cc_start: 0.8856 (mp) cc_final: 0.8462 (tm) REVERT: D 100 MET cc_start: 0.5900 (ptp) cc_final: 0.5645 (ptm) REVERT: E 18 MET cc_start: 0.9147 (mtm) cc_final: 0.8870 (mtm) REVERT: E 91 CYS cc_start: 0.9442 (t) cc_final: 0.8929 (p) REVERT: E 94 MET cc_start: 0.6414 (mmp) cc_final: 0.5772 (tpp) REVERT: E 125 TYR cc_start: 0.6286 (m-80) cc_final: 0.5966 (m-10) REVERT: E 126 ILE cc_start: 0.8333 (mt) cc_final: 0.7903 (pp) REVERT: E 127 LEU cc_start: 0.8324 (mp) cc_final: 0.7868 (mm) REVERT: F 51 ARG cc_start: 0.7277 (mtm-85) cc_final: 0.4762 (mmm160) REVERT: F 54 THR cc_start: 0.8903 (p) cc_final: 0.8494 (t) REVERT: F 56 TYR cc_start: 0.9175 (m-80) cc_final: 0.8852 (m-80) REVERT: G 7 MET cc_start: 0.8129 (mtp) cc_final: 0.7750 (mtm) REVERT: G 80 PHE cc_start: 0.7961 (p90) cc_final: 0.7588 (p90) REVERT: G 82 ASP cc_start: 0.8022 (t0) cc_final: 0.7126 (m-30) REVERT: G 104 PHE cc_start: 0.5574 (t80) cc_final: 0.5154 (t80) REVERT: H 37 MET cc_start: 0.8370 (mmm) cc_final: 0.7788 (mmt) REVERT: H 122 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8895 (mm) REVERT: J 19 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: J 36 ASP cc_start: 0.8917 (m-30) cc_final: 0.8502 (m-30) REVERT: J 47 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8770 (ttt-90) REVERT: K 59 ILE cc_start: 0.8586 (tt) cc_final: 0.8015 (mt) REVERT: K 64 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8618 (mt-10) REVERT: K 98 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8518 (ttp-170) REVERT: K 119 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7977 (ttpp) REVERT: L 50 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7559 (mmtm) REVERT: M 30 TYR cc_start: 0.7583 (m-80) cc_final: 0.7353 (m-80) REVERT: M 42 ILE cc_start: 0.8521 (mt) cc_final: 0.8177 (mt) REVERT: M 70 CYS cc_start: 0.8488 (t) cc_final: 0.8109 (t) REVERT: M 99 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6621 (ptmm) REVERT: M 102 PHE cc_start: 0.7335 (m-10) cc_final: 0.6899 (m-10) REVERT: M 105 SER cc_start: 0.7659 (t) cc_final: 0.6967 (p) REVERT: M 144 LYS cc_start: 0.8510 (mttt) cc_final: 0.8160 (tttt) REVERT: M 247 MET cc_start: 0.7216 (tpp) cc_final: 0.6795 (tpp) REVERT: M 286 MET cc_start: 0.9439 (mmm) cc_final: 0.8919 (mmm) REVERT: O 19 GLU cc_start: 0.7103 (tp30) cc_final: 0.6583 (tp30) REVERT: O 43 THR cc_start: 0.8137 (m) cc_final: 0.7738 (p) REVERT: O 259 MET cc_start: 0.4726 (mtp) cc_final: 0.3733 (ptp) REVERT: O 317 ASP cc_start: 0.7707 (m-30) cc_final: 0.7447 (m-30) REVERT: O 344 SER cc_start: 0.8553 (m) cc_final: 0.7695 (p) REVERT: O 347 THR cc_start: 0.7094 (m) cc_final: 0.6699 (p) REVERT: O 385 MET cc_start: 0.8342 (ttt) cc_final: 0.7621 (tmm) REVERT: O 490 MET cc_start: 0.2304 (pmm) cc_final: 0.1828 (pmm) REVERT: O 523 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7152 (mm) REVERT: P 151 MET cc_start: 0.1949 (OUTLIER) cc_final: 0.1605 (mmp) REVERT: P 217 TRP cc_start: 0.9339 (t60) cc_final: 0.8876 (t-100) REVERT: P 232 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: Q 49 LYS cc_start: 0.7554 (mtpp) cc_final: 0.6889 (tptp) REVERT: Q 68 MET cc_start: 0.6071 (tpp) cc_final: 0.5386 (tpt) REVERT: Q 71 MET cc_start: 0.8184 (tpp) cc_final: 0.7921 (tpp) REVERT: Q 85 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7176 (pt0) REVERT: Q 103 TRP cc_start: 0.6451 (OUTLIER) cc_final: 0.5998 (t-100) outliers start: 166 outliers final: 93 residues processed: 740 average time/residue: 0.4686 time to fit residues: 434.9738 Evaluate side-chains 742 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 620 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 277 optimal weight: 1.9990 chunk 456 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 402 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 366 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 418 optimal weight: 8.9990 chunk 189 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 434 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN H 46 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 371 GLN O 377 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.214368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126426 restraints weight = 53033.055| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.53 r_work: 0.3260 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 45690 Z= 0.140 Angle : 0.671 20.132 62189 Z= 0.337 Chirality : 0.044 0.292 6999 Planarity : 0.004 0.068 7608 Dihedral : 16.080 178.729 7125 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.38 % Allowed : 21.09 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5269 helix: 1.31 (0.12), residues: 2062 sheet: -0.56 (0.19), residues: 678 loop : -0.72 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 229 TYR 0.043 0.001 TYR G 40 PHE 0.023 0.001 PHE O 452 TRP 0.035 0.001 TRP G 200 HIS 0.011 0.001 HIS I 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (45660) covalent geometry : angle 0.65756 / 0.34 (62144) hydrogen bonds : bond 0.03726 / 2.45 ( 1986) hydrogen bonds : angle 4.64311 / 3.32 ( 5601) metal coordination : bond 0.00599 / 0.36 ( 28) metal coordination : angle 5.06180 / 2.93 ( 45) Misc. bond : bond 0.00224 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 645 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8454 (m110) cc_final: 0.8234 (m110) REVERT: A 75 ASN cc_start: 0.7857 (m-40) cc_final: 0.7497 (p0) REVERT: A 119 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7262 (tm-30) REVERT: A 151 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7428 (mtp85) REVERT: A 154 ASN cc_start: 0.8492 (m-40) cc_final: 0.8155 (t0) REVERT: A 215 GLN cc_start: 0.7813 (mm-40) cc_final: 0.6533 (mm-40) REVERT: A 217 ASN cc_start: 0.7644 (t0) cc_final: 0.7246 (p0) REVERT: A 225 ASN cc_start: 0.8144 (t0) cc_final: 0.7356 (m110) REVERT: A 307 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7342 (mpt) REVERT: A 312 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: A 349 GLN cc_start: 0.8533 (mp10) cc_final: 0.8288 (mp10) REVERT: A 406 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8050 (mmtt) REVERT: A 430 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8200 (mmt90) REVERT: A 523 MET cc_start: 0.9217 (mtp) cc_final: 0.8899 (mtm) REVERT: A 693 ASN cc_start: 0.8814 (m-40) cc_final: 0.8322 (m-40) REVERT: A 722 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7346 (ttmm) REVERT: A 729 GLU cc_start: 0.8181 (tp30) cc_final: 0.7356 (pt0) REVERT: A 738 GLN cc_start: 0.8338 (tt0) cc_final: 0.8012 (tt0) REVERT: A 871 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8587 (ttp) REVERT: A 920 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8449 (mt-10) REVERT: A 979 LYS cc_start: 0.7545 (mptt) cc_final: 0.7024 (mtpt) REVERT: A 1020 ASP cc_start: 0.8613 (t70) cc_final: 0.7979 (m-30) REVERT: A 1039 GLN cc_start: 0.8799 (mt0) cc_final: 0.8335 (mt0) REVERT: A 1129 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7592 (tm) REVERT: A 1141 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7886 (mmm160) REVERT: A 1150 ARG cc_start: 0.8520 (tmt170) cc_final: 0.8295 (tmt170) REVERT: A 1174 CYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6498 (m) REVERT: A 1191 PHE cc_start: 0.7645 (t80) cc_final: 0.7294 (t80) REVERT: A 1193 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7916 (mtmm) REVERT: A 1194 GLU cc_start: 0.7949 (pt0) cc_final: 0.7528 (pm20) REVERT: A 1228 GLU cc_start: 0.7738 (tt0) cc_final: 0.6728 (tm-30) REVERT: A 1275 MET cc_start: 0.8465 (tpp) cc_final: 0.8092 (mmt) REVERT: A 1313 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: B 136 MET cc_start: 0.8573 (tpt) cc_final: 0.8348 (tpp) REVERT: B 243 MET cc_start: 0.8321 (mtm) cc_final: 0.7977 (mtp) REVERT: B 253 GLN cc_start: 0.8161 (mt0) cc_final: 0.7855 (mt0) REVERT: B 271 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7261 (tt0) REVERT: B 280 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: B 282 GLN cc_start: 0.8432 (mt0) cc_final: 0.7786 (mt0) REVERT: B 303 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4311 (tmtt) REVERT: B 312 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7358 (tm) REVERT: B 344 LEU cc_start: 0.9249 (mm) cc_final: 0.8992 (mm) REVERT: B 363 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 408 GLN cc_start: 0.7311 (tt0) cc_final: 0.6599 (tp40) REVERT: B 413 ASN cc_start: 0.8075 (m-40) cc_final: 0.7156 (m110) REVERT: B 431 MET cc_start: 0.7681 (tmm) cc_final: 0.7401 (ttp) REVERT: B 452 MET cc_start: 0.8577 (mmp) cc_final: 0.8316 (mmm) REVERT: B 459 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.6061 (t80) REVERT: B 470 SER cc_start: 0.8002 (t) cc_final: 0.7691 (p) REVERT: B 553 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7406 (mmtt) REVERT: B 570 GLU cc_start: 0.8760 (pt0) cc_final: 0.8501 (pt0) REVERT: B 580 ASP cc_start: 0.8199 (m-30) cc_final: 0.7808 (t0) REVERT: B 600 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7838 (mttt) REVERT: B 609 LYS cc_start: 0.8476 (tmmt) cc_final: 0.8240 (tppp) REVERT: B 611 MET cc_start: 0.8758 (mmm) cc_final: 0.8505 (mmp) REVERT: B 628 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 652 LYS cc_start: 0.8970 (pmtt) cc_final: 0.8725 (pttp) REVERT: B 791 MET cc_start: 0.7700 (mpp) cc_final: 0.7402 (mpt) REVERT: B 805 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.8040 (mtp-110) REVERT: B 906 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8681 (p) REVERT: B 929 MET cc_start: 0.8457 (ptp) cc_final: 0.8024 (ttt) REVERT: B 936 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8842 (t) REVERT: C 28 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8145 (p0) REVERT: C 83 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: C 87 MET cc_start: 0.9449 (mmm) cc_final: 0.9184 (mmp) REVERT: C 125 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: C 135 ILE cc_start: 0.8471 (tp) cc_final: 0.8079 (pt) REVERT: C 138 LEU cc_start: 0.8623 (mt) cc_final: 0.8385 (mt) REVERT: C 141 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8259 (tpt-90) REVERT: C 143 GLN cc_start: 0.8571 (mt0) cc_final: 0.8314 (mt0) REVERT: C 195 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8482 (p0) REVERT: D 59 ARG cc_start: 0.8685 (mpp80) cc_final: 0.8361 (mpp80) REVERT: D 73 LEU cc_start: 0.8854 (mp) cc_final: 0.8455 (tm) REVERT: D 100 MET cc_start: 0.5625 (ptp) cc_final: 0.5329 (ptm) REVERT: E 18 MET cc_start: 0.9092 (mtm) cc_final: 0.8799 (mtm) REVERT: E 91 CYS cc_start: 0.9439 (t) cc_final: 0.8907 (p) REVERT: E 94 MET cc_start: 0.6793 (mmp) cc_final: 0.6201 (tpp) REVERT: E 125 TYR cc_start: 0.6414 (m-80) cc_final: 0.6080 (m-10) REVERT: E 126 ILE cc_start: 0.8327 (mt) cc_final: 0.7904 (pp) REVERT: E 127 LEU cc_start: 0.8253 (mp) cc_final: 0.7788 (mm) REVERT: F 51 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.4734 (mmm160) REVERT: F 54 THR cc_start: 0.8893 (p) cc_final: 0.8477 (t) REVERT: F 56 TYR cc_start: 0.9161 (m-80) cc_final: 0.8844 (m-80) REVERT: G 7 MET cc_start: 0.8109 (mtp) cc_final: 0.7721 (mtm) REVERT: G 80 PHE cc_start: 0.7963 (p90) cc_final: 0.7489 (p90) REVERT: G 82 ASP cc_start: 0.8033 (t0) cc_final: 0.7074 (m-30) REVERT: G 104 PHE cc_start: 0.5619 (t80) cc_final: 0.5330 (t80) REVERT: H 18 GLU cc_start: 0.8152 (mp0) cc_final: 0.7709 (mp0) REVERT: H 37 MET cc_start: 0.8355 (mmm) cc_final: 0.7774 (mmt) REVERT: H 62 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8750 (p) REVERT: H 122 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8906 (mm) REVERT: I 15 GLU cc_start: 0.6902 (tp30) cc_final: 0.6424 (tm-30) REVERT: I 16 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7523 (mm-30) REVERT: J 36 ASP cc_start: 0.8898 (m-30) cc_final: 0.8475 (m-30) REVERT: J 47 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (ttt-90) REVERT: K 59 ILE cc_start: 0.8393 (tt) cc_final: 0.7807 (mt) REVERT: K 64 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8576 (mt-10) REVERT: K 72 THR cc_start: 0.9090 (p) cc_final: 0.8778 (p) REVERT: K 98 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8561 (ttp-170) REVERT: K 119 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7971 (ttpp) REVERT: L 50 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7621 (mmtm) REVERT: M 30 TYR cc_start: 0.7573 (m-80) cc_final: 0.7326 (m-80) REVERT: M 42 ILE cc_start: 0.8523 (mt) cc_final: 0.8137 (mt) REVERT: M 70 CYS cc_start: 0.8476 (t) cc_final: 0.8090 (t) REVERT: M 80 ASN cc_start: 0.9360 (m110) cc_final: 0.9007 (OUTLIER) REVERT: M 99 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6602 (ptmm) REVERT: M 102 PHE cc_start: 0.7273 (m-10) cc_final: 0.6818 (m-10) REVERT: M 105 SER cc_start: 0.7733 (t) cc_final: 0.7039 (p) REVERT: M 144 LYS cc_start: 0.8513 (mttt) cc_final: 0.8147 (tttt) REVERT: M 247 MET cc_start: 0.7257 (tpp) cc_final: 0.6817 (tpp) REVERT: M 286 MET cc_start: 0.9437 (mmm) cc_final: 0.8914 (mmm) REVERT: O 43 THR cc_start: 0.8076 (m) cc_final: 0.7718 (p) REVERT: O 259 MET cc_start: 0.4948 (mtp) cc_final: 0.4179 (ptp) REVERT: O 306 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8799 (tp-100) REVERT: O 317 ASP cc_start: 0.7647 (m-30) cc_final: 0.7393 (m-30) REVERT: O 344 SER cc_start: 0.8555 (m) cc_final: 0.7705 (p) REVERT: O 347 THR cc_start: 0.7144 (m) cc_final: 0.6671 (p) REVERT: O 371 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: O 385 MET cc_start: 0.8491 (ttt) cc_final: 0.7761 (tmm) REVERT: O 490 MET cc_start: 0.2165 (pmm) cc_final: 0.1705 (pmm) REVERT: O 523 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7143 (mm) REVERT: P 151 MET cc_start: 0.1939 (OUTLIER) cc_final: 0.1440 (mmp) REVERT: P 217 TRP cc_start: 0.9349 (t60) cc_final: 0.8879 (t-100) REVERT: P 232 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7176 (tpt) REVERT: Q 49 LYS cc_start: 0.7468 (mtpp) cc_final: 0.6798 (tptp) REVERT: Q 60 LEU cc_start: 0.7172 (tp) cc_final: 0.6830 (mt) REVERT: Q 68 MET cc_start: 0.6044 (tpp) cc_final: 0.5458 (tpt) REVERT: Q 71 MET cc_start: 0.8282 (tpp) cc_final: 0.8032 (tpp) REVERT: Q 85 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7126 (pt0) REVERT: Q 103 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.6132 (t-100) outliers start: 159 outliers final: 95 residues processed: 748 average time/residue: 0.4494 time to fit residues: 420.3870 Evaluate side-chains 738 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 616 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 371 GLN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 335 optimal weight: 20.0000 chunk 438 optimal weight: 0.6980 chunk 273 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 210 optimal weight: 0.9980 chunk 473 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 494 optimal weight: 6.9990 chunk 365 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 157 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN B 327 ASN B 423 ASN B 434 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN G 36 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN O 371 GLN O 377 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.214241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127089 restraints weight = 53320.268| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.70 r_work: 0.3225 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 45690 Z= 0.169 Angle : 0.733 59.199 62189 Z= 0.384 Chirality : 0.044 0.292 6999 Planarity : 0.004 0.067 7608 Dihedral : 16.077 178.727 7125 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.98 % Allowed : 21.67 % Favored : 75.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5269 helix: 1.31 (0.12), residues: 2062 sheet: -0.56 (0.19), residues: 678 loop : -0.72 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 229 TYR 0.020 0.001 TYR G 40 PHE 0.021 0.001 PHE O 452 TRP 0.033 0.002 TRP G 200 HIS 0.010 0.001 HIS P 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (45660) covalent geometry : angle 0.72011 / 0.38 (62144) hydrogen bonds : bond 0.03743 / 2.46 ( 1986) hydrogen bonds : angle 4.64745 / 3.32 ( 5601) metal coordination : bond 0.00616 / 0.37 ( 28) metal coordination : angle 5.05211 / 2.93 ( 45) Misc. bond : bond 0.00230 / 0.12 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 615 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8471 (m110) cc_final: 0.8166 (m-40) REVERT: A 75 ASN cc_start: 0.7907 (m-40) cc_final: 0.7543 (p0) REVERT: A 119 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7271 (tm-30) REVERT: A 151 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.7437 (mtp85) REVERT: A 154 ASN cc_start: 0.8503 (m-40) cc_final: 0.8171 (t0) REVERT: A 215 GLN cc_start: 0.7809 (mm-40) cc_final: 0.6529 (mm-40) REVERT: A 217 ASN cc_start: 0.7667 (t0) cc_final: 0.7263 (p0) REVERT: A 225 ASN cc_start: 0.8211 (t0) cc_final: 0.7430 (m110) REVERT: A 233 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8422 (pp20) REVERT: A 307 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7372 (mpt) REVERT: A 312 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: A 349 GLN cc_start: 0.8561 (mp10) cc_final: 0.8319 (mp10) REVERT: A 406 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8114 (mmtt) REVERT: A 430 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8287 (mmt90) REVERT: A 523 MET cc_start: 0.9226 (mtp) cc_final: 0.8928 (mtm) REVERT: A 693 ASN cc_start: 0.8837 (m-40) cc_final: 0.8345 (m-40) REVERT: A 722 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7396 (ttmm) REVERT: A 729 GLU cc_start: 0.8223 (tp30) cc_final: 0.7391 (pt0) REVERT: A 738 GLN cc_start: 0.8357 (tt0) cc_final: 0.8033 (tt0) REVERT: A 760 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7391 (ttt-90) REVERT: A 871 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8641 (ttp) REVERT: A 920 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: A 979 LYS cc_start: 0.7626 (mptt) cc_final: 0.7101 (mtpt) REVERT: A 1020 ASP cc_start: 0.8706 (t70) cc_final: 0.8076 (m-30) REVERT: A 1039 GLN cc_start: 0.8850 (mt0) cc_final: 0.8385 (mt0) REVERT: A 1129 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7622 (tm) REVERT: A 1141 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7919 (mmm160) REVERT: A 1150 ARG cc_start: 0.8544 (tmt170) cc_final: 0.8302 (tmt170) REVERT: A 1174 CYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6542 (m) REVERT: A 1191 PHE cc_start: 0.7660 (t80) cc_final: 0.7270 (t80) REVERT: A 1193 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7932 (mtmm) REVERT: A 1194 GLU cc_start: 0.7965 (pt0) cc_final: 0.7535 (pm20) REVERT: A 1228 GLU cc_start: 0.7798 (tt0) cc_final: 0.6798 (tm-30) REVERT: A 1275 MET cc_start: 0.8521 (tpp) cc_final: 0.8136 (mmt) REVERT: A 1313 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: B 136 MET cc_start: 0.8646 (tpt) cc_final: 0.8424 (tpp) REVERT: B 243 MET cc_start: 0.8367 (mtm) cc_final: 0.8019 (mtp) REVERT: B 253 GLN cc_start: 0.8192 (mt0) cc_final: 0.7897 (mt0) REVERT: B 271 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7318 (tt0) REVERT: B 280 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: B 282 GLN cc_start: 0.8474 (mt0) cc_final: 0.7827 (mt0) REVERT: B 303 LYS cc_start: 0.4702 (OUTLIER) cc_final: 0.4307 (tmtt) REVERT: B 312 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7379 (tm) REVERT: B 344 LEU cc_start: 0.9259 (mm) cc_final: 0.8998 (mm) REVERT: B 363 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 408 GLN cc_start: 0.7321 (tt0) cc_final: 0.6616 (tp40) REVERT: B 413 ASN cc_start: 0.8144 (m-40) cc_final: 0.7234 (m110) REVERT: B 431 MET cc_start: 0.7686 (tmm) cc_final: 0.7397 (ttp) REVERT: B 459 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6080 (t80) REVERT: B 470 SER cc_start: 0.8062 (t) cc_final: 0.7760 (p) REVERT: B 553 LYS cc_start: 0.7813 (mmmt) cc_final: 0.7446 (mmtt) REVERT: B 570 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (pt0) REVERT: B 580 ASP cc_start: 0.8238 (m-30) cc_final: 0.7833 (t0) REVERT: B 600 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7863 (mttt) REVERT: B 609 LYS cc_start: 0.8504 (tmmt) cc_final: 0.8268 (tppp) REVERT: B 611 MET cc_start: 0.8817 (mmm) cc_final: 0.8553 (mmp) REVERT: B 628 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8679 (p) REVERT: B 652 LYS cc_start: 0.8990 (pmtt) cc_final: 0.8740 (pttp) REVERT: B 697 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9014 (mt) REVERT: B 776 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8567 (ptmm) REVERT: B 791 MET cc_start: 0.7764 (mpp) cc_final: 0.7469 (mpt) REVERT: B 805 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8116 (mtp-110) REVERT: B 906 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 929 MET cc_start: 0.8508 (ptp) cc_final: 0.8077 (ttt) REVERT: B 936 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 28 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8232 (p0) REVERT: C 83 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: C 87 MET cc_start: 0.9468 (mmm) cc_final: 0.9196 (mmp) REVERT: C 125 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7544 (mtm-85) REVERT: C 135 ILE cc_start: 0.8514 (tp) cc_final: 0.8118 (pt) REVERT: C 138 LEU cc_start: 0.8661 (mt) cc_final: 0.8415 (mt) REVERT: C 141 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8302 (tpt-90) REVERT: C 143 GLN cc_start: 0.8611 (mt0) cc_final: 0.8345 (mt0) REVERT: C 195 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8526 (p0) REVERT: D 59 ARG cc_start: 0.8674 (mpp80) cc_final: 0.8359 (mpp80) REVERT: D 73 LEU cc_start: 0.8851 (mp) cc_final: 0.8462 (tm) REVERT: D 100 MET cc_start: 0.5570 (ptp) cc_final: 0.5337 (ptm) REVERT: E 18 MET cc_start: 0.9118 (mtm) cc_final: 0.8854 (mtm) REVERT: E 91 CYS cc_start: 0.9441 (t) cc_final: 0.8907 (p) REVERT: E 94 MET cc_start: 0.6833 (mmp) cc_final: 0.6218 (tpp) REVERT: E 125 TYR cc_start: 0.6428 (m-80) cc_final: 0.6076 (m-10) REVERT: E 126 ILE cc_start: 0.8330 (mt) cc_final: 0.7894 (pp) REVERT: E 127 LEU cc_start: 0.8242 (mp) cc_final: 0.7785 (mm) REVERT: F 51 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.4790 (mmm160) REVERT: F 54 THR cc_start: 0.8925 (p) cc_final: 0.8512 (t) REVERT: F 56 TYR cc_start: 0.9199 (m-80) cc_final: 0.8892 (m-80) REVERT: G 7 MET cc_start: 0.8160 (mtp) cc_final: 0.7798 (mtm) REVERT: G 80 PHE cc_start: 0.7951 (p90) cc_final: 0.7502 (p90) REVERT: G 82 ASP cc_start: 0.8058 (t0) cc_final: 0.7096 (m-30) REVERT: G 104 PHE cc_start: 0.5711 (t80) cc_final: 0.5345 (t80) REVERT: H 18 GLU cc_start: 0.8141 (mp0) cc_final: 0.7744 (mp0) REVERT: H 37 MET cc_start: 0.8402 (mmm) cc_final: 0.7832 (mmt) REVERT: H 62 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8785 (p) REVERT: H 122 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8928 (mm) REVERT: I 15 GLU cc_start: 0.6930 (tp30) cc_final: 0.6450 (tm-30) REVERT: I 16 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7521 (mm-30) REVERT: J 36 ASP cc_start: 0.8941 (m-30) cc_final: 0.8526 (m-30) REVERT: J 47 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8858 (ttt-90) REVERT: K 59 ILE cc_start: 0.8410 (tt) cc_final: 0.7829 (mt) REVERT: K 64 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8648 (mt-10) REVERT: K 72 THR cc_start: 0.9122 (p) cc_final: 0.8812 (p) REVERT: K 98 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8629 (ttp-170) REVERT: K 119 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8017 (ttpp) REVERT: L 50 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7660 (mmtm) REVERT: M 30 TYR cc_start: 0.7566 (m-80) cc_final: 0.7360 (m-80) REVERT: M 42 ILE cc_start: 0.8519 (mt) cc_final: 0.8138 (mt) REVERT: M 70 CYS cc_start: 0.8509 (t) cc_final: 0.8124 (t) REVERT: M 80 ASN cc_start: 0.9357 (m110) cc_final: 0.9006 (OUTLIER) REVERT: M 99 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6606 (ptmm) REVERT: M 102 PHE cc_start: 0.7290 (m-10) cc_final: 0.6917 (m-10) REVERT: M 105 SER cc_start: 0.7768 (t) cc_final: 0.7087 (p) REVERT: M 144 LYS cc_start: 0.8538 (mttt) cc_final: 0.8169 (tttt) REVERT: M 247 MET cc_start: 0.7265 (tpp) cc_final: 0.6818 (tpp) REVERT: M 286 MET cc_start: 0.9420 (mmm) cc_final: 0.8930 (mmm) REVERT: O 43 THR cc_start: 0.8128 (m) cc_final: 0.7724 (p) REVERT: O 259 MET cc_start: 0.4958 (mtp) cc_final: 0.4102 (ptp) REVERT: O 317 ASP cc_start: 0.7652 (m-30) cc_final: 0.7396 (m-30) REVERT: O 344 SER cc_start: 0.8583 (m) cc_final: 0.7723 (p) REVERT: O 347 THR cc_start: 0.7186 (m) cc_final: 0.6702 (p) REVERT: O 490 MET cc_start: 0.2163 (pmm) cc_final: 0.1706 (pmm) REVERT: O 523 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7233 (mm) REVERT: P 151 MET cc_start: 0.1916 (OUTLIER) cc_final: 0.1401 (mmp) REVERT: P 217 TRP cc_start: 0.9344 (t60) cc_final: 0.8869 (t-100) REVERT: P 232 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7183 (tpt) REVERT: Q 49 LYS cc_start: 0.7480 (mtpp) cc_final: 0.6809 (tptp) REVERT: Q 60 LEU cc_start: 0.7281 (tp) cc_final: 0.6917 (mt) REVERT: Q 68 MET cc_start: 0.6063 (tpp) cc_final: 0.5458 (tpt) REVERT: Q 71 MET cc_start: 0.8277 (tpp) cc_final: 0.8046 (tpp) REVERT: Q 85 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7132 (pt0) REVERT: Q 103 TRP cc_start: 0.6402 (OUTLIER) cc_final: 0.6080 (t-100) outliers start: 140 outliers final: 97 residues processed: 704 average time/residue: 0.4517 time to fit residues: 396.3681 Evaluate side-chains 740 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 612 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 TYR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 151 MET Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 189 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 429 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 519 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 137 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 157 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN G 36 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 GLN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.217404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130217 restraints weight = 53462.816| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.55 r_work: 0.3255 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 45690 Z= 0.198 Angle : 0.784 59.200 62189 Z= 0.428 Chirality : 0.047 1.369 6999 Planarity : 0.005 0.067 7608 Dihedral : 16.080 178.726 7125 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.92 % Allowed : 21.82 % Favored : 75.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 5269 helix: 1.31 (0.12), residues: 2062 sheet: -0.58 (0.19), residues: 678 loop : -0.73 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 229 TYR 0.018 0.001 TYR I 30 PHE 0.024 0.001 PHE A 462 TRP 0.030 0.002 TRP G 200 HIS 0.009 0.001 HIS P 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (45660) covalent geometry : angle 0.77243 / 0.43 (62144) hydrogen bonds : bond 0.03752 / 2.48 ( 1986) hydrogen bonds : angle 4.64959 / 3.32 ( 5601) metal coordination : bond 0.00627 / 0.38 ( 28) metal coordination : angle 5.04620 / 2.92 ( 45) Misc. bond : bond 0.00230 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19601.44 seconds wall clock time: 332 minutes 42.89 seconds (19962.89 seconds total)