Starting phenix.real_space_refine on Sun Aug 9 06:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wq9_66163/08_2026/9wq9_66163.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wq9_66163/08_2026/9wq9_66163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wq9_66163/08_2026/9wq9_66163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wq9_66163/08_2026/9wq9_66163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wq9_66163/08_2026/9wq9_66163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wq9_66163/08_2026/9wq9_66163.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 43 5.49 5 Mg 1 5.21 5 S 179 5.16 5 C 20341 2.51 5 N 5660 2.21 5 O 6238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 32470 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1414, 11123 Classifications: {'peptide': 1414} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1347} Chain breaks: 4 Chain: "B" Number of atoms: 9335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 9335 Classifications: {'peptide': 1171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1118} Chain breaks: 5 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1326 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1113 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "P" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 135 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 6} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 430 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 87.343 76.848 23.942 1.00102.59 S ATOM 844 SG CYS A 110 89.105 80.118 22.946 1.00121.71 S ATOM 1149 SG CYS A 148 86.135 78.977 21.028 1.00111.20 S ATOM 1287 SG CYS A 167 89.308 76.953 20.711 1.00111.41 S ATOM 515 SG CYS A 67 107.234 84.778 65.962 1.00100.07 S ATOM 537 SG CYS A 70 106.244 88.387 66.814 1.00 91.20 S ATOM 590 SG CYS A 77 103.575 85.628 66.671 1.00 89.76 S ATOM 19964 SG CYS B1163 99.440 95.916 54.130 1.00 80.89 S ATOM 19982 SG CYS B1166 98.237 92.773 52.611 1.00 87.19 S ATOM 20107 SG CYS B1182 101.779 92.988 54.340 1.00 79.03 S ATOM 20126 SG CYS B1185 101.042 94.312 50.880 1.00 86.09 S ATOM 21105 SG CYS C 86 84.994 85.559 131.247 1.00129.19 S ATOM 21122 SG CYS C 88 86.865 83.166 128.884 1.00136.05 S ATOM 21155 SG CYS C 92 86.033 82.193 132.549 1.00110.84 S ATOM 21178 SG CYS C 95 83.328 82.571 129.797 1.00118.05 S ATOM 28832 SG CYS I 7 43.325 26.591 31.763 1.00134.04 S ATOM 28857 SG CYS I 10 47.146 27.123 32.503 1.00128.56 S ATOM 29023 SG CYS I 29 45.296 29.585 30.350 1.00145.90 S ATOM 29047 SG CYS I 32 45.806 26.113 29.057 1.00145.28 S ATOM 29374 SG CYS I 75 17.870 37.743 67.046 1.00 91.78 S ATOM 29396 SG CYS I 78 17.515 33.760 67.433 1.00110.12 S ATOM 29612 SG CYS I 103 20.447 35.876 68.988 1.00104.51 S ATOM 29632 SG CYS I 106 20.014 34.977 65.382 1.00106.67 S ATOM 29777 SG CYS J 7 57.844 69.560 117.553 1.00 84.17 S ATOM 29800 SG CYS J 10 56.866 71.979 120.400 1.00 83.91 S ATOM 30080 SG CYS J 45 54.194 70.861 117.912 1.00 98.38 S ATOM 30086 SG CYS J 46 55.750 68.656 120.661 1.00 80.77 S ATOM 31266 SG CYS L 31 91.844 44.129 106.909 1.00101.10 S ATOM 31286 SG CYS L 34 91.616 41.151 109.398 1.00 90.79 S ATOM 31390 SG CYS L 48 95.050 42.833 108.334 1.00 97.86 S ATOM 31413 SG CYS L 51 92.927 40.438 106.266 1.00108.97 S Time building chain proxies: 6.03, per 1000 atoms: 0.19 Number of scatterers: 32470 At special positions: 0 Unit cell: (153.45, 152.52, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 179 16.00 P 43 15.00 Mg 1 11.99 O 6238 8.00 N 5660 7.00 C 20341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7464 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 38.1% alpha, 19.9% beta 18 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.837A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.531A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.777A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.641A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.657A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.734A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.279A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.513A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.647A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.711A pdb=" N ALA A1125 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1176 Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.755A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A1188 " --> pdb=" O PHE A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1188' Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1269 Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.918A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.349A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.790A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.637A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.702A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.792A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.408A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.621A pdb=" N TYR B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 removed outlier: 3.512A pdb=" N LEU B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.826A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.487A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.672A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.887A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 51 through 72 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 4.048A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.517A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.555A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.529A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.635A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.615A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.933A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.506A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.121A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.563A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.289A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.757A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 200 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 185 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 198 " --> pdb=" O TRP A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.659A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.594A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.006A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.373A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.900A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.529A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB6, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.526A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.992A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 71 removed outlier: 4.923A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 71 removed outlier: 4.923A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.960A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.997A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.275A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.866A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.866A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.560A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.483A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.028A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 51 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.856A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.357A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.694A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE7, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.592A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.508A pdb=" N ARG G 60 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.713A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.617A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 137 " --> pdb=" O TYR G 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 14 through 17 removed outlier: 3.712A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.669A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) 1395 hydrogen bonds defined for protein. 3840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10652 1.34 - 1.46: 6361 1.46 - 1.58: 15754 1.58 - 1.70: 83 1.70 - 1.82: 286 Bond restraints: 33136 Sorted by residual: bond pdb=" P DC T 10 " pdb=" O5' DC T 10 " ideal model delta sigma weight residual 1.593 1.640 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" P DC T 12 " pdb=" O5' DC T 12 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" P DC T 9 " pdb=" O5' DC T 9 " ideal model delta sigma weight residual 1.593 1.624 -0.031 1.00e-02 1.00e+04 9.49e+00 bond pdb=" N1 DC T 12 " pdb=" C6 DC T 12 " ideal model delta sigma weight residual 1.367 1.349 0.018 6.00e-03 2.78e+04 9.18e+00 bond pdb=" P DT T 11 " pdb=" O5' DT T 11 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.00e-02 1.00e+04 9.05e+00 ... (remaining 33131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 44184 1.98 - 3.95: 605 3.95 - 5.93: 83 5.93 - 7.91: 44 7.91 - 9.88: 6 Bond angle restraints: 44922 Sorted by residual: angle pdb=" O3' DC T 9 " pdb=" P DC T 10 " pdb=" O5' DC T 10 " ideal model delta sigma weight residual 104.00 113.88 -9.88 1.90e+00 2.77e-01 2.71e+01 angle pdb=" N GLN B 776 " pdb=" CA GLN B 776 " pdb=" C GLN B 776 " ideal model delta sigma weight residual 113.17 106.99 6.18 1.26e+00 6.30e-01 2.40e+01 angle pdb=" O3' DG T 13 " pdb=" P DC T 14 " pdb=" O5' DC T 14 " ideal model delta sigma weight residual 104.00 113.23 -9.23 1.90e+00 2.77e-01 2.36e+01 angle pdb=" C1' DG N 12 " pdb=" N9 DG N 12 " pdb=" C8 DG N 12 " ideal model delta sigma weight residual 127.00 132.61 -5.61 1.30e+00 5.92e-01 1.86e+01 angle pdb=" O5' DC T 14 " pdb=" C5' DC T 14 " pdb=" C4' DC T 14 " ideal model delta sigma weight residual 109.40 112.85 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 44917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 19781 35.01 - 70.01: 377 70.01 - 105.02: 31 105.02 - 140.02: 1 140.02 - 175.03: 4 Dihedral angle restraints: 20194 sinusoidal: 8667 harmonic: 11527 Sorted by residual: dihedral pdb=" CA GLN B 115 " pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C4' DA N 13 " pdb=" C3' DA N 13 " pdb=" O3' DA N 13 " pdb=" P DG N 14 " ideal model delta sinusoidal sigma weight residual 220.00 44.97 175.03 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC T 14 " pdb=" C3' DC T 14 " pdb=" O3' DC T 14 " pdb=" P DT T 15 " ideal model delta sinusoidal sigma weight residual -140.00 34.79 -174.79 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 20191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 5004 0.149 - 0.297: 11 0.297 - 0.446: 5 0.446 - 0.594: 21 0.594 - 0.743: 9 Chirality restraints: 5050 Sorted by residual: chirality pdb=" P DC T 10 " pdb=" OP1 DC T 10 " pdb=" OP2 DC T 10 " pdb=" O5' DC T 10 " both_signs ideal model delta sigma weight residual True 2.34 -3.08 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" P DT T 4 " pdb=" OP1 DT T 4 " pdb=" OP2 DT T 4 " pdb=" O5' DT T 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DC T 5 " pdb=" OP1 DC T 5 " pdb=" OP2 DC T 5 " pdb=" O5' DC T 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 5047 not shown) Planarity restraints: 5678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T 10 " -0.018 2.00e-02 2.50e+03 1.88e-02 7.96e+00 pdb=" N1 DC T 10 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DC T 10 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC T 10 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC T 10 " -0.033 2.00e-02 2.50e+03 pdb=" C4 DC T 10 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC T 10 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DC T 10 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC T 10 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A 245 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 12 " 0.025 2.00e-02 2.50e+03 1.46e-02 6.37e+00 pdb=" N9 DG N 12 " -0.040 2.00e-02 2.50e+03 pdb=" C8 DG N 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG N 12 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG N 12 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG N 12 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG N 12 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DG N 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG N 12 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG N 12 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG N 12 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DG N 12 " 0.014 2.00e-02 2.50e+03 ... (remaining 5675 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 276 2.54 - 3.13: 25126 3.13 - 3.72: 53466 3.72 - 4.31: 75898 4.31 - 4.90: 125706 Nonbonded interactions: 280472 Sorted by model distance: nonbonded pdb=" O3' A P 6 " pdb="MG MG A1803 " model vdw 1.945 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1803 " model vdw 2.085 2.170 nonbonded pdb=" O GLU D 32 " pdb=" NZ LYS G 5 " model vdw 2.095 3.120 nonbonded pdb=" OG SER A1115 " pdb=" OD1 ASN A1330 " model vdw 2.149 3.040 nonbonded pdb=" NH2 ARG A 469 " pdb=" O GLY B 991 " model vdw 2.162 3.120 ... (remaining 280467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.820 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.003 0.081 33168 Z= 0.192 Angle : 0.618 13.440 44967 Z= 0.337 Chirality : 0.062 0.743 5050 Planarity : 0.004 0.070 5678 Dihedral : 14.433 175.031 12730 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.48 (0.14), residues: 3925 helix: 1.03 (0.15), residues: 1342 sheet: -0.13 (0.21), residues: 589 loop : 0.10 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 840 TYR 0.013 0.001 TYR B 797 PHE 0.023 0.001 PHE A 444 TRP 0.013 0.001 TRP C 170 HIS 0.005 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.19 (33136) covalent geometry : angle 0.59931 / 0.34 (44922) hydrogen bonds : bond 0.20766 / 13.80 ( 1402) hydrogen bonds : angle 7.29121 / 5.11 ( 3926) metal coordination : bond 0.00519 / 0.32 ( 32) metal coordination : angle 4.83922 / 3.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 799 time to evaluate : 1.202 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: A 124 GLN cc_start: 0.8651 (mt0) cc_final: 0.8188 (mm-40) REVERT: A 383 TYR cc_start: 0.7771 (m-80) cc_final: 0.7510 (m-80) REVERT: A 500 GLU cc_start: 0.7733 (pt0) cc_final: 0.7499 (mt-10) REVERT: A 826 ASP cc_start: 0.8273 (t70) cc_final: 0.7587 (m-30) REVERT: A 1259 MET cc_start: 0.8380 (tpt) cc_final: 0.8123 (mmm) REVERT: A 1287 TYR cc_start: 0.6588 (m-80) cc_final: 0.5863 (m-80) REVERT: A 1349 TYR cc_start: 0.9075 (t80) cc_final: 0.8709 (t80) REVERT: A 1442 ASP cc_start: 0.8388 (m-30) cc_final: 0.8074 (m-30) REVERT: B 96 TYR cc_start: 0.7775 (m-10) cc_final: 0.7560 (m-80) REVERT: B 151 LEU cc_start: 0.7389 (mt) cc_final: 0.7104 (tp) REVERT: B 353 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7896 (tppt) REVERT: B 432 MET cc_start: 0.7158 (ttp) cc_final: 0.6872 (tpt) REVERT: B 1101 ASP cc_start: 0.8441 (m-30) cc_final: 0.8151 (p0) REVERT: B 1125 ASP cc_start: 0.8852 (t0) cc_final: 0.8538 (t0) REVERT: C 75 MET cc_start: 0.8438 (tpp) cc_final: 0.8179 (tpp) REVERT: C 190 ASP cc_start: 0.8530 (t0) cc_final: 0.8278 (m-30) REVERT: F 72 LYS cc_start: 0.8736 (mmtp) cc_final: 0.7782 (mmtt) REVERT: F 85 MET cc_start: 0.9251 (ttm) cc_final: 0.9036 (ttp) REVERT: F 99 LEU cc_start: 0.9089 (tt) cc_final: 0.8840 (tp) REVERT: F 123 LYS cc_start: 0.8427 (tttm) cc_final: 0.7873 (tttp) REVERT: G 65 ASP cc_start: 0.7820 (t0) cc_final: 0.7564 (t0) REVERT: G 115 MET cc_start: 0.3668 (mpp) cc_final: 0.2956 (mtp) REVERT: H 2 SER cc_start: 0.7452 (p) cc_final: 0.7150 (m) REVERT: H 14 GLU cc_start: 0.7830 (tt0) cc_final: 0.7624 (tp30) REVERT: H 19 ARG cc_start: 0.8403 (mmt90) cc_final: 0.8162 (mtp85) REVERT: H 21 ASN cc_start: 0.9064 (m-40) cc_final: 0.8859 (m110) REVERT: H 33 GLN cc_start: 0.7762 (mp10) cc_final: 0.7272 (mp-120) REVERT: H 35 GLN cc_start: 0.7745 (mt0) cc_final: 0.7527 (mt0) REVERT: H 64 ASN cc_start: 0.8021 (p0) cc_final: 0.7784 (p0) REVERT: H 129 TYR cc_start: 0.6947 (p90) cc_final: 0.6123 (p90) REVERT: I 50 THR cc_start: 0.8511 (m) cc_final: 0.8124 (p) REVERT: K 29 ASN cc_start: 0.7222 (t0) cc_final: 0.6703 (t0) REVERT: K 79 GLU cc_start: 0.8057 (tp30) cc_final: 0.7527 (tm-30) REVERT: K 94 ILE cc_start: 0.8291 (mm) cc_final: 0.8007 (mp) outliers start: 0 outliers final: 3 residues processed: 799 average time/residue: 0.7522 time to fit residues: 700.4598 Evaluate side-chains 398 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 395 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain E residue 5 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN A 286 HIS A 515 GLN A 706 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS A1171 GLN A1364 ASN B 115 GLN B 309 GLN B 572 HIS B1013 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS C 214 ASN E 32 GLN E 104 ASN G 10 ASN I 22 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084454 restraints weight = 63333.847| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.59 r_work: 0.3140 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 33168 Z= 0.290 Angle : 0.772 35.195 44967 Z= 0.384 Chirality : 0.049 0.293 5050 Planarity : 0.006 0.072 5678 Dihedral : 12.028 179.323 4796 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.95 % Allowed : 12.34 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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 (0.13), residues: 3925 helix: 0.64 (0.14), residues: 1367 sheet: -0.49 (0.20), residues: 642 loop : 0.04 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1023 TYR 0.034 0.002 TYR H 129 PHE 0.039 0.002 PHE A 444 TRP 0.013 0.002 TRP A 430 HIS 0.009 0.002 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (33136) covalent geometry : angle 0.72212 / 0.38 (44922) hydrogen bonds : bond 0.05316 / 3.55 ( 1402) hydrogen bonds : angle 5.70081 / 4.00 ( 3926) metal coordination : bond 0.01324 / 0.86 ( 32) metal coordination : angle 8.67844 / 5.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 409 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8647 (m-40) cc_final: 0.8294 (p0) REVERT: A 124 GLN cc_start: 0.8978 (mt0) cc_final: 0.8382 (mm-40) REVERT: A 146 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7622 (mpp) REVERT: A 383 TYR cc_start: 0.8376 (m-80) cc_final: 0.8150 (m-80) REVERT: A 500 GLU cc_start: 0.7560 (pt0) cc_final: 0.7209 (mt-10) REVERT: A 1132 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7658 (mtmm) REVERT: A 1148 ILE cc_start: 0.8356 (mt) cc_final: 0.8000 (mt) REVERT: A 1218 GLN cc_start: 0.9035 (tt0) cc_final: 0.8747 (tm-30) REVERT: A 1285 MET cc_start: 0.7727 (ttm) cc_final: 0.6589 (tmm) REVERT: A 1287 TYR cc_start: 0.6728 (m-80) cc_final: 0.6427 (m-80) REVERT: A 1362 TYR cc_start: 0.8291 (t80) cc_final: 0.8048 (t80) REVERT: A 1375 MET cc_start: 0.8871 (ttm) cc_final: 0.8621 (mtp) REVERT: A 1442 ASP cc_start: 0.8639 (m-30) cc_final: 0.8331 (m-30) REVERT: A 1444 MET cc_start: 0.8597 (mtp) cc_final: 0.8379 (mtt) REVERT: B 96 TYR cc_start: 0.8240 (m-80) cc_final: 0.7617 (m-80) REVERT: B 101 MET cc_start: 0.8340 (tpp) cc_final: 0.8134 (tpp) REVERT: B 322 PHE cc_start: 0.8488 (t80) cc_final: 0.8279 (t80) REVERT: B 353 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7669 (tppt) REVERT: B 381 MET cc_start: 0.8037 (ttp) cc_final: 0.7814 (ttt) REVERT: B 432 MET cc_start: 0.7331 (ttp) cc_final: 0.6931 (tpt) REVERT: B 434 ARG cc_start: 0.7505 (tmm-80) cc_final: 0.7261 (tmm-80) REVERT: B 476 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6851 (ptp-170) REVERT: B 552 MET cc_start: 0.8881 (tpp) cc_final: 0.8669 (mmm) REVERT: B 837 ASP cc_start: 0.8741 (m-30) cc_final: 0.8336 (m-30) REVERT: B 961 LEU cc_start: 0.7820 (mp) cc_final: 0.7393 (tp) REVERT: B 1082 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9048 (tpt) REVERT: B 1124 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8415 (mtt180) REVERT: C 75 MET cc_start: 0.8813 (tpp) cc_final: 0.8433 (tpp) REVERT: C 190 ASP cc_start: 0.8996 (t0) cc_final: 0.8671 (m-30) REVERT: E 58 MET cc_start: 0.7774 (tpp) cc_final: 0.7529 (tpp) REVERT: E 121 MET cc_start: 0.8915 (mmp) cc_final: 0.8525 (mmp) REVERT: E 215 MET cc_start: 0.6377 (mmt) cc_final: 0.5479 (ptm) REVERT: F 72 LYS cc_start: 0.8601 (mmtp) cc_final: 0.7671 (mmtt) REVERT: F 76 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (ttmp) REVERT: F 111 LEU cc_start: 0.8387 (mp) cc_final: 0.7888 (mt) REVERT: F 114 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: G 3 PHE cc_start: 0.5752 (m-80) cc_final: 0.5449 (m-80) REVERT: G 65 ASP cc_start: 0.8596 (t0) cc_final: 0.7991 (t0) REVERT: G 69 GLU cc_start: 0.8381 (tt0) cc_final: 0.8050 (tt0) REVERT: G 115 MET cc_start: 0.3638 (mpp) cc_final: 0.2993 (mtp) REVERT: H 14 GLU cc_start: 0.7945 (tt0) cc_final: 0.7468 (tp30) REVERT: H 33 GLN cc_start: 0.7692 (mp10) cc_final: 0.7138 (mp10) REVERT: H 66 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: H 129 TYR cc_start: 0.7646 (p90) cc_final: 0.7119 (p90) REVERT: H 134 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8433 (m110) REVERT: I 13 MET cc_start: 0.8141 (pp-130) cc_final: 0.7854 (ppp) REVERT: I 77 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7609 (ttpt) REVERT: I 87 GLN cc_start: 0.7237 (pt0) cc_final: 0.6900 (mm110) REVERT: K 29 ASN cc_start: 0.7569 (t0) cc_final: 0.6814 (t0) REVERT: K 38 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8490 (mp0) REVERT: K 79 GLU cc_start: 0.8452 (tp30) cc_final: 0.7728 (tm-30) REVERT: L 62 LYS cc_start: 0.7416 (mmpt) cc_final: 0.7169 (mmpt) outliers start: 103 outliers final: 38 residues processed: 479 average time/residue: 0.7135 time to fit residues: 404.2336 Evaluate side-chains 379 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 236 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 386 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN A1124 HIS B1093 GLN E 32 GLN E 104 ASN G 102 GLN H 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.122298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087175 restraints weight = 62541.958| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.60 r_work: 0.3186 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33168 Z= 0.143 Angle : 0.628 24.529 44967 Z= 0.316 Chirality : 0.045 0.299 5050 Planarity : 0.004 0.069 5678 Dihedral : 11.862 179.194 4791 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.66 % Allowed : 14.49 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 3925 helix: 0.81 (0.14), residues: 1371 sheet: -0.50 (0.20), residues: 630 loop : 0.05 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 153 TYR 0.021 0.001 TYR E 46 PHE 0.023 0.002 PHE K 7 TRP 0.011 0.001 TRP B 308 HIS 0.008 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (33136) covalent geometry : angle 0.59251 / 0.31 (44922) hydrogen bonds : bond 0.04462 / 2.95 ( 1402) hydrogen bonds : angle 5.25879 / 3.70 ( 3926) metal coordination : bond 0.00736 / 0.45 ( 32) metal coordination : angle 6.56379 / 4.19 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 380 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.8978 (mt0) cc_final: 0.8379 (mm-40) REVERT: A 146 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7518 (mpp) REVERT: A 383 TYR cc_start: 0.8350 (m-80) cc_final: 0.8115 (m-80) REVERT: A 542 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: A 826 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: A 1132 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7636 (mtmm) REVERT: A 1148 ILE cc_start: 0.8342 (mt) cc_final: 0.8035 (mt) REVERT: A 1218 GLN cc_start: 0.9051 (tt0) cc_final: 0.8728 (tm-30) REVERT: A 1281 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7343 (mmm160) REVERT: A 1285 MET cc_start: 0.7592 (ttm) cc_final: 0.6486 (tmm) REVERT: A 1287 TYR cc_start: 0.6742 (m-80) cc_final: 0.6334 (m-80) REVERT: A 1362 TYR cc_start: 0.8305 (t80) cc_final: 0.8086 (t80) REVERT: A 1375 MET cc_start: 0.8804 (ttm) cc_final: 0.8582 (mtp) REVERT: A 1442 ASP cc_start: 0.8629 (m-30) cc_final: 0.8364 (m-30) REVERT: B 96 TYR cc_start: 0.8213 (m-80) cc_final: 0.7465 (m-80) REVERT: B 353 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7678 (tppt) REVERT: B 381 MET cc_start: 0.8143 (ttp) cc_final: 0.7909 (ttt) REVERT: B 432 MET cc_start: 0.7230 (ttp) cc_final: 0.6838 (tpt) REVERT: B 434 ARG cc_start: 0.7542 (tmm-80) cc_final: 0.7211 (tmm-80) REVERT: B 552 MET cc_start: 0.8795 (tpp) cc_final: 0.8594 (mmm) REVERT: B 572 HIS cc_start: 0.7535 (m-70) cc_final: 0.7331 (m-70) REVERT: B 837 ASP cc_start: 0.8680 (m-30) cc_final: 0.8164 (m-30) REVERT: B 1124 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8408 (mtt180) REVERT: C 50 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: D 31 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: E 25 ASP cc_start: 0.7057 (m-30) cc_final: 0.6849 (p0) REVERT: E 58 MET cc_start: 0.7667 (tpp) cc_final: 0.7448 (tpt) REVERT: E 121 MET cc_start: 0.8785 (mmp) cc_final: 0.8461 (mmp) REVERT: E 215 MET cc_start: 0.6538 (mmt) cc_final: 0.5481 (ptm) REVERT: F 72 LYS cc_start: 0.8446 (mmtp) cc_final: 0.7495 (mmtt) REVERT: F 78 GLN cc_start: 0.8964 (pt0) cc_final: 0.8726 (pm20) REVERT: F 111 LEU cc_start: 0.8396 (mp) cc_final: 0.7907 (mt) REVERT: F 114 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: G 1 MET cc_start: 0.7508 (ttm) cc_final: 0.6936 (ttt) REVERT: G 65 ASP cc_start: 0.8583 (t0) cc_final: 0.7971 (t0) REVERT: G 115 MET cc_start: 0.3856 (mpp) cc_final: 0.3125 (mtp) REVERT: H 2 SER cc_start: 0.7682 (p) cc_final: 0.6928 (m) REVERT: H 14 GLU cc_start: 0.7959 (tt0) cc_final: 0.7523 (tp30) REVERT: H 33 GLN cc_start: 0.7545 (mp10) cc_final: 0.6793 (mp-120) REVERT: H 35 GLN cc_start: 0.8018 (tt0) cc_final: 0.7764 (tt0) REVERT: H 64 ASN cc_start: 0.8251 (p0) cc_final: 0.7974 (p0) REVERT: H 87 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8231 (mmp-170) REVERT: H 129 TYR cc_start: 0.7627 (p90) cc_final: 0.7220 (p90) REVERT: I 77 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7469 (ttmt) REVERT: I 87 GLN cc_start: 0.7319 (pt0) cc_final: 0.6911 (mm110) REVERT: K 29 ASN cc_start: 0.7480 (t0) cc_final: 0.6739 (t0) REVERT: K 79 GLU cc_start: 0.8402 (tp30) cc_final: 0.7662 (tm-30) REVERT: K 94 ILE cc_start: 0.8279 (mm) cc_final: 0.7960 (mp) REVERT: L 62 LYS cc_start: 0.7433 (mmpt) cc_final: 0.7187 (mmpt) outliers start: 93 outliers final: 34 residues processed: 440 average time/residue: 0.6845 time to fit residues: 359.2035 Evaluate side-chains 373 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 332 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 391 optimal weight: 30.0000 chunk 167 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 216 optimal weight: 0.0980 chunk 222 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B1040 ASN B1093 GLN E 32 GLN E 104 ASN G 102 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085585 restraints weight = 62303.883| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.58 r_work: 0.3160 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33168 Z= 0.188 Angle : 0.642 31.733 44967 Z= 0.315 Chirality : 0.045 0.299 5050 Planarity : 0.004 0.070 5678 Dihedral : 11.702 178.565 4789 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.75 % Allowed : 16.43 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.21 (0.13), residues: 3925 helix: 0.87 (0.14), residues: 1370 sheet: -0.56 (0.20), residues: 621 loop : -0.01 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 63 TYR 0.022 0.002 TYR B 666 PHE 0.024 0.002 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.007 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (33136) covalent geometry : angle 0.59077 / 0.31 (44922) hydrogen bonds : bond 0.04225 / 2.79 ( 1402) hydrogen bonds : angle 5.09078 / 3.57 ( 3926) metal coordination : bond 0.01363 / 0.86 ( 32) metal coordination : angle 8.00148 / 5.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 357 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.9027 (mt0) cc_final: 0.8420 (mm-40) REVERT: A 146 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7463 (mpp) REVERT: A 383 TYR cc_start: 0.8368 (m-80) cc_final: 0.8165 (m-80) REVERT: A 515 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8901 (tt0) REVERT: A 542 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: A 705 LYS cc_start: 0.6657 (tmtt) cc_final: 0.6432 (pptt) REVERT: A 929 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6889 (mt) REVERT: A 961 ARG cc_start: 0.8917 (ttm-80) cc_final: 0.8486 (ttm110) REVERT: A 1132 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7674 (mtmm) REVERT: A 1218 GLN cc_start: 0.9046 (tt0) cc_final: 0.8722 (tm-30) REVERT: A 1285 MET cc_start: 0.7542 (ttm) cc_final: 0.6330 (tmm) REVERT: A 1287 TYR cc_start: 0.6724 (m-80) cc_final: 0.6199 (m-10) REVERT: A 1362 TYR cc_start: 0.8419 (t80) cc_final: 0.8196 (t80) REVERT: B 96 TYR cc_start: 0.8243 (m-80) cc_final: 0.7474 (m-80) REVERT: B 101 MET cc_start: 0.8446 (tpp) cc_final: 0.8216 (tpp) REVERT: B 353 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7581 (tppt) REVERT: B 381 MET cc_start: 0.8283 (ttp) cc_final: 0.8013 (ttt) REVERT: B 432 MET cc_start: 0.7165 (ttp) cc_final: 0.6779 (tpt) REVERT: B 434 ARG cc_start: 0.7559 (tmm-80) cc_final: 0.7171 (tmm-80) REVERT: B 572 HIS cc_start: 0.7613 (m-70) cc_final: 0.7332 (m-70) REVERT: B 592 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8241 (m110) REVERT: B 1082 MET cc_start: 0.9269 (tpp) cc_final: 0.9046 (tpt) REVERT: B 1124 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8432 (mtt180) REVERT: C 123 ASN cc_start: 0.8119 (t0) cc_final: 0.7887 (m-40) REVERT: E 58 MET cc_start: 0.7601 (tpp) cc_final: 0.7383 (tpt) REVERT: E 121 MET cc_start: 0.8821 (mmp) cc_final: 0.8477 (mmp) REVERT: E 215 MET cc_start: 0.6531 (mmt) cc_final: 0.5560 (ptm) REVERT: F 72 LYS cc_start: 0.8481 (mmtp) cc_final: 0.7540 (mmtt) REVERT: F 76 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: F 77 ASP cc_start: 0.8643 (p0) cc_final: 0.8342 (p0) REVERT: F 78 GLN cc_start: 0.8871 (pt0) cc_final: 0.8620 (pm20) REVERT: F 111 LEU cc_start: 0.8409 (mp) cc_final: 0.7938 (mt) REVERT: F 114 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: G 3 PHE cc_start: 0.4667 (m-80) cc_final: 0.4428 (m-80) REVERT: G 33 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7964 (tm-30) REVERT: G 65 ASP cc_start: 0.8636 (t0) cc_final: 0.7976 (t0) REVERT: G 115 MET cc_start: 0.3564 (mpp) cc_final: 0.2733 (mtp) REVERT: H 2 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7050 (m) REVERT: H 14 GLU cc_start: 0.7938 (tt0) cc_final: 0.7511 (tp30) REVERT: H 33 GLN cc_start: 0.7528 (mp10) cc_final: 0.7082 (mp-120) REVERT: H 35 GLN cc_start: 0.8028 (tt0) cc_final: 0.7774 (tt0) REVERT: H 64 ASN cc_start: 0.8217 (p0) cc_final: 0.7983 (p0) REVERT: H 115 TYR cc_start: 0.8419 (m-80) cc_final: 0.8186 (m-80) REVERT: H 129 TYR cc_start: 0.7647 (p90) cc_final: 0.7220 (p90) REVERT: I 77 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7468 (ttmt) REVERT: K 29 ASN cc_start: 0.7546 (t0) cc_final: 0.6806 (t0) REVERT: K 38 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8577 (mp0) REVERT: K 79 GLU cc_start: 0.8425 (tp30) cc_final: 0.7681 (tm-30) REVERT: K 94 ILE cc_start: 0.8365 (mm) cc_final: 0.8031 (mp) outliers start: 96 outliers final: 39 residues processed: 426 average time/residue: 0.6814 time to fit residues: 345.3099 Evaluate side-chains 379 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 330 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 34 optimal weight: 0.0670 chunk 66 optimal weight: 0.9990 chunk 225 optimal weight: 0.1980 chunk 344 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 153 optimal weight: 0.0980 chunk 239 optimal weight: 0.9980 chunk 289 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.123002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.088011 restraints weight = 62341.165| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.60 r_work: 0.3203 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33168 Z= 0.120 Angle : 0.601 24.917 44967 Z= 0.300 Chirality : 0.044 0.311 5050 Planarity : 0.004 0.070 5678 Dihedral : 11.658 179.840 4789 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.38 % Allowed : 17.52 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.29 (0.14), residues: 3925 helix: 0.97 (0.14), residues: 1377 sheet: -0.58 (0.20), residues: 621 loop : 0.02 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 63 TYR 0.019 0.001 TYR H 129 PHE 0.023 0.001 PHE B 322 TRP 0.012 0.001 TRP B 308 HIS 0.007 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (33136) covalent geometry : angle 0.56976 / 0.30 (44922) hydrogen bonds : bond 0.03823 / 2.51 ( 1402) hydrogen bonds : angle 4.89430 / 3.44 ( 3926) metal coordination : bond 0.00554 / 0.35 ( 32) metal coordination : angle 6.11702 / 3.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 352 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.9009 (mt0) cc_final: 0.8395 (mm-40) REVERT: A 383 TYR cc_start: 0.8348 (m-80) cc_final: 0.8148 (m-80) REVERT: A 456 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8842 (mtm) REVERT: A 705 LYS cc_start: 0.6751 (tmtt) cc_final: 0.6505 (pptt) REVERT: A 826 ASP cc_start: 0.8347 (t70) cc_final: 0.7518 (m-30) REVERT: A 929 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6871 (mt) REVERT: A 1132 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7701 (mtmm) REVERT: A 1218 GLN cc_start: 0.9068 (tt0) cc_final: 0.8718 (tm-30) REVERT: A 1285 MET cc_start: 0.7320 (ttm) cc_final: 0.6028 (tmm) REVERT: A 1287 TYR cc_start: 0.6677 (m-80) cc_final: 0.6117 (m-10) REVERT: B 96 TYR cc_start: 0.8196 (m-80) cc_final: 0.7422 (m-80) REVERT: B 173 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6705 (ptm) REVERT: B 353 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7560 (tppt) REVERT: B 381 MET cc_start: 0.8307 (ttp) cc_final: 0.8010 (ttt) REVERT: B 432 MET cc_start: 0.7123 (ttp) cc_final: 0.6768 (tpt) REVERT: B 434 ARG cc_start: 0.7597 (tmm-80) cc_final: 0.7184 (tmm-80) REVERT: B 572 HIS cc_start: 0.7640 (m-70) cc_final: 0.7384 (m-70) REVERT: B 837 ASP cc_start: 0.8578 (m-30) cc_final: 0.8171 (m-30) REVERT: B 884 ARG cc_start: 0.7480 (mmp-170) cc_final: 0.7236 (mmm160) REVERT: B 1026 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8726 (mt) REVERT: C 50 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: C 75 MET cc_start: 0.8577 (mmm) cc_final: 0.7984 (tmm) REVERT: C 123 ASN cc_start: 0.8092 (t0) cc_final: 0.7875 (m-40) REVERT: E 121 MET cc_start: 0.8757 (mmp) cc_final: 0.8447 (mmp) REVERT: E 215 MET cc_start: 0.6489 (mmt) cc_final: 0.5570 (ptm) REVERT: F 72 LYS cc_start: 0.8437 (mmtp) cc_final: 0.7497 (mmtt) REVERT: F 76 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8474 (ttmm) REVERT: F 77 ASP cc_start: 0.8618 (p0) cc_final: 0.8307 (p0) REVERT: F 78 GLN cc_start: 0.8825 (pt0) cc_final: 0.8592 (pm20) REVERT: F 111 LEU cc_start: 0.8399 (mp) cc_final: 0.7959 (mt) REVERT: F 114 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: G 3 PHE cc_start: 0.4727 (m-80) cc_final: 0.3724 (m-80) REVERT: G 65 ASP cc_start: 0.8619 (t0) cc_final: 0.7947 (t0) REVERT: G 115 MET cc_start: 0.3794 (mpp) cc_final: 0.2912 (mtp) REVERT: H 2 SER cc_start: 0.7782 (OUTLIER) cc_final: 0.7070 (m) REVERT: H 14 GLU cc_start: 0.7956 (tt0) cc_final: 0.7497 (tp30) REVERT: H 33 GLN cc_start: 0.7417 (mp10) cc_final: 0.6914 (mp-120) REVERT: H 35 GLN cc_start: 0.8019 (tt0) cc_final: 0.7788 (tt0) REVERT: H 64 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7875 (p0) REVERT: H 87 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8228 (mmp-170) REVERT: H 129 TYR cc_start: 0.7580 (p90) cc_final: 0.7226 (p90) REVERT: I 61 ASP cc_start: 0.6756 (m-30) cc_final: 0.6528 (m-30) REVERT: I 77 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7440 (ttmt) REVERT: I 87 GLN cc_start: 0.7231 (pt0) cc_final: 0.7000 (mm110) REVERT: K 29 ASN cc_start: 0.7530 (t0) cc_final: 0.6825 (t0) REVERT: K 38 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8454 (mp0) REVERT: K 94 ILE cc_start: 0.8289 (mm) cc_final: 0.7989 (mp) REVERT: L 57 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (mt) outliers start: 83 outliers final: 35 residues processed: 408 average time/residue: 0.6869 time to fit residues: 334.8366 Evaluate side-chains 379 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 247 optimal weight: 5.9990 chunk 293 optimal weight: 30.0000 chunk 273 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 291 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 0.0050 chunk 10 optimal weight: 5.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B 518 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.118939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083560 restraints weight = 62674.738| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.54 r_work: 0.3122 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 33168 Z= 0.270 Angle : 0.680 25.950 44967 Z= 0.339 Chirality : 0.047 0.295 5050 Planarity : 0.005 0.081 5678 Dihedral : 11.747 179.378 4789 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.89 % Allowed : 17.64 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.14 (0.13), residues: 3925 helix: 0.82 (0.14), residues: 1368 sheet: -0.59 (0.20), residues: 620 loop : -0.06 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 47 TYR 0.020 0.002 TYR B1092 PHE 0.024 0.002 PHE A 219 TRP 0.012 0.001 TRP B 681 HIS 0.007 0.001 HIS B1015 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.27 (33136) covalent geometry : angle 0.64619 / 0.34 (44922) hydrogen bonds : bond 0.04407 / 2.91 ( 1402) hydrogen bonds : angle 5.07876 / 3.57 ( 3926) metal coordination : bond 0.01032 / 0.59 ( 32) metal coordination : angle 6.73519 / 4.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 333 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.9040 (mt0) cc_final: 0.8445 (mm-40) REVERT: A 146 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8121 (mmt) REVERT: A 515 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8867 (tm-30) REVERT: A 542 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: A 695 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8481 (mmtm) REVERT: A 929 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7092 (mt) REVERT: A 961 ARG cc_start: 0.8900 (ttm-80) cc_final: 0.8468 (ttm110) REVERT: A 1132 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7714 (mtmm) REVERT: A 1218 GLN cc_start: 0.9069 (tt0) cc_final: 0.8433 (tm-30) REVERT: A 1285 MET cc_start: 0.7437 (ttm) cc_final: 0.7235 (ttm) REVERT: B 96 TYR cc_start: 0.8256 (m-80) cc_final: 0.7472 (m-80) REVERT: B 353 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7492 (tppt) REVERT: B 381 MET cc_start: 0.8307 (ttp) cc_final: 0.7991 (ttt) REVERT: B 432 MET cc_start: 0.7094 (ttp) cc_final: 0.6743 (tpt) REVERT: B 434 ARG cc_start: 0.7550 (tmm-80) cc_final: 0.7130 (tmm-80) REVERT: B 572 HIS cc_start: 0.7667 (m-70) cc_final: 0.7346 (m-70) REVERT: B 837 ASP cc_start: 0.8747 (m-30) cc_final: 0.8321 (m-30) REVERT: B 879 ARG cc_start: 0.7352 (mmt90) cc_final: 0.6660 (mmm-85) REVERT: C 50 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: C 123 ASN cc_start: 0.8139 (t0) cc_final: 0.7882 (m-40) REVERT: E 58 MET cc_start: 0.7576 (tpt) cc_final: 0.7002 (tpt) REVERT: E 121 MET cc_start: 0.8818 (mmp) cc_final: 0.8528 (mmp) REVERT: E 215 MET cc_start: 0.6617 (mmt) cc_final: 0.5664 (ptm) REVERT: F 71 GLU cc_start: 0.8509 (mp0) cc_final: 0.8083 (pm20) REVERT: F 72 LYS cc_start: 0.8457 (mmtp) cc_final: 0.7338 (mmtt) REVERT: F 111 LEU cc_start: 0.8407 (mp) cc_final: 0.7993 (mt) REVERT: F 114 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: G 1 MET cc_start: 0.7437 (ptm) cc_final: 0.7144 (ppp) REVERT: G 3 PHE cc_start: 0.5339 (m-80) cc_final: 0.4251 (m-80) REVERT: G 33 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 115 MET cc_start: 0.3643 (mpp) cc_final: 0.2784 (mtp) REVERT: H 2 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7066 (m) REVERT: H 14 GLU cc_start: 0.7974 (tt0) cc_final: 0.7537 (tp30) REVERT: H 33 GLN cc_start: 0.7529 (mp10) cc_final: 0.6993 (mp-120) REVERT: H 35 GLN cc_start: 0.7988 (tt0) cc_final: 0.7728 (tt0) REVERT: H 64 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7894 (p0) REVERT: H 87 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8342 (mmp-170) REVERT: H 129 TYR cc_start: 0.7699 (p90) cc_final: 0.7325 (p90) REVERT: I 13 MET cc_start: 0.8105 (pp-130) cc_final: 0.7820 (ppp) REVERT: I 77 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7533 (ttpt) REVERT: I 87 GLN cc_start: 0.7255 (pt0) cc_final: 0.6976 (mm110) REVERT: J 42 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7712 (ptmt) REVERT: K 29 ASN cc_start: 0.7619 (t0) cc_final: 0.6856 (t0) REVERT: K 38 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8568 (mp0) REVERT: K 79 GLU cc_start: 0.8283 (tp30) cc_final: 0.7473 (tm-30) REVERT: L 57 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8383 (mt) outliers start: 101 outliers final: 49 residues processed: 395 average time/residue: 0.6801 time to fit residues: 319.9043 Evaluate side-chains 378 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 317 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 53 optimal weight: 0.1980 chunk 372 optimal weight: 0.0980 chunk 263 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 202 optimal weight: 7.9990 chunk 332 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.121970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086959 restraints weight = 62428.275| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.61 r_work: 0.3184 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33168 Z= 0.125 Angle : 0.613 25.916 44967 Z= 0.304 Chirality : 0.044 0.312 5050 Planarity : 0.004 0.071 5678 Dihedral : 11.657 177.570 4789 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.23 % Allowed : 18.78 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.26 (0.13), residues: 3925 helix: 0.97 (0.14), residues: 1379 sheet: -0.54 (0.20), residues: 608 loop : -0.04 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 47 TYR 0.013 0.001 TYR G 51 PHE 0.022 0.001 PHE A 219 TRP 0.012 0.001 TRP C 201 HIS 0.008 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (33136) covalent geometry : angle 0.57806 / 0.30 (44922) hydrogen bonds : bond 0.03771 / 2.47 ( 1402) hydrogen bonds : angle 4.84141 / 3.40 ( 3926) metal coordination : bond 0.00591 / 0.37 ( 32) metal coordination : angle 6.44705 / 4.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 353 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.9020 (mt0) cc_final: 0.8425 (mm-40) REVERT: A 515 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9065 (tm-30) REVERT: A 542 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: A 676 MET cc_start: 0.8130 (mmt) cc_final: 0.7703 (mmm) REVERT: A 695 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8380 (mmtm) REVERT: A 826 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: A 929 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7037 (mt) REVERT: A 992 ASP cc_start: 0.7730 (t0) cc_final: 0.7288 (p0) REVERT: A 1132 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7740 (mtmm) REVERT: A 1218 GLN cc_start: 0.9101 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 1285 MET cc_start: 0.7512 (ttm) cc_final: 0.6506 (ttm) REVERT: A 1287 TYR cc_start: 0.7002 (m-80) cc_final: 0.6513 (m-10) REVERT: B 96 TYR cc_start: 0.8210 (m-80) cc_final: 0.7427 (m-80) REVERT: B 353 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7458 (tppt) REVERT: B 381 MET cc_start: 0.8283 (ttp) cc_final: 0.7996 (ttt) REVERT: B 432 MET cc_start: 0.6988 (ttp) cc_final: 0.6651 (tpt) REVERT: B 434 ARG cc_start: 0.7577 (tmm-80) cc_final: 0.7116 (tmm-80) REVERT: B 572 HIS cc_start: 0.7680 (m-70) cc_final: 0.7360 (m-70) REVERT: B 705 MET cc_start: 0.9015 (tpp) cc_final: 0.8632 (tpt) REVERT: B 837 ASP cc_start: 0.8634 (m-30) cc_final: 0.8153 (m-30) REVERT: B 879 ARG cc_start: 0.7438 (mmt90) cc_final: 0.7191 (mmm-85) REVERT: B 884 ARG cc_start: 0.7430 (mmp-170) cc_final: 0.7141 (mmm160) REVERT: B 908 GLU cc_start: 0.8138 (tp30) cc_final: 0.7911 (tp30) REVERT: B 963 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6604 (p90) REVERT: B 1026 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8745 (mt) REVERT: C 50 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: C 123 ASN cc_start: 0.8097 (t0) cc_final: 0.7875 (m-40) REVERT: E 58 MET cc_start: 0.7618 (tpt) cc_final: 0.7037 (tpt) REVERT: E 75 MET cc_start: 0.8143 (ppp) cc_final: 0.7562 (ppp) REVERT: E 121 MET cc_start: 0.8733 (mmp) cc_final: 0.8486 (mmp) REVERT: E 215 MET cc_start: 0.6534 (mmt) cc_final: 0.5604 (ptm) REVERT: F 71 GLU cc_start: 0.8454 (mp0) cc_final: 0.8080 (pm20) REVERT: F 72 LYS cc_start: 0.8445 (mmtp) cc_final: 0.7348 (mmtt) REVERT: F 77 ASP cc_start: 0.8738 (p0) cc_final: 0.8504 (p0) REVERT: F 78 GLN cc_start: 0.8916 (pt0) cc_final: 0.8679 (pm20) REVERT: F 111 LEU cc_start: 0.8354 (mp) cc_final: 0.8010 (mt) REVERT: F 114 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: G 3 PHE cc_start: 0.5467 (m-80) cc_final: 0.4801 (m-80) REVERT: G 65 ASP cc_start: 0.8836 (m-30) cc_final: 0.8191 (t0) REVERT: G 115 MET cc_start: 0.3618 (mpp) cc_final: 0.2955 (mtp) REVERT: H 2 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.6845 (m) REVERT: H 14 GLU cc_start: 0.7938 (tt0) cc_final: 0.7420 (tp30) REVERT: H 33 GLN cc_start: 0.7451 (mp10) cc_final: 0.7052 (mp10) REVERT: H 35 GLN cc_start: 0.8022 (tt0) cc_final: 0.7755 (tt0) REVERT: H 64 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.6977 (p0) REVERT: H 87 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8314 (mmp-170) REVERT: I 13 MET cc_start: 0.8092 (pp-130) cc_final: 0.7825 (ppp) REVERT: I 77 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7427 (ttpt) REVERT: I 87 GLN cc_start: 0.7244 (pt0) cc_final: 0.7037 (mm110) REVERT: K 29 ASN cc_start: 0.7617 (t0) cc_final: 0.6873 (t0) REVERT: K 38 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8469 (mp0) REVERT: L 53 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7548 (t-170) outliers start: 78 outliers final: 34 residues processed: 403 average time/residue: 0.6782 time to fit residues: 326.2234 Evaluate side-chains 373 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 117 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 146 optimal weight: 30.0000 chunk 375 optimal weight: 0.9980 chunk 391 optimal weight: 40.0000 chunk 244 optimal weight: 2.9990 chunk 355 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086933 restraints weight = 62334.060| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.60 r_work: 0.3184 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33168 Z= 0.135 Angle : 0.615 25.332 44967 Z= 0.306 Chirality : 0.044 0.307 5050 Planarity : 0.004 0.071 5678 Dihedral : 11.621 176.708 4789 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.12 % Allowed : 19.35 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.33 (0.14), residues: 3925 helix: 1.04 (0.14), residues: 1380 sheet: -0.44 (0.20), residues: 616 loop : -0.03 (0.15), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 47 TYR 0.018 0.001 TYR B 137 PHE 0.022 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (33136) covalent geometry : angle 0.58380 / 0.30 (44922) hydrogen bonds : bond 0.03696 / 2.42 ( 1402) hydrogen bonds : angle 4.76490 / 3.35 ( 3926) metal coordination : bond 0.00603 / 0.37 ( 32) metal coordination : angle 6.18662 / 3.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 341 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8376 (t0) cc_final: 0.8148 (t0) REVERT: A 124 GLN cc_start: 0.9003 (mt0) cc_final: 0.8411 (mm-40) REVERT: A 515 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8825 (tm-30) REVERT: A 542 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: A 676 MET cc_start: 0.8159 (mmt) cc_final: 0.7723 (mmm) REVERT: A 695 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8355 (mmtm) REVERT: A 826 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: A 929 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7037 (mt) REVERT: A 992 ASP cc_start: 0.7718 (t0) cc_final: 0.7202 (p0) REVERT: A 1132 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7752 (mtmm) REVERT: A 1218 GLN cc_start: 0.9104 (tt0) cc_final: 0.8632 (tm-30) REVERT: A 1284 MET cc_start: 0.8005 (ttp) cc_final: 0.7798 (tmt) REVERT: A 1285 MET cc_start: 0.7547 (ttm) cc_final: 0.6562 (ttm) REVERT: A 1287 TYR cc_start: 0.6986 (m-80) cc_final: 0.6486 (m-10) REVERT: B 96 TYR cc_start: 0.8203 (m-80) cc_final: 0.7432 (m-80) REVERT: B 353 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7457 (tppt) REVERT: B 432 MET cc_start: 0.7006 (ttp) cc_final: 0.6649 (tpt) REVERT: B 434 ARG cc_start: 0.7603 (tmm-80) cc_final: 0.7152 (tmm-80) REVERT: B 572 HIS cc_start: 0.7659 (m-70) cc_final: 0.7323 (m-70) REVERT: B 705 MET cc_start: 0.9016 (tpp) cc_final: 0.8653 (tpt) REVERT: B 837 ASP cc_start: 0.8654 (m-30) cc_final: 0.8157 (m-30) REVERT: B 879 ARG cc_start: 0.7472 (mmt90) cc_final: 0.7211 (mmm-85) REVERT: B 884 ARG cc_start: 0.7406 (mmp-170) cc_final: 0.7142 (mmm160) REVERT: B 908 GLU cc_start: 0.8137 (tp30) cc_final: 0.7917 (tp30) REVERT: B 963 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6552 (p90) REVERT: B 1190 ASP cc_start: 0.8455 (t70) cc_final: 0.8224 (t0) REVERT: B 1206 GLU cc_start: 0.8345 (tt0) cc_final: 0.8043 (mt-10) REVERT: C 50 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 123 ASN cc_start: 0.8102 (t0) cc_final: 0.7889 (m-40) REVERT: E 75 MET cc_start: 0.8079 (ppp) cc_final: 0.7524 (ppp) REVERT: E 121 MET cc_start: 0.8758 (mmp) cc_final: 0.8525 (mmp) REVERT: E 215 MET cc_start: 0.6598 (mmt) cc_final: 0.5661 (ptm) REVERT: F 71 GLU cc_start: 0.8458 (mp0) cc_final: 0.8091 (pm20) REVERT: F 72 LYS cc_start: 0.8443 (mmtp) cc_final: 0.7355 (mmtt) REVERT: F 111 LEU cc_start: 0.8365 (mp) cc_final: 0.8017 (mt) REVERT: F 114 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: G 3 PHE cc_start: 0.5573 (m-80) cc_final: 0.4665 (m-80) REVERT: G 33 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7798 (tm-30) REVERT: G 65 ASP cc_start: 0.8817 (m-30) cc_final: 0.8169 (t0) REVERT: G 115 MET cc_start: 0.3614 (mpp) cc_final: 0.2951 (mtp) REVERT: H 2 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.6922 (m) REVERT: H 14 GLU cc_start: 0.7912 (tt0) cc_final: 0.7424 (tp30) REVERT: H 33 GLN cc_start: 0.7361 (mp10) cc_final: 0.6821 (mp-120) REVERT: H 35 GLN cc_start: 0.7986 (tt0) cc_final: 0.7724 (tt0) REVERT: H 64 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.6924 (p0) REVERT: H 87 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8318 (mmp-170) REVERT: H 130 ARG cc_start: 0.8840 (tpp80) cc_final: 0.8640 (tpp80) REVERT: I 13 MET cc_start: 0.8104 (pp-130) cc_final: 0.7857 (ppp) REVERT: I 77 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7563 (ttpt) REVERT: J 42 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7575 (ptmt) REVERT: K 29 ASN cc_start: 0.7608 (t0) cc_final: 0.6865 (t0) REVERT: K 38 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8506 (mp0) REVERT: K 94 ILE cc_start: 0.8381 (mm) cc_final: 0.8059 (mp) REVERT: L 53 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7608 (t-170) REVERT: L 57 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (mt) outliers start: 74 outliers final: 38 residues processed: 390 average time/residue: 0.6376 time to fit residues: 298.3058 Evaluate side-chains 380 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 380 optimal weight: 6.9990 chunk 214 optimal weight: 0.6980 chunk 390 optimal weight: 3.9990 chunk 314 optimal weight: 0.0030 chunk 371 optimal weight: 8.9990 chunk 247 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 706 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.119837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084679 restraints weight = 62381.153| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.53 r_work: 0.3143 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33168 Z= 0.226 Angle : 0.687 29.701 44967 Z= 0.334 Chirality : 0.046 0.301 5050 Planarity : 0.005 0.071 5678 Dihedral : 11.669 176.263 4789 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.03 % Allowed : 19.61 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3925 helix: 0.98 (0.14), residues: 1373 sheet: -0.56 (0.20), residues: 619 loop : -0.07 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 63 TYR 0.014 0.002 TYR B 486 PHE 0.024 0.002 PHE A 219 TRP 0.012 0.001 TRP B 681 HIS 0.007 0.001 HIS A1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (33136) covalent geometry : angle 0.63734 / 0.33 (44922) hydrogen bonds : bond 0.04042 / 2.66 ( 1402) hydrogen bonds : angle 4.88511 / 3.43 ( 3926) metal coordination : bond 0.01295 / 0.62 ( 32) metal coordination : angle 8.16596 / 5.11 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 320 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8426 (t0) cc_final: 0.8223 (t0) REVERT: A 124 GLN cc_start: 0.9020 (mt0) cc_final: 0.8433 (mm-40) REVERT: A 146 MET cc_start: 0.8425 (mpp) cc_final: 0.8104 (mmt) REVERT: A 456 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8989 (mtm) REVERT: A 515 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9066 (tm-30) REVERT: A 542 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: A 929 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 992 ASP cc_start: 0.7720 (t0) cc_final: 0.7177 (p0) REVERT: A 1132 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7762 (ptpt) REVERT: A 1218 GLN cc_start: 0.9111 (tt0) cc_final: 0.8684 (tm-30) REVERT: A 1281 ARG cc_start: 0.7619 (mmm160) cc_final: 0.7349 (mmm160) REVERT: A 1285 MET cc_start: 0.7548 (ttm) cc_final: 0.7293 (ttm) REVERT: B 96 TYR cc_start: 0.8222 (m-80) cc_final: 0.7412 (m-80) REVERT: B 432 MET cc_start: 0.7025 (ttp) cc_final: 0.6714 (tpt) REVERT: B 434 ARG cc_start: 0.7612 (tmm-80) cc_final: 0.7155 (tmm-80) REVERT: B 572 HIS cc_start: 0.7698 (m-70) cc_final: 0.7360 (m-70) REVERT: B 792 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7563 (mpp) REVERT: B 837 ASP cc_start: 0.8760 (m-30) cc_final: 0.8263 (m-30) REVERT: B 879 ARG cc_start: 0.7508 (mmt90) cc_final: 0.7235 (mmm-85) REVERT: B 908 GLU cc_start: 0.8163 (tp30) cc_final: 0.7947 (tp30) REVERT: B 935 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.7761 (tpt90) REVERT: B 963 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6606 (p90) REVERT: B 1026 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8800 (mt) REVERT: B 1206 GLU cc_start: 0.8384 (tt0) cc_final: 0.8102 (mt-10) REVERT: C 50 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: C 123 ASN cc_start: 0.8097 (t0) cc_final: 0.7854 (m-40) REVERT: E 58 MET cc_start: 0.7449 (tpt) cc_final: 0.7059 (tpt) REVERT: E 75 MET cc_start: 0.8139 (ppp) cc_final: 0.7563 (ppp) REVERT: E 121 MET cc_start: 0.8749 (mmp) cc_final: 0.8475 (mmp) REVERT: E 215 MET cc_start: 0.6573 (mmt) cc_final: 0.5630 (ptm) REVERT: F 71 GLU cc_start: 0.8519 (mp0) cc_final: 0.8061 (pm20) REVERT: F 72 LYS cc_start: 0.8480 (mmtp) cc_final: 0.7421 (mmtt) REVERT: F 111 LEU cc_start: 0.8383 (mp) cc_final: 0.8056 (mt) REVERT: F 114 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: G 1 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (ppp) REVERT: G 3 PHE cc_start: 0.5670 (m-80) cc_final: 0.5278 (m-80) REVERT: G 33 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7938 (tm-30) REVERT: G 69 GLU cc_start: 0.8343 (tt0) cc_final: 0.8010 (tt0) REVERT: G 115 MET cc_start: 0.3636 (mpp) cc_final: 0.3053 (mtp) REVERT: H 2 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7029 (m) REVERT: H 14 GLU cc_start: 0.7948 (tt0) cc_final: 0.7463 (tp30) REVERT: H 33 GLN cc_start: 0.7352 (mp10) cc_final: 0.6800 (mp-120) REVERT: H 35 GLN cc_start: 0.7940 (tt0) cc_final: 0.7659 (tt0) REVERT: H 64 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.6942 (p0) REVERT: H 87 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8358 (mmp-170) REVERT: I 13 MET cc_start: 0.8129 (pp-130) cc_final: 0.7858 (ppp) REVERT: I 77 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7489 (ttpt) REVERT: J 42 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7647 (ptmt) REVERT: K 29 ASN cc_start: 0.7610 (t0) cc_final: 0.6897 (t0) REVERT: K 38 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8519 (mp0) REVERT: L 53 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7640 (t-170) outliers start: 71 outliers final: 38 residues processed: 366 average time/residue: 0.6711 time to fit residues: 294.0175 Evaluate side-chains 363 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 297 optimal weight: 30.0000 chunk 375 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 356 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 326 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 353 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 150 ASN E 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086440 restraints weight = 62697.898| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.59 r_work: 0.3175 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33168 Z= 0.142 Angle : 0.650 26.341 44967 Z= 0.315 Chirality : 0.044 0.310 5050 Planarity : 0.004 0.071 5678 Dihedral : 11.640 177.633 4789 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.63 % Allowed : 20.13 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.33 (0.14), residues: 3925 helix: 1.08 (0.14), residues: 1372 sheet: -0.52 (0.21), residues: 613 loop : -0.04 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 63 TYR 0.017 0.001 TYR D 147 PHE 0.022 0.001 PHE J 8 TRP 0.010 0.001 TRP E 79 HIS 0.007 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (33136) covalent geometry : angle 0.60249 / 0.31 (44922) hydrogen bonds : bond 0.03739 / 2.45 ( 1402) hydrogen bonds : angle 4.76566 / 3.35 ( 3926) metal coordination : bond 0.00757 / 0.41 ( 32) metal coordination : angle 7.77040 / 4.87 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7850 Ramachandran restraints generated. 3925 Oldfield, 0 Emsley, 3925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8384 (t0) cc_final: 0.8153 (t0) REVERT: A 124 GLN cc_start: 0.9004 (mt0) cc_final: 0.8425 (mm-40) REVERT: A 146 MET cc_start: 0.8324 (mpp) cc_final: 0.8023 (mmt) REVERT: A 515 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8935 (tm-30) REVERT: A 542 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: A 676 MET cc_start: 0.8282 (mmt) cc_final: 0.7818 (mmm) REVERT: A 929 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7117 (mt) REVERT: A 992 ASP cc_start: 0.7712 (t0) cc_final: 0.7168 (p0) REVERT: A 1132 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7787 (ptpt) REVERT: A 1218 GLN cc_start: 0.9107 (tt0) cc_final: 0.8706 (tm-30) REVERT: A 1281 ARG cc_start: 0.7539 (mmm160) cc_final: 0.7251 (mmm160) REVERT: A 1284 MET cc_start: 0.8049 (ttp) cc_final: 0.7811 (tmt) REVERT: A 1285 MET cc_start: 0.7504 (ttm) cc_final: 0.7253 (ttm) REVERT: B 96 TYR cc_start: 0.8196 (m-80) cc_final: 0.7414 (m-80) REVERT: B 381 MET cc_start: 0.8047 (ttp) cc_final: 0.7845 (ttt) REVERT: B 432 MET cc_start: 0.6914 (ttp) cc_final: 0.6596 (tpt) REVERT: B 434 ARG cc_start: 0.7640 (tmm-80) cc_final: 0.7082 (tmm-80) REVERT: B 572 HIS cc_start: 0.7706 (m-70) cc_final: 0.7390 (m-70) REVERT: B 705 MET cc_start: 0.9038 (tpp) cc_final: 0.8609 (tpt) REVERT: B 837 ASP cc_start: 0.8712 (m-30) cc_final: 0.8235 (m-30) REVERT: B 879 ARG cc_start: 0.7530 (mmt90) cc_final: 0.7283 (mmm-85) REVERT: B 908 GLU cc_start: 0.8187 (tp30) cc_final: 0.7965 (tp30) REVERT: B 935 ARG cc_start: 0.8122 (ttt-90) cc_final: 0.7429 (tpt90) REVERT: B 963 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.6404 (p90) REVERT: B 1026 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 1190 ASP cc_start: 0.8484 (t70) cc_final: 0.8259 (t0) REVERT: B 1206 GLU cc_start: 0.8342 (tt0) cc_final: 0.8059 (mt-10) REVERT: C 123 ASN cc_start: 0.8108 (t0) cc_final: 0.7890 (m-40) REVERT: E 104 ASN cc_start: 0.8524 (t0) cc_final: 0.8212 (m110) REVERT: E 121 MET cc_start: 0.8708 (mmp) cc_final: 0.8465 (mmp) REVERT: E 215 MET cc_start: 0.6599 (mmt) cc_final: 0.5714 (ptm) REVERT: F 71 GLU cc_start: 0.8507 (mp0) cc_final: 0.8059 (pm20) REVERT: F 72 LYS cc_start: 0.8498 (mmtp) cc_final: 0.7458 (mmtt) REVERT: F 103 MET cc_start: 0.8577 (ptp) cc_final: 0.8045 (ptp) REVERT: F 111 LEU cc_start: 0.8371 (mp) cc_final: 0.8037 (mt) REVERT: F 114 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: G 3 PHE cc_start: 0.5884 (m-80) cc_final: 0.5524 (m-80) REVERT: G 33 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7822 (tm-30) REVERT: G 69 GLU cc_start: 0.8301 (tt0) cc_final: 0.7976 (tt0) REVERT: G 115 MET cc_start: 0.3512 (mpp) cc_final: 0.2913 (mtp) REVERT: H 2 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7163 (m) REVERT: H 14 GLU cc_start: 0.7939 (tt0) cc_final: 0.7447 (tp30) REVERT: H 33 GLN cc_start: 0.7232 (mp10) cc_final: 0.6697 (mp-120) REVERT: H 35 GLN cc_start: 0.7918 (tt0) cc_final: 0.7656 (tt0) REVERT: H 64 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.6806 (p0) REVERT: H 66 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6558 (tm-30) REVERT: H 87 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.8355 (mmp-170) REVERT: I 13 MET cc_start: 0.8113 (pp-130) cc_final: 0.7844 (ppp) REVERT: I 77 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7580 (ttpt) REVERT: J 42 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7650 (ptmt) REVERT: K 29 ASN cc_start: 0.7592 (t0) cc_final: 0.6883 (t0) REVERT: K 38 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8497 (mp0) REVERT: K 54 ARG cc_start: 0.8791 (ttp-110) cc_final: 0.8549 (ttt-90) REVERT: L 53 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7637 (t-170) outliers start: 57 outliers final: 34 residues processed: 373 average time/residue: 0.6782 time to fit residues: 301.6476 Evaluate side-chains 365 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 172 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 chunk 392 optimal weight: 40.0000 chunk 264 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 322 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 326 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 150 ASN E 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085882 restraints weight = 62631.964| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.55 r_work: 0.3163 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33168 Z= 0.170 Angle : 0.652 24.916 44967 Z= 0.318 Chirality : 0.044 0.307 5050 Planarity : 0.004 0.071 5678 Dihedral : 11.624 177.886 4789 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.69 % Allowed : 20.33 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.33 (0.14), residues: 3925 helix: 1.09 (0.14), residues: 1372 sheet: -0.53 (0.21), residues: 607 loop : -0.05 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 63 TYR 0.015 0.001 TYR E 46 PHE 0.022 0.001 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.007 0.001 HIS A1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (33136) covalent geometry : angle 0.60972 / 0.32 (44922) hydrogen bonds : bond 0.03772 / 2.47 ( 1402) hydrogen bonds : angle 4.76490 / 3.35 ( 3926) metal coordination : bond 0.00756 / 0.42 ( 32) metal coordination : angle 7.36336 / 4.65 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13025.90 seconds wall clock time: 222 minutes 11.04 seconds (13331.04 seconds total)