Starting phenix.real_space_refine on Mon Sep 14 21:11:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sb0_54708/09_2026/9sb0_54708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sb0_54708/09_2026/9sb0_54708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sb0_54708/09_2026/9sb0_54708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sb0_54708/09_2026/9sb0_54708.map" model { file = "/net/cci-nas-00/data/ceres_data/9sb0_54708/09_2026/9sb0_54708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sb0_54708/09_2026/9sb0_54708.cif" } resolution = 3.04 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= 0.000 sd= 0.044 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 56 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20301 2.51 5 N 5655 2.21 5 O 6265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32469 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11091 Classifications: {'peptide': 1409} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1344} Chain breaks: 6 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' MG': 2, ' ZN': 2, 'PPV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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 457 SG CYS A 67 57.375 70.238 86.076 1.00 71.27 S ATOM 479 SG CYS A 70 56.823 73.370 84.008 1.00 70.79 S ATOM 532 SG CYS A 77 60.298 71.717 84.285 1.00 68.06 S ATOM 762 SG CYS A 107 75.742 80.102 128.988 1.00105.03 S ATOM 786 SG CYS A 110 73.341 82.805 128.321 1.00 95.30 S ATOM 1091 SG CYS A 148 76.157 83.264 131.030 1.00111.71 S ATOM 1190 SG CYS A 167 73.011 81.212 131.604 1.00 98.53 S ATOM 19865 SG CYS B1163 58.794 86.030 93.965 1.00 66.91 S ATOM 19883 SG CYS B1166 61.293 83.716 95.515 1.00 63.50 S ATOM 20008 SG CYS B1182 57.846 82.423 94.233 1.00 77.92 S ATOM 20027 SG CYS B1185 58.204 84.470 97.455 1.00 71.68 S ATOM 21015 SG CYS C 86 83.801 60.531 21.219 1.00 85.51 S ATOM 21032 SG CYS C 88 82.505 57.840 23.584 1.00101.39 S ATOM 21065 SG CYS C 92 84.414 56.833 20.515 1.00 84.62 S ATOM 21088 SG CYS C 95 86.209 58.554 23.424 1.00 77.34 S ATOM 28673 SG CYS I 7 131.633 48.923 136.568 1.00153.52 S ATOM 28698 SG CYS I 10 128.000 48.429 135.655 1.00156.17 S ATOM 28864 SG CYS I 29 129.419 52.106 136.062 1.00157.44 S ATOM 28888 SG CYS I 32 128.891 49.810 138.933 1.00155.81 S ATOM 29215 SG CYS I 75 158.906 59.337 97.522 1.00192.88 S ATOM 29237 SG CYS I 78 159.947 56.062 98.485 1.00216.46 S ATOM 29453 SG CYS I 103 156.255 56.693 97.168 1.00192.82 S ATOM 29473 SG CYS I 106 157.122 57.402 100.646 1.00179.64 S ATOM 29592 SG CYS J 7 113.949 59.341 39.034 1.00 30.77 S ATOM 29615 SG CYS J 10 114.317 61.008 35.678 1.00 35.94 S ATOM 29895 SG CYS J 45 116.944 61.670 38.338 1.00 42.50 S ATOM 29901 SG CYS J 46 116.738 58.316 36.598 1.00 30.41 S ATOM 31024 SG CYS L 31 88.319 27.252 55.948 1.00113.26 S ATOM 31044 SG CYS L 34 89.482 24.589 53.408 1.00114.71 S ATOM 31148 SG CYS L 48 86.058 24.451 55.106 1.00119.55 S ATOM 31171 SG CYS L 51 89.308 23.722 57.059 1.00117.71 S Time building chain proxies: 6.00, per 1000 atoms: 0.18 Number of scatterers: 32469 At special positions: 0 Unit cell: (172.167, 154.842, 160.256, 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 182 16.00 P 56 15.00 Mg 2 11.99 O 6265 8.00 N 5655 7.00 C 20301 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " 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 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7410 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 46 sheets defined 38.1% alpha, 18.7% beta 25 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.504A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 288 through 305 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: 3.743A 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 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.647A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.809A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.682A 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 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.599A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) 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 removed outlier: 3.582A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.868A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 845 removed outlier: 3.777A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.570A 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 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.556A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.601A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1082 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1083 through 1086 Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1147 removed outlier: 3.563A pdb=" N THR A1147 " --> pdb=" O LYS A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.668A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 4.116A pdb=" N ASP A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.579A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.881A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.667A 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 1447 through 1452 removed outlier: 3.764A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.903A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 4.665A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' 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 303 removed outlier: 3.886A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.578A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) 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 438 removed outlier: 3.587A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.658A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.509A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.560A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.966A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.558A pdb=" N ILE B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.659A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.728A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.119A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.708A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.464A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.915A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 removed outlier: 3.768A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) 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 removed outlier: 3.526A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 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: 4.049A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.884A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.158A pdb=" N GLN D 132 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.841A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.980A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.551A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.569A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 103 Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.570A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.043A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.505A pdb=" N MET F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.573A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) 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 '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: 3.638A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.780A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.646A 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 84 through 91 removed outlier: 11.415A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.683A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.650A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.713A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.521A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (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 588 through 590 removed outlier: 6.903A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 removed outlier: 3.616A pdb=" N GLY A 766 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.811A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.815A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1226 removed outlier: 4.407A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 71 removed outlier: 5.058A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 71 removed outlier: 5.058A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.205A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.643A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.824A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.400A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.588A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.588A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.028A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.761A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD5, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD6, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.449A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.791A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AD9, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.783A pdb=" N GLN D 37 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.608A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS G 5 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR G 74 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 44 through 45 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.355A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.860A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 86 through 95 removed outlier: 6.475A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU G 100 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE G 143 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY G 89 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 121 through 122 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.566A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE9, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.586A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 86 " --> pdb=" O PHE I 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.626A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 13996 1.44 - 1.67: 18860 1.67 - 1.90: 295 1.90 - 2.13: 1 2.13 - 2.36: 4 Bond restraints: 33156 Sorted by residual: bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.528 2.088 -0.560 1.59e-02 3.96e+03 1.24e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.358 -0.976 3.00e-02 1.11e+03 1.06e+03 bond pdb=" CE1 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.343 -0.961 3.00e-02 1.11e+03 1.03e+03 bond pdb=" CD1 PHE D 70 " pdb=" CE1 PHE D 70 " ideal model delta sigma weight residual 1.382 2.340 -0.958 3.00e-02 1.11e+03 1.02e+03 bond pdb=" CE2 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.319 -0.937 3.00e-02 1.11e+03 9.76e+02 ... (remaining 33151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 44968 4.92 - 9.83: 26 9.83 - 14.75: 2 14.75 - 19.66: 2 19.66 - 24.58: 1 Bond angle restraints: 44999 Sorted by residual: angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 110.50 135.08 -24.58 1.70e+00 3.46e-01 2.09e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 128.10 -18.50 1.50e+00 4.44e-01 1.52e+02 angle pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" C THR D 133 " ideal model delta sigma weight residual 111.36 102.13 9.23 1.09e+00 8.42e-01 7.18e+01 angle pdb=" OG1 THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 109.30 92.41 16.89 2.00e+00 2.50e-01 7.13e+01 angle pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 110.85 124.20 -13.35 1.70e+00 3.46e-01 6.17e+01 ... (remaining 44994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 19587 26.42 - 52.84: 498 52.84 - 79.26: 81 79.26 - 105.69: 7 105.69 - 132.11: 1 Dihedral angle restraints: 20174 sinusoidal: 8732 harmonic: 11442 Sorted by residual: dihedral pdb=" C THR D 133 " pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual -122.00 -141.66 19.66 0 2.50e+00 1.60e-01 6.18e+01 dihedral pdb=" N THR D 133 " pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual 123.40 139.33 -15.93 0 2.50e+00 1.60e-01 4.06e+01 dihedral pdb=" CA ALA C 39 " pdb=" C ALA C 39 " pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta harmonic sigma weight residual 180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 20171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 5062 0.193 - 0.387: 0 0.387 - 0.580: 0 0.580 - 0.773: 0 0.773 - 0.967: 1 Chirality restraints: 5063 Sorted by residual: chirality pdb=" CB THR D 133 " pdb=" CA THR D 133 " pdb=" OG1 THR D 133 " pdb=" CG2 THR D 133 " both_signs ideal model delta sigma weight residual False 2.55 1.59 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA HIS A 287 " pdb=" N HIS A 287 " pdb=" C HIS A 287 " pdb=" CB HIS A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 5060 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " -0.001 2.00e-02 2.50e+03 5.33e-02 4.97e+01 pdb=" CG PHE D 70 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.090 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 133 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C THR D 133 " 0.041 2.00e-02 2.50e+03 pdb=" O THR D 133 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 134 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 245 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.027 5.00e-02 4.00e+02 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 276 2.58 - 3.16: 26504 3.16 - 3.74: 49768 3.74 - 4.32: 71226 4.32 - 4.90: 118476 Nonbonded interactions: 266250 Sorted by model distance: nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1803 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1802 " model vdw 2.005 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1802 " model vdw 2.005 2.170 nonbonded pdb=" O32 PPV A1801 " pdb="MG MG A1803 " model vdw 2.042 2.170 nonbonded pdb=" CE2 PHE D 70 " pdb=" OG1 THR D 133 " model vdw 2.046 3.340 ... (remaining 266245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 35.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.012 0.976 33188 Z= 0.474 Angle : 0.564 24.580 45044 Z= 0.330 Chirality : 0.045 0.967 5063 Planarity : 0.004 0.053 5640 Dihedral : 11.806 132.107 12764 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.03 (0.14), residues: 3893 helix: 1.22 (0.15), residues: 1314 sheet: -0.43 (0.22), residues: 574 loop : -0.62 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.027 0.001 TYR B 797 PHE 0.090 0.002 PHE D 70 TRP 0.023 0.001 TRP B 561 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.01209 / 0.47 (33156) covalent geometry : angle 0.55015 / 0.33 (44999) hydrogen bonds : bond 0.17751 / 11.77 ( 1336) hydrogen bonds : angle 6.74434 / 4.86 ( 3711) metal coordination : bond 0.00474 / 0.30 ( 32) metal coordination : angle 4.01712 / 2.72 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6240 (mmt) cc_final: 0.5924 (mmm) REVERT: A 71 GLN cc_start: 0.7979 (mm110) cc_final: 0.7716 (mm-40) REVERT: A 199 LEU cc_start: 0.6865 (mt) cc_final: 0.6539 (tp) REVERT: A 453 MET cc_start: 0.8599 (mpp) cc_final: 0.8132 (mpp) REVERT: A 688 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6813 (ttpt) REVERT: A 830 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8302 (mtpp) REVERT: A 1077 THR cc_start: 0.8995 (m) cc_final: 0.8576 (m) REVERT: A 1110 ASN cc_start: 0.8373 (m-40) cc_final: 0.7969 (p0) REVERT: A 1259 MET cc_start: 0.5741 (mtp) cc_final: 0.5065 (mmp) REVERT: A 1263 ILE cc_start: 0.7254 (mm) cc_final: 0.6968 (mm) REVERT: B 89 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6683 (tm-30) REVERT: B 272 THR cc_start: 0.8874 (m) cc_final: 0.8672 (p) REVERT: B 357 GLN cc_start: 0.7505 (tt0) cc_final: 0.7111 (tt0) REVERT: B 422 LYS cc_start: 0.7528 (mmtm) cc_final: 0.7131 (mtpp) REVERT: B 531 GLN cc_start: 0.7665 (pm20) cc_final: 0.7308 (mm-40) REVERT: B 552 MET cc_start: 0.8120 (mmm) cc_final: 0.7319 (ttp) REVERT: B 621 GLU cc_start: 0.8405 (tp30) cc_final: 0.7872 (tp30) REVERT: B 916 THR cc_start: 0.8077 (t) cc_final: 0.7839 (p) REVERT: B 951 GLN cc_start: 0.7781 (mt0) cc_final: 0.7555 (mm-40) REVERT: B 957 ASN cc_start: 0.7610 (t0) cc_final: 0.7406 (t0) REVERT: B 1082 MET cc_start: 0.8416 (tpp) cc_final: 0.8195 (tpt) REVERT: B 1124 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8443 (mtp180) REVERT: C 89 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6972 (pm20) REVERT: C 123 ASN cc_start: 0.8034 (t0) cc_final: 0.7774 (m-40) REVERT: C 264 GLN cc_start: 0.7699 (tp40) cc_final: 0.7275 (mt0) REVERT: E 46 TYR cc_start: 0.8525 (m-80) cc_final: 0.8237 (m-80) REVERT: E 90 VAL cc_start: 0.6952 (t) cc_final: 0.6737 (m) REVERT: E 95 THR cc_start: 0.8131 (m) cc_final: 0.7771 (p) REVERT: F 119 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7822 (mmm160) REVERT: F 128 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8667 (mmmt) REVERT: H 14 GLU cc_start: 0.8340 (tt0) cc_final: 0.7986 (tt0) REVERT: I 13 MET cc_start: 0.7440 (ptt) cc_final: 0.7210 (ptp) REVERT: I 17 ARG cc_start: 0.5829 (ttt180) cc_final: 0.5571 (ptm-80) REVERT: I 45 ARG cc_start: 0.7360 (tmm-80) cc_final: 0.6696 (tmm-80) REVERT: K 16 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7399 (mt-10) REVERT: L 27 LEU cc_start: 0.6774 (mm) cc_final: 0.6425 (mm) outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.2311 time to fit residues: 253.5876 Evaluate side-chains 409 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 706 HIS A 926 GLN B 513 GLN B 887 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN C 224 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 114 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN K 2 ASN L 66 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.152828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107239 restraints weight = 47276.314| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.38 r_work: 0.3233 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.025 33188 Z= 0.463 Angle : 0.610 24.184 45044 Z= 0.323 Chirality : 0.045 0.788 5063 Planarity : 0.004 0.046 5640 Dihedral : 11.981 133.811 4901 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 1.04 % Allowed : 6.14 % Favored : 92.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.05 (0.13), residues: 3893 helix: 1.08 (0.14), residues: 1363 sheet: -0.53 (0.22), residues: 541 loop : -0.62 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A1241 TYR 0.017 0.001 TYR B 797 PHE 0.077 0.002 PHE D 70 TRP 0.016 0.001 TRP A1044 HIS 0.009 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01219 / 0.46 (33156) covalent geometry : angle 0.59477 / 0.32 (44999) hydrogen bonds : bond 0.04630 / 3.10 ( 1336) hydrogen bonds : angle 5.12598 / 3.71 ( 3711) metal coordination : bond 0.00505 / 0.33 ( 32) metal coordination : angle 4.26399 / 2.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 430 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.6872 (m-30) cc_final: 0.6285 (p0) REVERT: A 199 LEU cc_start: 0.6652 (mt) cc_final: 0.6303 (tp) REVERT: A 453 MET cc_start: 0.8908 (mpp) cc_final: 0.8221 (mpp) REVERT: A 455 MET cc_start: 0.9319 (ttm) cc_final: 0.9068 (ttm) REVERT: A 688 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6238 (ttpt) REVERT: A 830 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7757 (mtpp) REVERT: A 1063 MET cc_start: 0.9111 (mmm) cc_final: 0.8805 (mmm) REVERT: A 1110 ASN cc_start: 0.8646 (m-40) cc_final: 0.7892 (p0) REVERT: A 1259 MET cc_start: 0.5578 (mtp) cc_final: 0.5100 (mmp) REVERT: A 1285 MET cc_start: 0.7483 (mtp) cc_final: 0.7201 (mtp) REVERT: A 1444 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7601 (mtp) REVERT: B 89 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6169 (tm-30) REVERT: B 272 THR cc_start: 0.8610 (m) cc_final: 0.8290 (p) REVERT: B 331 LEU cc_start: 0.8596 (mt) cc_final: 0.8375 (mp) REVERT: B 422 LYS cc_start: 0.7048 (mmtm) cc_final: 0.6564 (mtpp) REVERT: B 432 MET cc_start: 0.6931 (mtt) cc_final: 0.6597 (mtp) REVERT: B 531 GLN cc_start: 0.7522 (pm20) cc_final: 0.6918 (mm-40) REVERT: B 552 MET cc_start: 0.7693 (mmm) cc_final: 0.6623 (ttp) REVERT: B 621 GLU cc_start: 0.8594 (tp30) cc_final: 0.8002 (tp30) REVERT: B 837 ASP cc_start: 0.8631 (m-30) cc_final: 0.8335 (m-30) REVERT: B 916 THR cc_start: 0.7881 (t) cc_final: 0.7484 (p) REVERT: B 950 ASP cc_start: 0.8545 (t0) cc_final: 0.8208 (t0) REVERT: B 951 GLN cc_start: 0.7999 (mt0) cc_final: 0.7087 (mm-40) REVERT: B 1072 MET cc_start: 0.9213 (mtp) cc_final: 0.9009 (mtp) REVERT: B 1124 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8113 (mtp180) REVERT: C 89 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6772 (pm20) REVERT: C 123 ASN cc_start: 0.7974 (t0) cc_final: 0.7475 (m-40) REVERT: C 154 LYS cc_start: 0.8267 (ttpp) cc_final: 0.8003 (tttt) REVERT: E 50 MET cc_start: 0.7763 (tmm) cc_final: 0.7034 (mpp) REVERT: E 102 GLU cc_start: 0.7483 (pt0) cc_final: 0.6616 (tm-30) REVERT: F 119 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7521 (mmm160) REVERT: F 128 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7796 (mmtt) REVERT: G 106 MET cc_start: -0.1352 (ttp) cc_final: -0.1727 (mpp) REVERT: H 97 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8789 (mtt) REVERT: H 129 TYR cc_start: 0.8206 (p90) cc_final: 0.7914 (p90) REVERT: I 17 ARG cc_start: 0.6115 (ttt180) cc_final: 0.5518 (ptm160) REVERT: I 45 ARG cc_start: 0.6899 (tmm-80) cc_final: 0.6650 (tmm-80) REVERT: J 26 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8213 (tm-30) REVERT: K 16 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7156 (mt-10) REVERT: K 54 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8351 (mmm-85) REVERT: L 27 LEU cc_start: 0.6205 (mm) cc_final: 0.5810 (mm) outliers start: 36 outliers final: 17 residues processed: 446 average time/residue: 0.2085 time to fit residues: 147.2869 Evaluate side-chains 390 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 371 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 354 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 386 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A1203 ASN B 115 GLN B 395 GLN B 484 ASN B 763 GLN B 822 ASN C 224 GLN E 54 GLN E 101 GLN E 114 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 HIS H 64 ASN K 2 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103632 restraints weight = 47513.810| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.31 r_work: 0.3197 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.022 33188 Z= 0.541 Angle : 0.704 24.110 45044 Z= 0.368 Chirality : 0.049 0.767 5063 Planarity : 0.005 0.054 5640 Dihedral : 12.164 132.724 4901 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 1.76 % Allowed : 8.45 % Favored : 89.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.47 (0.13), residues: 3893 helix: 0.74 (0.14), residues: 1347 sheet: -0.78 (0.21), residues: 560 loop : -0.87 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 857 TYR 0.028 0.002 TYR A1154 PHE 0.079 0.003 PHE D 70 TRP 0.020 0.002 TRP B 561 HIS 0.009 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01396 / 0.54 (33156) covalent geometry : angle 0.68866 / 0.37 (44999) hydrogen bonds : bond 0.04961 / 3.30 ( 1336) hydrogen bonds : angle 5.02350 / 3.62 ( 3711) metal coordination : bond 0.00915 / 0.62 ( 32) metal coordination : angle 4.67349 / 3.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 386 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9023 (m-10) REVERT: A 199 LEU cc_start: 0.6781 (mt) cc_final: 0.6376 (tp) REVERT: A 437 MET cc_start: 0.8467 (mmm) cc_final: 0.8197 (mmm) REVERT: A 453 MET cc_start: 0.8815 (mpp) cc_final: 0.8179 (mpp) REVERT: A 455 MET cc_start: 0.9388 (ttm) cc_final: 0.9130 (ttm) REVERT: A 688 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6481 (ttpt) REVERT: A 830 LYS cc_start: 0.8640 (mmtt) cc_final: 0.7954 (mtpp) REVERT: A 838 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8547 (tt0) REVERT: A 912 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7034 (pp) REVERT: A 1039 LYS cc_start: 0.8436 (tttt) cc_final: 0.8124 (ttpt) REVERT: A 1110 ASN cc_start: 0.8631 (m-40) cc_final: 0.8032 (p0) REVERT: A 1259 MET cc_start: 0.5970 (mtp) cc_final: 0.5328 (mmp) REVERT: A 1404 GLU cc_start: 0.8016 (tp30) cc_final: 0.7751 (tp30) REVERT: B 88 TYR cc_start: 0.6068 (m-10) cc_final: 0.5538 (m-80) REVERT: B 89 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 115 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 272 THR cc_start: 0.8714 (m) cc_final: 0.8343 (p) REVERT: B 331 LEU cc_start: 0.8801 (mt) cc_final: 0.8588 (mp) REVERT: B 413 LEU cc_start: 0.8889 (mm) cc_final: 0.8659 (mt) REVERT: B 422 LYS cc_start: 0.7307 (mmtm) cc_final: 0.6778 (mtpp) REVERT: B 531 GLN cc_start: 0.7626 (pm20) cc_final: 0.7181 (mm-40) REVERT: B 552 MET cc_start: 0.7977 (mmm) cc_final: 0.6976 (ttp) REVERT: B 597 MET cc_start: 0.8649 (tpt) cc_final: 0.8284 (tpt) REVERT: B 621 GLU cc_start: 0.8566 (tp30) cc_final: 0.7863 (tp30) REVERT: B 641 GLU cc_start: 0.7831 (tt0) cc_final: 0.7593 (tt0) REVERT: B 878 GLN cc_start: 0.6230 (mt0) cc_final: 0.6008 (tp40) REVERT: B 950 ASP cc_start: 0.8522 (t0) cc_final: 0.8208 (t0) REVERT: B 951 GLN cc_start: 0.8244 (mt0) cc_final: 0.7374 (mm-40) REVERT: C 89 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6797 (pm20) REVERT: C 123 ASN cc_start: 0.8032 (t0) cc_final: 0.7523 (m-40) REVERT: C 154 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8259 (tttt) REVERT: E 50 MET cc_start: 0.7637 (tmm) cc_final: 0.7062 (mpp) REVERT: E 102 GLU cc_start: 0.7748 (pt0) cc_final: 0.6783 (tm-30) REVERT: F 119 ARG cc_start: 0.8436 (tpp80) cc_final: 0.7555 (mmm160) REVERT: F 128 LYS cc_start: 0.8443 (mmtp) cc_final: 0.8032 (mmtt) REVERT: H 52 GLN cc_start: 0.8626 (mp10) cc_final: 0.7970 (mp10) REVERT: H 129 TYR cc_start: 0.8375 (p90) cc_final: 0.8126 (p90) REVERT: I 13 MET cc_start: 0.7522 (ptp) cc_final: 0.7104 (ptp) REVERT: I 17 ARG cc_start: 0.6053 (ttt180) cc_final: 0.5390 (ptm-80) REVERT: I 45 ARG cc_start: 0.6981 (tmm-80) cc_final: 0.6737 (tmm-80) REVERT: K 54 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8370 (mmm-85) REVERT: L 27 LEU cc_start: 0.6509 (mm) cc_final: 0.6077 (mm) outliers start: 61 outliers final: 36 residues processed: 425 average time/residue: 0.2120 time to fit residues: 142.7643 Evaluate side-chains 395 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 22 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 347 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 chunk 391 optimal weight: 40.0000 chunk 167 optimal weight: 6.9990 chunk 373 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 216 optimal weight: 0.6980 chunk 222 optimal weight: 0.2980 chunk 217 optimal weight: 0.9990 chunk 253 optimal weight: 0.4980 chunk 164 optimal weight: 9.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 760 GLN B 73 GLN B 395 GLN B 887 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 3 GLN E 54 GLN E 101 GLN E 114 ASN G 57 GLN G 71 ASN G 158 HIS H 64 ASN I 46 HIS K 2 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108199 restraints weight = 47057.322| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.34 r_work: 0.3264 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.023 33188 Z= 0.451 Angle : 0.556 24.143 45044 Z= 0.296 Chirality : 0.044 0.777 5063 Planarity : 0.004 0.049 5640 Dihedral : 12.064 134.245 4901 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 1.61 % Allowed : 9.57 % Favored : 88.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.16 (0.13), residues: 3893 helix: 1.04 (0.14), residues: 1357 sheet: -0.57 (0.22), residues: 529 loop : -0.73 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1124 TYR 0.025 0.001 TYR A1154 PHE 0.080 0.001 PHE D 70 TRP 0.011 0.001 TRP A1044 HIS 0.005 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.45 (33156) covalent geometry : angle 0.54224 / 0.30 (44999) hydrogen bonds : bond 0.03666 / 2.44 ( 1336) hydrogen bonds : angle 4.60982 / 3.32 ( 3711) metal coordination : bond 0.00421 / 0.26 ( 32) metal coordination : angle 3.97861 / 2.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 398 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8974 (m-10) REVERT: A 65 LEU cc_start: 0.8462 (mt) cc_final: 0.7925 (mm) REVERT: A 199 LEU cc_start: 0.6805 (mt) cc_final: 0.6479 (tp) REVERT: A 437 MET cc_start: 0.8416 (mmm) cc_final: 0.8111 (mmm) REVERT: A 453 MET cc_start: 0.8821 (mpp) cc_final: 0.8185 (mpp) REVERT: A 688 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6487 (ttmt) REVERT: A 830 LYS cc_start: 0.8604 (mmtt) cc_final: 0.7867 (mtpp) REVERT: A 838 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8408 (tt0) REVERT: A 873 MET cc_start: 0.8624 (mmm) cc_final: 0.7965 (mmm) REVERT: A 912 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6827 (pp) REVERT: A 1039 LYS cc_start: 0.8334 (tttt) cc_final: 0.8022 (ttpt) REVERT: A 1110 ASN cc_start: 0.8592 (m-40) cc_final: 0.8070 (p0) REVERT: A 1259 MET cc_start: 0.5894 (mtp) cc_final: 0.5243 (mmp) REVERT: A 1285 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7265 (ttp) REVERT: B 61 ASP cc_start: 0.7808 (m-30) cc_final: 0.7459 (m-30) REVERT: B 89 GLU cc_start: 0.6605 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 272 THR cc_start: 0.8584 (m) cc_final: 0.8216 (p) REVERT: B 413 LEU cc_start: 0.8703 (mm) cc_final: 0.8502 (mt) REVERT: B 422 LYS cc_start: 0.7187 (mmtm) cc_final: 0.6701 (mtpp) REVERT: B 531 GLN cc_start: 0.7594 (pm20) cc_final: 0.7133 (mm-40) REVERT: B 552 MET cc_start: 0.7843 (mmm) cc_final: 0.6750 (ttp) REVERT: B 620 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7062 (ttt180) REVERT: B 621 GLU cc_start: 0.8440 (tp30) cc_final: 0.7592 (tp30) REVERT: B 641 GLU cc_start: 0.7865 (tt0) cc_final: 0.7663 (tt0) REVERT: B 878 GLN cc_start: 0.6182 (mt0) cc_final: 0.5970 (tp40) REVERT: B 950 ASP cc_start: 0.8469 (t0) cc_final: 0.8185 (t0) REVERT: B 951 GLN cc_start: 0.8165 (mt0) cc_final: 0.7306 (mm-40) REVERT: C 89 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6832 (pm20) REVERT: C 123 ASN cc_start: 0.7983 (t0) cc_final: 0.7502 (m-40) REVERT: C 154 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8207 (tttt) REVERT: E 48 ASP cc_start: 0.7659 (t70) cc_final: 0.7228 (t70) REVERT: E 50 MET cc_start: 0.7686 (tmm) cc_final: 0.6993 (mpp) REVERT: E 102 GLU cc_start: 0.7740 (pt0) cc_final: 0.6704 (tm-30) REVERT: F 119 ARG cc_start: 0.8342 (tpp80) cc_final: 0.7453 (mmm160) REVERT: F 128 LYS cc_start: 0.8384 (mmtp) cc_final: 0.8009 (mmmt) REVERT: H 52 GLN cc_start: 0.8606 (mp10) cc_final: 0.7873 (mp10) REVERT: H 97 MET cc_start: 0.9234 (mtp) cc_final: 0.8889 (mtt) REVERT: H 130 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8390 (mmt-90) REVERT: I 13 MET cc_start: 0.7456 (ptp) cc_final: 0.7130 (ptp) REVERT: I 17 ARG cc_start: 0.6029 (ttt180) cc_final: 0.5391 (ptm160) REVERT: K 54 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8393 (mmm-85) REVERT: L 27 LEU cc_start: 0.6488 (mm) cc_final: 0.6053 (mm) outliers start: 56 outliers final: 29 residues processed: 429 average time/residue: 0.2196 time to fit residues: 149.8478 Evaluate side-chains 402 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 369 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 325 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 359 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 994 GLN A1173 HIS B 115 GLN E 101 GLN E 114 ASN G 158 HIS H 64 ASN I 12 ASN K 2 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104506 restraints weight = 47337.203| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.29 r_work: 0.3212 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.020 33188 Z= 0.502 Angle : 0.634 24.080 45044 Z= 0.331 Chirality : 0.047 0.775 5063 Planarity : 0.005 0.051 5640 Dihedral : 12.108 133.866 4901 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.76 % Allowed : 10.61 % Favored : 87.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.32 (0.13), residues: 3893 helix: 0.90 (0.14), residues: 1353 sheet: -0.70 (0.21), residues: 570 loop : -0.80 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 287 TYR 0.021 0.002 TYR A1154 PHE 0.078 0.002 PHE D 70 TRP 0.016 0.002 TRP B 561 HIS 0.010 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01311 / 0.50 (33156) covalent geometry : angle 0.61606 / 0.33 (44999) hydrogen bonds : bond 0.04265 / 2.84 ( 1336) hydrogen bonds : angle 4.68196 / 3.38 ( 3711) metal coordination : bond 0.00829 / 0.56 ( 32) metal coordination : angle 4.74193 / 3.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 371 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8992 (m-10) REVERT: A 199 LEU cc_start: 0.6744 (mt) cc_final: 0.6348 (tp) REVERT: A 437 MET cc_start: 0.8507 (mmm) cc_final: 0.8204 (mmm) REVERT: A 453 MET cc_start: 0.8720 (mpp) cc_final: 0.8180 (mpp) REVERT: A 618 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: A 688 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6655 (ttpt) REVERT: A 830 LYS cc_start: 0.8615 (mmtt) cc_final: 0.7942 (mtpp) REVERT: A 838 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8515 (tt0) REVERT: A 890 ASP cc_start: 0.7870 (t0) cc_final: 0.7658 (t0) REVERT: A 912 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.6999 (pp) REVERT: A 1039 LYS cc_start: 0.8438 (tttt) cc_final: 0.7950 (ttpp) REVERT: A 1110 ASN cc_start: 0.8633 (m-40) cc_final: 0.8207 (p0) REVERT: A 1259 MET cc_start: 0.5960 (mtp) cc_final: 0.5275 (mmp) REVERT: A 1285 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7142 (ttt) REVERT: B 89 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6417 (tm-30) REVERT: B 272 THR cc_start: 0.8588 (m) cc_final: 0.8252 (p) REVERT: B 413 LEU cc_start: 0.8763 (mm) cc_final: 0.8542 (mt) REVERT: B 422 LYS cc_start: 0.7282 (mmtm) cc_final: 0.6752 (mtpp) REVERT: B 432 MET cc_start: 0.6799 (mtt) cc_final: 0.6303 (mtp) REVERT: B 531 GLN cc_start: 0.7471 (pm20) cc_final: 0.7027 (tp40) REVERT: B 542 MET cc_start: 0.8920 (mmm) cc_final: 0.8544 (mtt) REVERT: B 552 MET cc_start: 0.7912 (mmm) cc_final: 0.6882 (ttp) REVERT: B 621 GLU cc_start: 0.8507 (tp30) cc_final: 0.7648 (tp30) REVERT: B 641 GLU cc_start: 0.7891 (tt0) cc_final: 0.7653 (tt0) REVERT: B 950 ASP cc_start: 0.8479 (t0) cc_final: 0.8195 (t0) REVERT: B 951 GLN cc_start: 0.8261 (mt0) cc_final: 0.7382 (mm-40) REVERT: C 89 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6804 (pm20) REVERT: C 123 ASN cc_start: 0.8008 (t0) cc_final: 0.7483 (m-40) REVERT: C 154 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8253 (tttt) REVERT: E 48 ASP cc_start: 0.7667 (t70) cc_final: 0.7236 (t0) REVERT: E 50 MET cc_start: 0.7717 (tmm) cc_final: 0.7057 (mpp) REVERT: E 102 GLU cc_start: 0.7804 (pt0) cc_final: 0.6763 (tm-30) REVERT: F 119 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7515 (mmm160) REVERT: F 128 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8073 (mmtt) REVERT: H 52 GLN cc_start: 0.8615 (mp10) cc_final: 0.7871 (mp10) REVERT: H 97 MET cc_start: 0.9282 (mtp) cc_final: 0.9031 (mtt) REVERT: H 128 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7619 (p0) REVERT: I 13 MET cc_start: 0.7585 (ptp) cc_final: 0.7224 (ptp) REVERT: I 17 ARG cc_start: 0.6042 (ttt180) cc_final: 0.5403 (ptm-80) REVERT: K 54 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8428 (mmm-85) REVERT: L 27 LEU cc_start: 0.6528 (mm) cc_final: 0.6066 (mm) outliers start: 61 outliers final: 39 residues processed: 407 average time/residue: 0.2318 time to fit residues: 149.8941 Evaluate side-chains 401 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 357 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 85 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 291 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 224 GLN E 114 ASN H 64 ASN K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106019 restraints weight = 47200.445| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.30 r_work: 0.3238 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.019 33188 Z= 0.464 Angle : 0.575 24.088 45044 Z= 0.303 Chirality : 0.044 0.779 5063 Planarity : 0.004 0.050 5640 Dihedral : 12.070 134.442 4901 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 1.67 % Allowed : 11.04 % Favored : 87.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.16 (0.13), residues: 3893 helix: 1.08 (0.14), residues: 1340 sheet: -0.66 (0.22), residues: 549 loop : -0.73 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1124 TYR 0.030 0.001 TYR A1154 PHE 0.079 0.002 PHE D 70 TRP 0.019 0.001 TRP A1191 HIS 0.010 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01224 / 0.46 (33156) covalent geometry : angle 0.55823 / 0.30 (44999) hydrogen bonds : bond 0.03760 / 2.51 ( 1336) hydrogen bonds : angle 4.53180 / 3.27 ( 3711) metal coordination : bond 0.00576 / 0.37 ( 32) metal coordination : angle 4.33646 / 2.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 379 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.6211 (tp30) cc_final: 0.5997 (tp30) REVERT: A 199 LEU cc_start: 0.6858 (mt) cc_final: 0.6525 (tp) REVERT: A 437 MET cc_start: 0.8439 (mmm) cc_final: 0.8120 (mmm) REVERT: A 453 MET cc_start: 0.8681 (mpp) cc_final: 0.8125 (mpp) REVERT: A 500 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: A 688 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6626 (ttpt) REVERT: A 830 LYS cc_start: 0.8593 (mmtt) cc_final: 0.7873 (mtpp) REVERT: A 838 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8545 (tt0) REVERT: A 873 MET cc_start: 0.8650 (mmm) cc_final: 0.7939 (mmm) REVERT: A 890 ASP cc_start: 0.7855 (t0) cc_final: 0.7615 (t0) REVERT: A 912 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6857 (pp) REVERT: A 969 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: A 1039 LYS cc_start: 0.8370 (tttt) cc_final: 0.7909 (ttpp) REVERT: A 1110 ASN cc_start: 0.8614 (m-40) cc_final: 0.8271 (p0) REVERT: A 1259 MET cc_start: 0.5872 (mtp) cc_final: 0.5318 (mmp) REVERT: A 1285 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7150 (ttt) REVERT: B 61 ASP cc_start: 0.7791 (m-30) cc_final: 0.7470 (m-30) REVERT: B 89 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6444 (tm-30) REVERT: B 272 THR cc_start: 0.8550 (m) cc_final: 0.8239 (p) REVERT: B 315 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7556 (pttp) REVERT: B 413 LEU cc_start: 0.8749 (mm) cc_final: 0.8544 (mt) REVERT: B 422 LYS cc_start: 0.7231 (mmtm) cc_final: 0.6710 (mtpp) REVERT: B 432 MET cc_start: 0.6868 (mtt) cc_final: 0.6482 (mtp) REVERT: B 531 GLN cc_start: 0.7411 (pm20) cc_final: 0.7056 (tp40) REVERT: B 542 MET cc_start: 0.8929 (mmm) cc_final: 0.8558 (mtt) REVERT: B 552 MET cc_start: 0.7886 (mmm) cc_final: 0.6786 (ttp) REVERT: B 621 GLU cc_start: 0.8474 (tp30) cc_final: 0.7577 (tp30) REVERT: B 641 GLU cc_start: 0.7900 (tt0) cc_final: 0.7683 (tt0) REVERT: B 950 ASP cc_start: 0.8450 (t0) cc_final: 0.8136 (t0) REVERT: B 951 GLN cc_start: 0.8191 (mt0) cc_final: 0.7338 (mm-40) REVERT: B 958 GLN cc_start: 0.7832 (tt0) cc_final: 0.7298 (tp40) REVERT: C 89 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6841 (pm20) REVERT: C 123 ASN cc_start: 0.7990 (t0) cc_final: 0.7467 (m-40) REVERT: E 48 ASP cc_start: 0.7641 (t70) cc_final: 0.7147 (t0) REVERT: E 50 MET cc_start: 0.7603 (tmm) cc_final: 0.7054 (mpp) REVERT: E 102 GLU cc_start: 0.7738 (pt0) cc_final: 0.6694 (tm-30) REVERT: F 119 ARG cc_start: 0.8333 (tpp80) cc_final: 0.7428 (mmm160) REVERT: F 128 LYS cc_start: 0.8393 (mmtp) cc_final: 0.8037 (mmtt) REVERT: G 115 MET cc_start: 0.5196 (ppp) cc_final: 0.4212 (ptt) REVERT: H 52 GLN cc_start: 0.8628 (mp10) cc_final: 0.7817 (mp10) REVERT: H 97 MET cc_start: 0.9262 (mtp) cc_final: 0.9040 (mtt) REVERT: H 128 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7440 (p0) REVERT: I 13 MET cc_start: 0.7555 (ptp) cc_final: 0.7217 (ptp) REVERT: I 17 ARG cc_start: 0.6024 (ttt180) cc_final: 0.5369 (ptm-80) REVERT: L 27 LEU cc_start: 0.6555 (mm) cc_final: 0.6110 (mm) outliers start: 58 outliers final: 33 residues processed: 415 average time/residue: 0.2209 time to fit residues: 147.1303 Evaluate side-chains 404 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 365 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 68 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 372 optimal weight: 0.3980 chunk 263 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 114 ASN K 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.150277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106042 restraints weight = 47381.283| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.32 r_work: 0.3238 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.019 33188 Z= 0.464 Angle : 0.575 24.090 45044 Z= 0.302 Chirality : 0.045 0.782 5063 Planarity : 0.004 0.049 5640 Dihedral : 12.041 134.869 4901 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 1.73 % Allowed : 11.39 % Favored : 86.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 3893 helix: 1.11 (0.14), residues: 1345 sheet: -0.57 (0.22), residues: 516 loop : -0.75 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 434 TYR 0.025 0.001 TYR A1154 PHE 0.078 0.002 PHE D 70 TRP 0.021 0.001 TRP A1191 HIS 0.007 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01224 / 0.46 (33156) covalent geometry : angle 0.55998 / 0.30 (44999) hydrogen bonds : bond 0.03691 / 2.46 ( 1336) hydrogen bonds : angle 4.48011 / 3.23 ( 3711) metal coordination : bond 0.00554 / 0.36 ( 32) metal coordination : angle 4.17142 / 2.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LEU cc_start: 0.6857 (mt) cc_final: 0.6495 (tp) REVERT: A 404 TYR cc_start: 0.8855 (m-80) cc_final: 0.8608 (m-80) REVERT: A 437 MET cc_start: 0.8446 (mmm) cc_final: 0.8122 (mmm) REVERT: A 453 MET cc_start: 0.8732 (mpp) cc_final: 0.8156 (mpp) REVERT: A 618 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: A 688 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6614 (ttpt) REVERT: A 712 GLU cc_start: 0.8194 (tt0) cc_final: 0.7976 (tp30) REVERT: A 830 LYS cc_start: 0.8604 (mmtt) cc_final: 0.7879 (mtpp) REVERT: A 838 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8561 (tt0) REVERT: A 873 MET cc_start: 0.8612 (mmm) cc_final: 0.7886 (mmm) REVERT: A 890 ASP cc_start: 0.7857 (t0) cc_final: 0.7603 (t0) REVERT: A 912 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6834 (pp) REVERT: A 969 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: A 1039 LYS cc_start: 0.8382 (tttt) cc_final: 0.7888 (ttpp) REVERT: A 1110 ASN cc_start: 0.8647 (m-40) cc_final: 0.8310 (p0) REVERT: A 1259 MET cc_start: 0.5832 (mtp) cc_final: 0.5260 (mmp) REVERT: A 1285 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7394 (ttp) REVERT: A 1404 GLU cc_start: 0.8062 (tp30) cc_final: 0.7815 (tp30) REVERT: B 61 ASP cc_start: 0.7790 (m-30) cc_final: 0.7458 (m-30) REVERT: B 89 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6469 (tm-30) REVERT: B 272 THR cc_start: 0.8505 (m) cc_final: 0.8190 (p) REVERT: B 413 LEU cc_start: 0.8785 (mm) cc_final: 0.8579 (mt) REVERT: B 422 LYS cc_start: 0.7132 (mmtm) cc_final: 0.6592 (mtpp) REVERT: B 531 GLN cc_start: 0.7421 (pm20) cc_final: 0.7093 (tp40) REVERT: B 542 MET cc_start: 0.8932 (mmm) cc_final: 0.8525 (mtt) REVERT: B 552 MET cc_start: 0.7895 (mmm) cc_final: 0.6791 (ttp) REVERT: B 621 GLU cc_start: 0.8490 (tp30) cc_final: 0.7633 (tp30) REVERT: B 950 ASP cc_start: 0.8483 (t0) cc_final: 0.8172 (t0) REVERT: B 951 GLN cc_start: 0.8175 (mt0) cc_final: 0.7308 (mm-40) REVERT: B 958 GLN cc_start: 0.7789 (tt0) cc_final: 0.7273 (tp40) REVERT: C 89 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6853 (pm20) REVERT: C 123 ASN cc_start: 0.7989 (t0) cc_final: 0.7457 (m-40) REVERT: E 48 ASP cc_start: 0.7663 (t70) cc_final: 0.7144 (t0) REVERT: E 50 MET cc_start: 0.7581 (tmm) cc_final: 0.7056 (mpp) REVERT: E 117 THR cc_start: 0.7452 (t) cc_final: 0.7246 (p) REVERT: F 76 LYS cc_start: 0.8752 (tppt) cc_final: 0.8545 (tppp) REVERT: F 119 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7421 (mmm160) REVERT: F 128 LYS cc_start: 0.8408 (mmtp) cc_final: 0.8063 (mmtt) REVERT: G 106 MET cc_start: -0.1010 (ttp) cc_final: -0.1635 (mpp) REVERT: G 115 MET cc_start: 0.5047 (ppp) cc_final: 0.4090 (ptt) REVERT: H 52 GLN cc_start: 0.8633 (mp10) cc_final: 0.7814 (mp10) REVERT: H 97 MET cc_start: 0.9262 (mtp) cc_final: 0.9041 (mtt) REVERT: H 128 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7446 (p0) REVERT: I 13 MET cc_start: 0.7568 (ptp) cc_final: 0.7222 (ptp) REVERT: I 17 ARG cc_start: 0.6020 (ttt180) cc_final: 0.5291 (ptm-80) REVERT: L 27 LEU cc_start: 0.6551 (mm) cc_final: 0.6090 (mm) outliers start: 60 outliers final: 42 residues processed: 412 average time/residue: 0.2308 time to fit residues: 152.4449 Evaluate side-chains 410 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 363 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 8 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 114 ASN K 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.148926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104715 restraints weight = 47381.821| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.30 r_work: 0.3218 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.018 33188 Z= 0.483 Angle : 0.612 24.070 45044 Z= 0.320 Chirality : 0.046 0.782 5063 Planarity : 0.004 0.050 5640 Dihedral : 12.062 134.612 4901 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 1.87 % Allowed : 11.48 % Favored : 86.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.25 (0.13), residues: 3893 helix: 1.00 (0.14), residues: 1342 sheet: -0.65 (0.22), residues: 528 loop : -0.80 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 434 TYR 0.022 0.002 TYR A1154 PHE 0.078 0.002 PHE D 70 TRP 0.023 0.001 TRP A1191 HIS 0.009 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01268 / 0.48 (33156) covalent geometry : angle 0.59584 / 0.32 (44999) hydrogen bonds : bond 0.03965 / 2.64 ( 1336) hydrogen bonds : angle 4.54014 / 3.27 ( 3711) metal coordination : bond 0.00695 / 0.47 ( 32) metal coordination : angle 4.39136 / 2.90 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LEU cc_start: 0.6904 (mt) cc_final: 0.6543 (tp) REVERT: A 437 MET cc_start: 0.8479 (mmm) cc_final: 0.8154 (mmm) REVERT: A 453 MET cc_start: 0.8787 (mpp) cc_final: 0.8103 (mpp) REVERT: A 500 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: A 618 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: A 688 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6645 (ttpt) REVERT: A 830 LYS cc_start: 0.8581 (mmtt) cc_final: 0.7919 (mtpp) REVERT: A 838 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8583 (tt0) REVERT: A 873 MET cc_start: 0.8708 (mmm) cc_final: 0.8004 (mmm) REVERT: A 890 ASP cc_start: 0.7886 (t0) cc_final: 0.7610 (t0) REVERT: A 912 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6806 (pp) REVERT: A 969 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: A 1039 LYS cc_start: 0.8363 (tttt) cc_final: 0.7903 (ttpp) REVERT: A 1110 ASN cc_start: 0.8657 (m-40) cc_final: 0.8332 (p0) REVERT: A 1259 MET cc_start: 0.5780 (mtp) cc_final: 0.5360 (mmp) REVERT: A 1285 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7411 (ttp) REVERT: B 61 ASP cc_start: 0.7822 (m-30) cc_final: 0.7494 (m-30) REVERT: B 89 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6326 (tm-30) REVERT: B 272 THR cc_start: 0.8483 (m) cc_final: 0.8132 (p) REVERT: B 413 LEU cc_start: 0.8777 (mm) cc_final: 0.8558 (mt) REVERT: B 422 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6691 (mtpp) REVERT: B 451 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8235 (ptpp) REVERT: B 531 GLN cc_start: 0.7420 (pm20) cc_final: 0.7121 (tp40) REVERT: B 542 MET cc_start: 0.8966 (mmm) cc_final: 0.8605 (mtt) REVERT: B 552 MET cc_start: 0.7928 (mmm) cc_final: 0.6822 (ttp) REVERT: B 621 GLU cc_start: 0.8508 (tp30) cc_final: 0.7646 (tp30) REVERT: B 950 ASP cc_start: 0.8496 (t0) cc_final: 0.8202 (t0) REVERT: B 951 GLN cc_start: 0.8230 (mt0) cc_final: 0.7372 (mm-40) REVERT: B 958 GLN cc_start: 0.7801 (tt0) cc_final: 0.7444 (tp40) REVERT: C 89 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6879 (pm20) REVERT: C 123 ASN cc_start: 0.8001 (t0) cc_final: 0.7457 (m-40) REVERT: E 48 ASP cc_start: 0.7701 (t70) cc_final: 0.7136 (t0) REVERT: E 50 MET cc_start: 0.7576 (tmm) cc_final: 0.7054 (mpp) REVERT: E 117 THR cc_start: 0.7471 (t) cc_final: 0.7252 (p) REVERT: F 119 ARG cc_start: 0.8369 (tpp80) cc_final: 0.7433 (mmm160) REVERT: F 128 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8089 (mmtt) REVERT: G 106 MET cc_start: -0.1009 (ttp) cc_final: -0.1710 (mpp) REVERT: G 115 MET cc_start: 0.5283 (ppp) cc_final: 0.4318 (ptt) REVERT: H 52 GLN cc_start: 0.8625 (mp10) cc_final: 0.7811 (mp10) REVERT: H 97 MET cc_start: 0.9266 (mtp) cc_final: 0.9063 (mtt) REVERT: H 128 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7458 (p0) REVERT: I 13 MET cc_start: 0.7568 (ptp) cc_final: 0.7241 (ptp) REVERT: I 17 ARG cc_start: 0.5915 (ttt180) cc_final: 0.5273 (ptm-80) REVERT: L 27 LEU cc_start: 0.6631 (mm) cc_final: 0.6164 (mm) outliers start: 65 outliers final: 47 residues processed: 409 average time/residue: 0.2304 time to fit residues: 150.7264 Evaluate side-chains 416 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 363 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 262 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 363 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 380 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 114 ASN K 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.149986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105945 restraints weight = 47058.648| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.27 r_work: 0.3237 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.018 33188 Z= 0.464 Angle : 0.579 24.069 45044 Z= 0.305 Chirality : 0.045 0.783 5063 Planarity : 0.004 0.050 5640 Dihedral : 12.026 135.091 4901 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 1.79 % Allowed : 11.97 % Favored : 86.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: -0.15 (0.13), residues: 3893 helix: 1.08 (0.14), residues: 1344 sheet: -0.55 (0.22), residues: 514 loop : -0.75 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 434 TYR 0.021 0.001 TYR C 193 PHE 0.078 0.002 PHE D 70 TRP 0.018 0.001 TRP A1191 HIS 0.008 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01224 / 0.46 (33156) covalent geometry : angle 0.56413 / 0.30 (44999) hydrogen bonds : bond 0.03680 / 2.45 ( 1336) hydrogen bonds : angle 4.44596 / 3.21 ( 3711) metal coordination : bond 0.00576 / 0.37 ( 32) metal coordination : angle 4.19130 / 2.75 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 378 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LEU cc_start: 0.6860 (mt) cc_final: 0.6493 (tp) REVERT: A 437 MET cc_start: 0.8510 (mmm) cc_final: 0.8178 (mmm) REVERT: A 453 MET cc_start: 0.8815 (mpp) cc_final: 0.8140 (mpp) REVERT: A 618 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: A 688 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6655 (ttpt) REVERT: A 830 LYS cc_start: 0.8528 (mmtt) cc_final: 0.7867 (mtpp) REVERT: A 838 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8578 (tt0) REVERT: A 873 MET cc_start: 0.8586 (mmm) cc_final: 0.7858 (mmm) REVERT: A 890 ASP cc_start: 0.7867 (t0) cc_final: 0.7589 (t0) REVERT: A 912 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6764 (pp) REVERT: A 969 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: A 1039 LYS cc_start: 0.8342 (tttt) cc_final: 0.7879 (ttpp) REVERT: A 1110 ASN cc_start: 0.8629 (m-40) cc_final: 0.8261 (p0) REVERT: A 1111 MET cc_start: 0.8494 (ttp) cc_final: 0.8225 (tmm) REVERT: A 1259 MET cc_start: 0.5831 (mtp) cc_final: 0.5442 (mmp) REVERT: A 1285 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7411 (ttp) REVERT: B 61 ASP cc_start: 0.7808 (m-30) cc_final: 0.7469 (m-30) REVERT: B 89 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6358 (tm-30) REVERT: B 272 THR cc_start: 0.8362 (m) cc_final: 0.8058 (p) REVERT: B 422 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6637 (mtpp) REVERT: B 434 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6885 (mtm110) REVERT: B 451 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8150 (ptpp) REVERT: B 531 GLN cc_start: 0.7408 (pm20) cc_final: 0.7122 (tp40) REVERT: B 542 MET cc_start: 0.8954 (mmm) cc_final: 0.8584 (mtt) REVERT: B 552 MET cc_start: 0.7910 (mmm) cc_final: 0.6800 (ttp) REVERT: B 621 GLU cc_start: 0.8471 (tp30) cc_final: 0.7498 (tp30) REVERT: B 950 ASP cc_start: 0.8480 (t0) cc_final: 0.8175 (t0) REVERT: B 951 GLN cc_start: 0.8250 (mt0) cc_final: 0.7348 (mm-40) REVERT: B 958 GLN cc_start: 0.7764 (tt0) cc_final: 0.7345 (tp40) REVERT: C 89 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6838 (pm20) REVERT: C 123 ASN cc_start: 0.7987 (t0) cc_final: 0.7445 (m-40) REVERT: E 48 ASP cc_start: 0.7680 (t70) cc_final: 0.7338 (t0) REVERT: E 50 MET cc_start: 0.7527 (tmm) cc_final: 0.7046 (mpp) REVERT: E 132 ILE cc_start: 0.9260 (mm) cc_final: 0.9016 (mm) REVERT: F 119 ARG cc_start: 0.8336 (tpp80) cc_final: 0.7420 (mmm160) REVERT: F 128 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8078 (mmtt) REVERT: G 115 MET cc_start: 0.5294 (ppp) cc_final: 0.4468 (ptt) REVERT: H 52 GLN cc_start: 0.8621 (mp10) cc_final: 0.7809 (mp10) REVERT: H 128 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7464 (p0) REVERT: I 13 MET cc_start: 0.7562 (ptp) cc_final: 0.7235 (ptp) REVERT: I 17 ARG cc_start: 0.6030 (ttt180) cc_final: 0.5351 (ptm-80) REVERT: L 27 LEU cc_start: 0.6658 (mm) cc_final: 0.6212 (mm) outliers start: 62 outliers final: 46 residues processed: 414 average time/residue: 0.2280 time to fit residues: 150.7513 Evaluate side-chains 414 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 274 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 chunk 375 optimal weight: 0.0060 chunk 160 optimal weight: 8.9990 chunk 356 optimal weight: 8.9990 chunk 220 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 GLN A 587 HIS E 114 ASN K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108612 restraints weight = 47213.685| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.31 r_work: 0.3276 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.019 33188 Z= 0.449 Angle : 0.554 24.075 45044 Z= 0.293 Chirality : 0.043 0.788 5063 Planarity : 0.004 0.049 5640 Dihedral : 11.930 136.305 4901 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 1.24 % Allowed : 12.63 % Favored : 86.13 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.01 (0.14), residues: 3893 helix: 1.25 (0.15), residues: 1351 sheet: -0.52 (0.22), residues: 513 loop : -0.68 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 434 TYR 0.027 0.001 TYR B 769 PHE 0.078 0.001 PHE D 70 TRP 0.013 0.001 TRP A1191 HIS 0.009 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01188 / 0.45 (33156) covalent geometry : angle 0.54105 / 0.29 (44999) hydrogen bonds : bond 0.03273 / 2.20 ( 1336) hydrogen bonds : angle 4.31724 / 3.11 ( 3711) metal coordination : bond 0.00359 / 0.22 ( 32) metal coordination : angle 3.87165 / 2.51 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7786 Ramachandran restraints generated. 3893 Oldfield, 0 Emsley, 3893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 396 time to evaluate : 1.341 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: A 65 LEU cc_start: 0.8490 (mt) cc_final: 0.7913 (mm) REVERT: A 199 LEU cc_start: 0.6712 (mt) cc_final: 0.6318 (tp) REVERT: A 293 GLU cc_start: 0.8224 (tt0) cc_final: 0.7858 (tt0) REVERT: A 437 MET cc_start: 0.8457 (mmm) cc_final: 0.8114 (mmm) REVERT: A 453 MET cc_start: 0.8795 (mpp) cc_final: 0.8099 (mpp) REVERT: A 618 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: A 688 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6611 (ttpt) REVERT: A 830 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7782 (mtpp) REVERT: A 838 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8576 (tt0) REVERT: A 873 MET cc_start: 0.8447 (mmm) cc_final: 0.7703 (mmm) REVERT: A 890 ASP cc_start: 0.7823 (t0) cc_final: 0.7554 (t0) REVERT: A 912 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6791 (pp) REVERT: A 1039 LYS cc_start: 0.8335 (tttt) cc_final: 0.7788 (ttpp) REVERT: A 1110 ASN cc_start: 0.8606 (m-40) cc_final: 0.8267 (p0) REVERT: A 1259 MET cc_start: 0.5780 (mtp) cc_final: 0.5422 (mmp) REVERT: A 1285 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7308 (ttp) REVERT: B 272 THR cc_start: 0.8338 (m) cc_final: 0.8014 (p) REVERT: B 381 MET cc_start: 0.8902 (mtp) cc_final: 0.8642 (mtp) REVERT: B 422 LYS cc_start: 0.7122 (mmtm) cc_final: 0.6568 (mtpp) REVERT: B 451 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8120 (ptpp) REVERT: B 531 GLN cc_start: 0.7426 (pm20) cc_final: 0.7145 (tp40) REVERT: B 552 MET cc_start: 0.7875 (mmm) cc_final: 0.6737 (ttp) REVERT: B 621 GLU cc_start: 0.8414 (tp30) cc_final: 0.7631 (tp30) REVERT: B 951 GLN cc_start: 0.8174 (mt0) cc_final: 0.7369 (mm-40) REVERT: B 958 GLN cc_start: 0.7622 (tt0) cc_final: 0.7283 (tp40) REVERT: C 47 ASP cc_start: 0.9017 (t70) cc_final: 0.8731 (t0) REVERT: C 89 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6926 (pm20) REVERT: C 123 ASN cc_start: 0.7992 (t0) cc_final: 0.7456 (m-40) REVERT: E 48 ASP cc_start: 0.7879 (t70) cc_final: 0.7472 (t0) REVERT: E 50 MET cc_start: 0.7480 (tmm) cc_final: 0.7010 (mpp) REVERT: F 119 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7385 (mmm160) REVERT: F 128 LYS cc_start: 0.8352 (mmtp) cc_final: 0.8029 (mmtt) REVERT: G 115 MET cc_start: 0.5187 (ppp) cc_final: 0.4401 (ptt) REVERT: H 52 GLN cc_start: 0.8675 (mp10) cc_final: 0.7849 (mp10) REVERT: H 128 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7461 (p0) REVERT: I 13 MET cc_start: 0.7518 (ptp) cc_final: 0.7219 (ptp) REVERT: I 17 ARG cc_start: 0.6023 (ttt180) cc_final: 0.5339 (ptm-80) REVERT: I 97 MET cc_start: 0.4903 (mtt) cc_final: 0.4580 (mtt) REVERT: J 32 GLU cc_start: 0.7700 (mp0) cc_final: 0.7230 (mp0) outliers start: 43 outliers final: 25 residues processed: 420 average time/residue: 0.2236 time to fit residues: 150.7187 Evaluate side-chains 399 residues out of total 3468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 370 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 305 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 chunk 392 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS E 54 GLN E 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105075 restraints weight = 47256.900| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.23 r_work: 0.3220 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.017 33188 Z= 0.496 Angle : 0.642 24.043 45044 Z= 0.333 Chirality : 0.047 0.781 5063 Planarity : 0.004 0.050 5640 Dihedral : 12.017 135.087 4901 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 13.18 % Favored : 85.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 3893 helix: 1.06 (0.14), residues: 1344 sheet: -0.67 (0.22), residues: 544 loop : -0.75 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 434 TYR 0.026 0.002 TYR B 769 PHE 0.077 0.002 PHE D 70 TRP 0.034 0.002 TRP A1191 HIS 0.011 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01299 / 0.50 (33156) covalent geometry : angle 0.62551 / 0.33 (44999) hydrogen bonds : bond 0.04016 / 2.67 ( 1336) hydrogen bonds : angle 4.49178 / 3.24 ( 3711) metal coordination : bond 0.00767 / 0.51 ( 32) metal coordination : angle 4.62136 / 3.06 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11817.75 seconds wall clock time: 202 minutes 0.69 seconds (12120.69 seconds total)