Starting phenix.real_space_refine on Sat Feb 7 14:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7f_62148/02_2026/9k7f_62148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7f_62148/02_2026/9k7f_62148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k7f_62148/02_2026/9k7f_62148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7f_62148/02_2026/9k7f_62148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k7f_62148/02_2026/9k7f_62148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7f_62148/02_2026/9k7f_62148.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.061 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 64 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 20620 2.51 5 N 5744 2.21 5 O 6394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33011 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11153 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1351} Chain breaks: 4 Chain: "B" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9400 Classifications: {'peptide': 1179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1126} Chain breaks: 5 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 436 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 92.020 78.068 24.396 1.00124.39 S ATOM 844 SG CYS A 110 94.348 80.942 23.839 1.00128.12 S ATOM 1149 SG CYS A 148 91.202 80.792 21.761 1.00135.65 S ATOM 1287 SG CYS A 167 93.866 78.148 21.207 1.00141.84 S ATOM 515 SG CYS A 67 112.206 77.288 67.565 1.00110.82 S ATOM 537 SG CYS A 70 111.991 80.856 68.857 1.00122.04 S ATOM 590 SG CYS A 77 108.791 78.817 68.416 1.00112.13 S ATOM 20059 SG CYS B1163 107.570 91.155 56.873 1.00105.54 S ATOM 20077 SG CYS B1166 105.919 88.368 55.191 1.00102.96 S ATOM 20202 SG CYS B1182 109.567 88.013 56.782 1.00 87.28 S ATOM 20221 SG CYS B1185 108.838 89.794 53.462 1.00115.81 S ATOM 21200 SG CYS C 86 88.291 76.314 132.737 1.00128.79 S ATOM 21217 SG CYS C 88 89.910 73.846 130.321 1.00129.78 S ATOM 21250 SG CYS C 92 88.641 72.849 133.824 1.00117.97 S ATOM 21273 SG CYS C 95 86.178 73.637 130.988 1.00112.20 S ATOM 28940 SG CYS I 7 35.991 38.530 26.403 1.00169.75 S ATOM 28965 SG CYS I 10 39.784 38.003 26.578 1.00173.46 S ATOM 29131 SG CYS I 29 38.426 41.221 25.073 1.00181.55 S ATOM 29155 SG CYS I 32 37.969 37.973 23.256 1.00170.71 S ATOM 29482 SG CYS I 75 12.942 51.273 61.986 1.00112.08 S ATOM 29504 SG CYS I 78 11.404 47.634 62.283 1.00121.21 S ATOM 29720 SG CYS I 103 14.787 48.777 64.036 1.00120.72 S ATOM 29740 SG CYS I 106 14.096 48.054 60.279 1.00121.92 S ATOM 29885 SG CYS J 7 58.364 68.302 117.344 1.00 79.40 S ATOM 29908 SG CYS J 10 57.855 70.449 120.421 1.00 76.10 S ATOM 30188 SG CYS J 45 55.071 70.181 117.785 1.00 95.73 S ATOM 30194 SG CYS J 46 56.042 67.377 120.309 1.00 82.36 S ATOM 31374 SG CYS L 31 86.540 36.963 105.081 1.00 96.23 S ATOM 31394 SG CYS L 34 86.054 33.590 107.044 1.00 90.44 S ATOM 31498 SG CYS L 48 89.514 34.679 105.730 1.00 92.93 S ATOM 31521 SG CYS L 51 86.682 33.399 103.595 1.00102.36 S Time building chain proxies: 6.62, per 1000 atoms: 0.20 Number of scatterers: 33011 At special positions: 0 Unit cell: (165.54, 156.24, 155.31, 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 180 16.00 P 64 15.00 Mg 1 11.99 O 6394 8.00 N 5744 7.00 C 20620 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: 2.88 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7492 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 50 sheets defined 39.4% alpha, 19.8% beta 30 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 4.090A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.514A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 418 through 422 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: 3.706A 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: 3.776A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.769A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.615A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.527A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.127A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix removed outlier: 3.644A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.664A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.588A pdb=" N ALA A1125 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.590A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 3.578A pdb=" N GLU A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.981A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.586A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.075A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.661A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.929A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.690A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.464A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.301A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.853A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.582A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.556A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.229A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.640A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.636A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.168A pdb=" N THR B 882 " --> pdb=" O ARG B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.824A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 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: 3.809A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.595A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 3 through 27 removed outlier: 3.562A 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 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 137 through 141 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: 3.733A 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 75 through 79 removed outlier: 3.678A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.553A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.551A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 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 53 removed outlier: 4.191A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.669A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.594A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.548A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 6.070A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 5.936A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.564A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.211A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.411A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.668A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.815A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 6.238A pdb=" N ILE A1238 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A1193 " --> pdb=" O ILE A1238 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS A1240 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP A1191 " --> pdb=" O CYS A1240 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL A1242 " --> pdb=" O SER A1189 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE A1148 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU I 47 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.041A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.041A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.972A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.358A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.808A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.808A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.987A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.562A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.524A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.867A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.261A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.567A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF1, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.958A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF3, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 1440 hydrogen bonds defined for protein. 3945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 9.17 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9949 1.33 - 1.45: 5112 1.45 - 1.57: 18256 1.57 - 1.69: 124 1.69 - 1.81: 288 Bond restraints: 33729 Sorted by residual: bond pdb=" CA VAL E 124 " pdb=" CB VAL E 124 " ideal model delta sigma weight residual 1.534 1.557 -0.022 6.80e-03 2.16e+04 1.09e+01 bond pdb=" CA PRO A 242 " pdb=" C PRO A 242 " ideal model delta sigma weight residual 1.514 1.504 0.010 5.50e-03 3.31e+04 3.62e+00 bond pdb=" CB VAL B 952 " pdb=" CG2 VAL B 952 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.08e+00 bond pdb=" C ALA B 900 " pdb=" N PRO B 901 " ideal model delta sigma weight residual 1.330 1.349 -0.018 1.19e-02 7.06e+03 2.39e+00 bond pdb=" C GLN E 174 " pdb=" N LEU E 175 " ideal model delta sigma weight residual 1.331 1.291 0.040 2.83e-02 1.25e+03 2.03e+00 ... (remaining 33724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 45164 2.02 - 4.04: 606 4.04 - 6.05: 40 6.05 - 8.07: 4 8.07 - 10.09: 1 Bond angle restraints: 45815 Sorted by residual: angle pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta sigma weight residual 122.15 132.24 -10.09 2.83e+00 1.25e-01 1.27e+01 angle pdb=" N VAL G 92 " pdb=" CA VAL G 92 " pdb=" C VAL G 92 " ideal model delta sigma weight residual 113.53 110.10 3.43 9.80e-01 1.04e+00 1.23e+01 angle pdb=" C SER B 732 " pdb=" N HIS B 733 " pdb=" CA HIS B 733 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" CA ASP B 894 " pdb=" C ASP B 894 " pdb=" O ASP B 894 " ideal model delta sigma weight residual 121.50 117.39 4.11 1.25e+00 6.40e-01 1.08e+01 angle pdb=" CA ASP B 894 " pdb=" C ASP B 894 " pdb=" N ASP B 895 " ideal model delta sigma weight residual 116.58 121.06 -4.48 1.55e+00 4.16e-01 8.37e+00 ... (remaining 45810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 20010 34.74 - 69.47: 487 69.47 - 104.21: 36 104.21 - 138.94: 0 138.94 - 173.68: 3 Dihedral angle restraints: 20536 sinusoidal: 8967 harmonic: 11569 Sorted by residual: dihedral pdb=" CA GLN B 115 " pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO I 76 " pdb=" C PRO I 76 " pdb=" N LYS I 77 " pdb=" CA LYS I 77 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 20533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3157 0.034 - 0.069: 1362 0.069 - 0.103: 436 0.103 - 0.137: 192 0.137 - 0.171: 9 Chirality restraints: 5156 Sorted by residual: chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE A 607 " pdb=" N ILE A 607 " pdb=" C ILE A 607 " pdb=" CB ILE A 607 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CB THR A1266 " pdb=" CA THR A1266 " pdb=" OG1 THR A1266 " pdb=" CG2 THR A1266 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 5153 not shown) Planarity restraints: 5718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO A 245 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1264 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C GLU A1264 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU A1264 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A1265 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 99 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ILE A 99 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE A 99 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 100 " 0.013 2.00e-02 2.50e+03 ... (remaining 5715 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 579 2.66 - 3.22: 31608 3.22 - 3.78: 52266 3.78 - 4.34: 73944 4.34 - 4.90: 119392 Nonbonded interactions: 277789 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.103 2.170 nonbonded pdb=" OG1 THR B 487 " pdb=" O ALA B 777 " model vdw 2.130 3.040 nonbonded pdb=" NH2 ARG A 469 " pdb=" O GLY B 991 " model vdw 2.148 3.120 nonbonded pdb=" OD1 ASP B 837 " pdb=" NH2 ARG B1020 " model vdw 2.169 3.120 nonbonded pdb=" OD1 ASP A 485 " pdb=" O2' C P 12 " model vdw 2.173 3.040 ... (remaining 277784 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: 2.110 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 37.840 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33761 Z= 0.179 Angle : 0.590 16.058 45860 Z= 0.311 Chirality : 0.044 0.171 5156 Planarity : 0.004 0.056 5718 Dihedral : 14.923 173.679 13044 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.81 (0.14), residues: 3939 helix: 1.50 (0.14), residues: 1339 sheet: -0.22 (0.20), residues: 674 loop : 0.27 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 123 TYR 0.026 0.002 TYR B 797 PHE 0.022 0.002 PHE B 963 TRP 0.017 0.002 TRP E 79 HIS 0.007 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00402 (33729) covalent geometry : angle 0.57247 (45815) hydrogen bonds : bond 0.13049 ( 1477) hydrogen bonds : angle 5.92064 ( 4083) metal coordination : bond 0.00601 ( 32) metal coordination : angle 4.63228 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7969 (mmm) cc_final: 0.7342 (mmm) REVERT: A 63 ARG cc_start: 0.7906 (tpm170) cc_final: 0.7623 (tpm170) REVERT: A 75 ASN cc_start: 0.8622 (t0) cc_final: 0.8293 (t0) REVERT: A 234 MET cc_start: 0.9121 (mtm) cc_final: 0.8909 (mtp) REVERT: A 290 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 593 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8770 (tm-30) REVERT: A 727 ASP cc_start: 0.8778 (m-30) cc_final: 0.8424 (m-30) REVERT: A 829 VAL cc_start: 0.7832 (t) cc_final: 0.7613 (m) REVERT: A 838 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8706 (tp-100) REVERT: A 966 ASN cc_start: 0.8547 (m-40) cc_final: 0.8311 (m-40) REVERT: A 1144 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8869 (pptt) REVERT: A 1209 MET cc_start: 0.8685 (mmm) cc_final: 0.8205 (tpp) REVERT: A 1241 ARG cc_start: 0.6491 (mtt-85) cc_final: 0.6164 (mmt180) REVERT: A 1281 ARG cc_start: 0.8033 (tmm-80) cc_final: 0.7722 (tmm160) REVERT: B 65 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7488 (tp30) REVERT: B 96 TYR cc_start: 0.8577 (m-10) cc_final: 0.8372 (m-80) REVERT: B 309 GLN cc_start: 0.8162 (mp10) cc_final: 0.7550 (mp10) REVERT: B 332 ASP cc_start: 0.9061 (t0) cc_final: 0.8689 (t0) REVERT: B 358 LYS cc_start: 0.9127 (mttt) cc_final: 0.8843 (tptt) REVERT: B 370 PHE cc_start: 0.8124 (m-80) cc_final: 0.7897 (m-80) REVERT: B 391 ASP cc_start: 0.8144 (m-30) cc_final: 0.7793 (p0) REVERT: B 422 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7691 (ttmm) REVERT: B 426 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7407 (tppt) REVERT: B 592 ASN cc_start: 0.8362 (t0) cc_final: 0.7577 (t0) REVERT: B 622 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8210 (mtpt) REVERT: B 665 GLU cc_start: 0.8412 (tt0) cc_final: 0.8107 (tm-30) REVERT: B 959 ASP cc_start: 0.8642 (t0) cc_final: 0.8068 (t0) REVERT: B 1153 GLU cc_start: 0.8121 (mp0) cc_final: 0.7908 (mp0) REVERT: C 106 GLU cc_start: 0.8347 (pm20) cc_final: 0.8077 (pm20) REVERT: C 121 VAL cc_start: 0.9001 (t) cc_final: 0.8783 (m) REVERT: D 58 VAL cc_start: 0.7820 (t) cc_final: 0.7424 (p) REVERT: E 50 MET cc_start: 0.8135 (mpp) cc_final: 0.7730 (tmm) REVERT: E 121 MET cc_start: 0.8745 (mmp) cc_final: 0.8492 (tpp) REVERT: E 192 ARG cc_start: 0.8507 (ptm-80) cc_final: 0.8214 (ttp80) REVERT: E 215 MET cc_start: 0.7744 (mmt) cc_final: 0.6668 (pp-130) REVERT: H 100 THR cc_start: 0.9309 (t) cc_final: 0.9005 (p) REVERT: H 105 GLU cc_start: 0.8440 (tt0) cc_final: 0.8205 (tt0) REVERT: H 106 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8015 (mm-30) REVERT: I 47 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7818 (tp30) REVERT: J 26 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8330 (tp-100) REVERT: J 32 GLU cc_start: 0.8748 (mp0) cc_final: 0.8484 (mp0) REVERT: K 88 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7868 (mttm) REVERT: L 38 LEU cc_start: 0.8116 (mt) cc_final: 0.7769 (mt) outliers start: 0 outliers final: 1 residues processed: 724 average time/residue: 0.8652 time to fit residues: 719.0759 Evaluate side-chains 447 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 896 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 776 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN B1104 HIS E 5 ASN E 101 GLN E 114 ASN E 179 GLN F 104 ASN G 158 HIS H 137 GLN I 90 GLN J 23 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.120389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078751 restraints weight = 56797.458| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.64 r_work: 0.3031 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33761 Z= 0.182 Angle : 0.633 16.065 45860 Z= 0.326 Chirality : 0.044 0.176 5156 Planarity : 0.005 0.064 5718 Dihedral : 13.207 173.425 5074 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.54 % Allowed : 11.29 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.80 (0.14), residues: 3939 helix: 1.49 (0.14), residues: 1348 sheet: -0.25 (0.20), residues: 687 loop : 0.28 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 7 TYR 0.020 0.002 TYR H 129 PHE 0.024 0.002 PHE A 219 TRP 0.016 0.002 TRP B 308 HIS 0.009 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00425 (33729) covalent geometry : angle 0.61489 (45815) hydrogen bonds : bond 0.04463 ( 1477) hydrogen bonds : angle 4.91519 ( 4083) metal coordination : bond 0.00597 ( 32) metal coordination : angle 4.81627 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 503 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8123 (mmm) cc_final: 0.7509 (mmm) REVERT: A 63 ARG cc_start: 0.7875 (tpm170) cc_final: 0.7580 (tpm170) REVERT: A 75 ASN cc_start: 0.8640 (t0) cc_final: 0.8284 (t0) REVERT: A 234 MET cc_start: 0.9106 (mtm) cc_final: 0.8887 (mtp) REVERT: A 264 PHE cc_start: 0.8619 (m-80) cc_final: 0.8331 (m-10) REVERT: A 281 HIS cc_start: 0.9041 (t-90) cc_final: 0.8821 (t-90) REVERT: A 291 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8290 (pt0) REVERT: A 593 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8904 (tm-30) REVERT: A 727 ASP cc_start: 0.8934 (m-30) cc_final: 0.8604 (m-30) REVERT: A 838 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8625 (tp-100) REVERT: A 1144 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8876 (pptt) REVERT: A 1151 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7091 (mt-10) REVERT: A 1191 TRP cc_start: 0.7798 (m100) cc_final: 0.7449 (m100) REVERT: A 1196 GLU cc_start: 0.7162 (mp0) cc_final: 0.6866 (mp0) REVERT: A 1209 MET cc_start: 0.8582 (mmm) cc_final: 0.7937 (tpp) REVERT: A 1285 MET cc_start: 0.8361 (ttm) cc_final: 0.8022 (ttm) REVERT: A 1442 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8280 (t0) REVERT: B 135 ARG cc_start: 0.8688 (mmt90) cc_final: 0.8363 (mmt90) REVERT: B 309 GLN cc_start: 0.8265 (mp10) cc_final: 0.7952 (mp10) REVERT: B 332 ASP cc_start: 0.9113 (t0) cc_final: 0.8889 (t70) REVERT: B 336 ARG cc_start: 0.8536 (ttm110) cc_final: 0.7941 (mmt-90) REVERT: B 358 LYS cc_start: 0.9039 (mttt) cc_final: 0.8803 (tptt) REVERT: B 391 ASP cc_start: 0.8294 (m-30) cc_final: 0.7604 (p0) REVERT: B 393 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8506 (mttm) REVERT: B 422 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7696 (ttmm) REVERT: B 426 LYS cc_start: 0.7548 (ttpt) cc_final: 0.7300 (tppt) REVERT: B 552 MET cc_start: 0.9088 (tpp) cc_final: 0.8658 (mpp) REVERT: B 615 MET cc_start: 0.8913 (mtp) cc_final: 0.8708 (mtm) REVERT: B 622 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8183 (mtmt) REVERT: B 665 GLU cc_start: 0.8291 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 943 SER cc_start: 0.9297 (m) cc_final: 0.8921 (t) REVERT: B 959 ASP cc_start: 0.8890 (t0) cc_final: 0.8566 (t0) REVERT: B 1189 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7975 (pp) REVERT: C 16 ASP cc_start: 0.8276 (p0) cc_final: 0.7998 (p0) REVERT: C 19 ASP cc_start: 0.8264 (t0) cc_final: 0.7931 (t0) REVERT: C 106 GLU cc_start: 0.8574 (pm20) cc_final: 0.8200 (pm20) REVERT: C 121 VAL cc_start: 0.9012 (t) cc_final: 0.8735 (m) REVERT: C 125 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: C 152 GLU cc_start: 0.8278 (tp30) cc_final: 0.7850 (tp30) REVERT: C 217 ASP cc_start: 0.9189 (m-30) cc_final: 0.8987 (m-30) REVERT: D 156 ASP cc_start: 0.8120 (p0) cc_final: 0.7649 (p0) REVERT: D 158 GLU cc_start: 0.8736 (mp0) cc_final: 0.8283 (mp0) REVERT: E 50 MET cc_start: 0.8288 (mpp) cc_final: 0.8032 (tmm) REVERT: E 52 ARG cc_start: 0.9001 (mpt180) cc_final: 0.8602 (mmt180) REVERT: E 192 ARG cc_start: 0.8884 (ptm-80) cc_final: 0.8497 (ttp80) REVERT: E 215 MET cc_start: 0.7803 (mmt) cc_final: 0.6565 (pp-130) REVERT: F 70 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8591 (pptt) REVERT: F 110 ASP cc_start: 0.7989 (t0) cc_final: 0.7739 (t0) REVERT: G 17 PHE cc_start: 0.9055 (m-10) cc_final: 0.8747 (m-10) REVERT: G 71 ASN cc_start: 0.8485 (t0) cc_final: 0.8222 (t0) REVERT: H 80 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8616 (mtm180) REVERT: H 87 ARG cc_start: 0.8119 (mmp-170) cc_final: 0.7890 (mmp80) REVERT: H 100 THR cc_start: 0.9343 (t) cc_final: 0.9123 (p) REVERT: H 106 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8091 (mm-30) REVERT: I 74 GLU cc_start: 0.8266 (tp30) cc_final: 0.7920 (tp30) REVERT: I 92 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7056 (ttp-170) REVERT: J 26 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8394 (tp-100) REVERT: J 32 GLU cc_start: 0.8736 (mp0) cc_final: 0.8536 (mp0) REVERT: K 2 ASN cc_start: 0.8979 (m-40) cc_final: 0.8645 (m110) REVERT: L 28 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8307 (mmmt) REVERT: L 38 LEU cc_start: 0.7427 (mt) cc_final: 0.6887 (mt) REVERT: L 47 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8071 (mtp180) outliers start: 54 outliers final: 17 residues processed: 525 average time/residue: 0.8803 time to fit residues: 534.9287 Evaluate side-chains 454 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 433 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 186 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 347 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN B1093 GLN E 179 GLN F 104 ASN G 71 ASN I 90 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077313 restraints weight = 56698.419| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.62 r_work: 0.2993 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33761 Z= 0.200 Angle : 0.617 15.631 45860 Z= 0.316 Chirality : 0.045 0.211 5156 Planarity : 0.005 0.065 5718 Dihedral : 13.131 172.351 5072 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.94 % Allowed : 12.89 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.71 (0.14), residues: 3939 helix: 1.36 (0.14), residues: 1351 sheet: -0.29 (0.19), residues: 687 loop : 0.26 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1274 TYR 0.021 0.001 TYR B1092 PHE 0.026 0.002 PHE A 219 TRP 0.012 0.001 TRP B 308 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00470 (33729) covalent geometry : angle 0.59917 (45815) hydrogen bonds : bond 0.04345 ( 1477) hydrogen bonds : angle 4.81077 ( 4083) metal coordination : bond 0.00670 ( 32) metal coordination : angle 4.76013 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 461 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8188 (mmm) cc_final: 0.7628 (mmm) REVERT: A 63 ARG cc_start: 0.7709 (tpm170) cc_final: 0.7442 (tpm170) REVERT: A 124 GLN cc_start: 0.8636 (mp10) cc_final: 0.8408 (mp10) REVERT: A 234 MET cc_start: 0.9096 (mtm) cc_final: 0.8876 (mtp) REVERT: A 264 PHE cc_start: 0.8592 (m-80) cc_final: 0.8315 (m-10) REVERT: A 281 HIS cc_start: 0.9037 (t-90) cc_final: 0.8834 (t-90) REVERT: A 593 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 727 ASP cc_start: 0.8948 (m-30) cc_final: 0.8645 (m-30) REVERT: A 838 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8623 (tp-100) REVERT: A 1144 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8933 (pptt) REVERT: A 1151 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 1209 MET cc_start: 0.8555 (mmm) cc_final: 0.7954 (tpp) REVERT: A 1285 MET cc_start: 0.8272 (ttm) cc_final: 0.7897 (ttm) REVERT: A 1442 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8403 (t0) REVERT: B 135 ARG cc_start: 0.8674 (mmt90) cc_final: 0.8319 (mmt90) REVERT: B 309 GLN cc_start: 0.8387 (mp10) cc_final: 0.8139 (mp10) REVERT: B 322 PHE cc_start: 0.8449 (t80) cc_final: 0.8078 (OUTLIER) REVERT: B 336 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8339 (tpp-160) REVERT: B 358 LYS cc_start: 0.9026 (mttt) cc_final: 0.8784 (tptt) REVERT: B 391 ASP cc_start: 0.8269 (m-30) cc_final: 0.7702 (p0) REVERT: B 426 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7319 (tppt) REVERT: B 468 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: B 615 MET cc_start: 0.8929 (mtp) cc_final: 0.8676 (mtm) REVERT: B 622 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8237 (mtmt) REVERT: B 665 GLU cc_start: 0.8294 (tt0) cc_final: 0.7985 (tm-30) REVERT: B 666 TYR cc_start: 0.8562 (m-80) cc_final: 0.8119 (m-80) REVERT: B 908 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8144 (tp30) REVERT: B 943 SER cc_start: 0.9308 (m) cc_final: 0.8969 (t) REVERT: B 959 ASP cc_start: 0.8939 (t0) cc_final: 0.8631 (t0) REVERT: B 1189 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8136 (pp) REVERT: C 16 ASP cc_start: 0.8337 (p0) cc_final: 0.8114 (p0) REVERT: C 125 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: C 152 GLU cc_start: 0.8329 (tp30) cc_final: 0.7902 (tp30) REVERT: C 217 ASP cc_start: 0.9159 (m-30) cc_final: 0.8903 (m-30) REVERT: D 51 ASN cc_start: 0.7314 (p0) cc_final: 0.7110 (p0) REVERT: D 145 MET cc_start: 0.8030 (ppp) cc_final: 0.7808 (ppp) REVERT: D 155 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7308 (tpp80) REVERT: D 158 GLU cc_start: 0.8749 (mp0) cc_final: 0.8533 (mp0) REVERT: E 50 MET cc_start: 0.8329 (mpp) cc_final: 0.8065 (tmm) REVERT: E 52 ARG cc_start: 0.8973 (mpt180) cc_final: 0.8693 (mmt180) REVERT: E 192 ARG cc_start: 0.8909 (ptm-80) cc_final: 0.8506 (ttp80) REVERT: E 215 MET cc_start: 0.7771 (mmt) cc_final: 0.6564 (pp-130) REVERT: F 70 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8578 (pptt) REVERT: F 110 ASP cc_start: 0.8101 (t0) cc_final: 0.7831 (t0) REVERT: F 122 MET cc_start: 0.8837 (mtm) cc_final: 0.8609 (mtp) REVERT: G 21 ARG cc_start: 0.8713 (pmm-80) cc_final: 0.8420 (ptm-80) REVERT: G 69 GLU cc_start: 0.8539 (tt0) cc_final: 0.8260 (pt0) REVERT: G 71 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8079 (t0) REVERT: H 80 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8590 (mtm180) REVERT: H 106 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8224 (mm-30) REVERT: I 8 ARG cc_start: 0.8099 (ppt170) cc_final: 0.7591 (pmt-80) REVERT: I 17 ARG cc_start: 0.5152 (tpm-80) cc_final: 0.4576 (tpp-160) REVERT: I 74 GLU cc_start: 0.8281 (tp30) cc_final: 0.7946 (tp30) REVERT: I 77 LYS cc_start: 0.9206 (mtpp) cc_final: 0.8775 (ttpp) REVERT: I 91 ARG cc_start: 0.8548 (tpp-160) cc_final: 0.8324 (tpp-160) REVERT: I 94 ASP cc_start: 0.8509 (p0) cc_final: 0.8076 (p0) REVERT: J 26 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8414 (tp-100) REVERT: L 28 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8337 (mmmt) REVERT: L 38 LEU cc_start: 0.7445 (mt) cc_final: 0.6896 (mt) REVERT: L 47 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8284 (mtp85) REVERT: L 57 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (mt) REVERT: L 63 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7621 (ptp-170) outliers start: 68 outliers final: 22 residues processed: 491 average time/residue: 0.8762 time to fit residues: 499.7673 Evaluate side-chains 439 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 411 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 376 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 GLN B 932 HIS B1093 GLN E 114 ASN E 179 GLN F 104 ASN H 43 ASN H 133 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077036 restraints weight = 56646.361| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.62 r_work: 0.2998 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33761 Z= 0.185 Angle : 0.597 14.679 45860 Z= 0.307 Chirality : 0.044 0.235 5156 Planarity : 0.004 0.066 5718 Dihedral : 13.110 171.613 5072 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 1.94 % Allowed : 14.38 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.72 (0.14), residues: 3939 helix: 1.39 (0.14), residues: 1345 sheet: -0.29 (0.19), residues: 687 loop : 0.25 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 68 TYR 0.021 0.001 TYR I 15 PHE 0.026 0.002 PHE A 219 TRP 0.022 0.002 TRP A1191 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00436 (33729) covalent geometry : angle 0.58007 (45815) hydrogen bonds : bond 0.04176 ( 1477) hydrogen bonds : angle 4.73891 ( 4083) metal coordination : bond 0.00621 ( 32) metal coordination : angle 4.52715 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 434 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7731 (tpm170) cc_final: 0.7451 (tpm170) REVERT: A 124 GLN cc_start: 0.8655 (mp10) cc_final: 0.8325 (mp10) REVERT: A 175 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7422 (mmt90) REVERT: A 234 MET cc_start: 0.9097 (mtm) cc_final: 0.8882 (mtp) REVERT: A 264 PHE cc_start: 0.8583 (m-80) cc_final: 0.8331 (m-10) REVERT: A 291 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8212 (pt0) REVERT: A 593 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8882 (tm-30) REVERT: A 727 ASP cc_start: 0.8951 (m-30) cc_final: 0.8657 (m-30) REVERT: A 838 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8653 (tp-100) REVERT: A 1144 LYS cc_start: 0.9313 (ttmt) cc_final: 0.8926 (pptt) REVERT: A 1151 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 1209 MET cc_start: 0.8565 (mmm) cc_final: 0.7936 (tpp) REVERT: A 1442 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8370 (t0) REVERT: B 309 GLN cc_start: 0.8393 (mp10) cc_final: 0.8160 (mp10) REVERT: B 322 PHE cc_start: 0.8495 (t80) cc_final: 0.8162 (t80) REVERT: B 336 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8318 (tpp-160) REVERT: B 358 LYS cc_start: 0.9012 (mttt) cc_final: 0.8782 (tptt) REVERT: B 391 ASP cc_start: 0.8291 (m-30) cc_final: 0.7780 (p0) REVERT: B 426 LYS cc_start: 0.7676 (ttpt) cc_final: 0.7360 (tppt) REVERT: B 468 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: B 622 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8257 (mtmt) REVERT: B 665 GLU cc_start: 0.8332 (tt0) cc_final: 0.8006 (tm-30) REVERT: B 666 TYR cc_start: 0.8580 (m-80) cc_final: 0.8182 (m-80) REVERT: B 908 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8141 (tp30) REVERT: B 943 SER cc_start: 0.9334 (m) cc_final: 0.8997 (t) REVERT: B 959 ASP cc_start: 0.8959 (t0) cc_final: 0.8648 (t0) REVERT: B 1189 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8208 (pp) REVERT: C 16 ASP cc_start: 0.8358 (p0) cc_final: 0.8114 (p0) REVERT: C 125 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: C 152 GLU cc_start: 0.8379 (tp30) cc_final: 0.7962 (tp30) REVERT: C 217 ASP cc_start: 0.9186 (m-30) cc_final: 0.8914 (m-30) REVERT: D 51 ASN cc_start: 0.7289 (p0) cc_final: 0.7024 (p0) REVERT: D 145 MET cc_start: 0.8037 (ppp) cc_final: 0.7763 (ppp) REVERT: D 158 GLU cc_start: 0.8765 (mp0) cc_final: 0.8548 (mp0) REVERT: E 5 ASN cc_start: 0.9508 (t0) cc_final: 0.9080 (t160) REVERT: E 50 MET cc_start: 0.8363 (mpp) cc_final: 0.8080 (tmm) REVERT: E 52 ARG cc_start: 0.8995 (mpt180) cc_final: 0.8371 (mpt180) REVERT: E 192 ARG cc_start: 0.8903 (ptm-80) cc_final: 0.8480 (ttp80) REVERT: E 215 MET cc_start: 0.7774 (mmt) cc_final: 0.6585 (pp-130) REVERT: F 70 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8624 (pptt) REVERT: F 103 MET cc_start: 0.9047 (mtt) cc_final: 0.8806 (mtt) REVERT: F 110 ASP cc_start: 0.8192 (t0) cc_final: 0.7879 (t0) REVERT: F 122 MET cc_start: 0.8876 (mtm) cc_final: 0.8616 (mtp) REVERT: F 127 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: G 4 ILE cc_start: 0.8188 (pp) cc_final: 0.7800 (mp) REVERT: G 21 ARG cc_start: 0.8718 (pmm-80) cc_final: 0.8369 (ptm-80) REVERT: G 71 ASN cc_start: 0.8270 (t0) cc_final: 0.8039 (t0) REVERT: G 75 ARG cc_start: 0.8398 (mmt90) cc_final: 0.8019 (mmt90) REVERT: H 80 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8577 (mtm180) REVERT: H 100 THR cc_start: 0.9296 (m) cc_final: 0.8955 (p) REVERT: H 106 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8246 (mm-30) REVERT: H 138 GLU cc_start: 0.8202 (pt0) cc_final: 0.7725 (pm20) REVERT: I 8 ARG cc_start: 0.8171 (ppt170) cc_final: 0.7666 (pmt-80) REVERT: I 17 ARG cc_start: 0.5388 (tpm-80) cc_final: 0.4915 (tpp-160) REVERT: I 65 ASP cc_start: 0.8339 (t0) cc_final: 0.8134 (t0) REVERT: I 74 GLU cc_start: 0.8292 (tp30) cc_final: 0.7923 (tp30) REVERT: I 91 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8407 (tpp-160) REVERT: I 92 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7761 (ttm170) REVERT: J 26 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8503 (tp-100) REVERT: K 108 GLU cc_start: 0.8933 (tp30) cc_final: 0.8598 (tp30) REVERT: L 28 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8330 (mmmt) REVERT: L 38 LEU cc_start: 0.7460 (mt) cc_final: 0.6800 (mt) REVERT: L 47 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8459 (mtp85) outliers start: 68 outliers final: 26 residues processed: 469 average time/residue: 0.8266 time to fit residues: 452.1904 Evaluate side-chains 450 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 418 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain L residue 43 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 249 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 283 optimal weight: 0.8980 chunk 329 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1093 GLN E 179 GLN F 104 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.117370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076002 restraints weight = 56539.699| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.61 r_work: 0.2983 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33761 Z= 0.226 Angle : 0.620 14.348 45860 Z= 0.317 Chirality : 0.045 0.175 5156 Planarity : 0.004 0.066 5718 Dihedral : 13.107 170.718 5072 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 2.03 % Allowed : 15.29 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.62 (0.14), residues: 3939 helix: 1.28 (0.14), residues: 1357 sheet: -0.40 (0.19), residues: 694 loop : 0.23 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1239 TYR 0.021 0.001 TYR I 15 PHE 0.026 0.002 PHE A 219 TRP 0.024 0.002 TRP A1191 HIS 0.006 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00534 (33729) covalent geometry : angle 0.60237 (45815) hydrogen bonds : bond 0.04292 ( 1477) hydrogen bonds : angle 4.77138 ( 4083) metal coordination : bond 0.00786 ( 32) metal coordination : angle 4.66374 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 445 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7746 (tpm170) cc_final: 0.7469 (tpm170) REVERT: A 124 GLN cc_start: 0.8713 (mp10) cc_final: 0.8326 (mp10) REVERT: A 151 ASP cc_start: 0.8258 (m-30) cc_final: 0.7953 (p0) REVERT: A 175 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7485 (mmt90) REVERT: A 234 MET cc_start: 0.9102 (mtm) cc_final: 0.8890 (mtp) REVERT: A 316 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7279 (tm-30) REVERT: A 593 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 609 ASP cc_start: 0.8956 (t0) cc_final: 0.8541 (t70) REVERT: A 727 ASP cc_start: 0.8946 (m-30) cc_final: 0.8634 (m-30) REVERT: A 1144 LYS cc_start: 0.9340 (ttmt) cc_final: 0.8917 (pptt) REVERT: A 1151 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 1209 MET cc_start: 0.8534 (mmm) cc_final: 0.7887 (tpp) REVERT: B 96 TYR cc_start: 0.8983 (m-80) cc_final: 0.8750 (m-80) REVERT: B 101 MET cc_start: 0.9057 (mtm) cc_final: 0.8680 (mtm) REVERT: B 309 GLN cc_start: 0.8425 (mp10) cc_final: 0.8223 (mp10) REVERT: B 322 PHE cc_start: 0.8556 (t80) cc_final: 0.8253 (t80) REVERT: B 336 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8333 (tpp-160) REVERT: B 358 LYS cc_start: 0.9029 (mttt) cc_final: 0.8762 (tptt) REVERT: B 391 ASP cc_start: 0.8376 (m-30) cc_final: 0.7860 (p0) REVERT: B 426 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7370 (tppt) REVERT: B 468 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: B 615 MET cc_start: 0.8915 (mtp) cc_final: 0.8678 (mtm) REVERT: B 662 MET cc_start: 0.9221 (mmm) cc_final: 0.8813 (mtp) REVERT: B 666 TYR cc_start: 0.8623 (m-80) cc_final: 0.8325 (m-80) REVERT: B 884 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8567 (mtm-85) REVERT: B 908 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8147 (tp30) REVERT: B 943 SER cc_start: 0.9374 (m) cc_final: 0.9054 (t) REVERT: B 959 ASP cc_start: 0.8963 (t0) cc_final: 0.8648 (t0) REVERT: B 1189 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8347 (pp) REVERT: C 16 ASP cc_start: 0.8366 (p0) cc_final: 0.8160 (p0) REVERT: C 106 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: C 125 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8365 (mmm) REVERT: C 152 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: C 217 ASP cc_start: 0.9181 (m-30) cc_final: 0.8924 (m-30) REVERT: D 141 LEU cc_start: 0.8468 (mm) cc_final: 0.7567 (pp) REVERT: D 145 MET cc_start: 0.8060 (ppp) cc_final: 0.7810 (ppp) REVERT: D 158 GLU cc_start: 0.8781 (mp0) cc_final: 0.8535 (mp0) REVERT: E 5 ASN cc_start: 0.9500 (t0) cc_final: 0.9197 (t160) REVERT: E 50 MET cc_start: 0.8350 (mpp) cc_final: 0.8130 (tmm) REVERT: E 52 ARG cc_start: 0.9012 (mpt180) cc_final: 0.8575 (mmt180) REVERT: E 192 ARG cc_start: 0.8868 (ptm-80) cc_final: 0.8478 (ttp80) REVERT: E 215 MET cc_start: 0.7798 (mmt) cc_final: 0.6654 (pp-130) REVERT: F 110 ASP cc_start: 0.8178 (t0) cc_final: 0.7879 (t0) REVERT: F 118 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8251 (tp) REVERT: F 122 MET cc_start: 0.8883 (mtm) cc_final: 0.8568 (mtp) REVERT: G 1 MET cc_start: 0.7414 (tmt) cc_final: 0.7078 (ptm) REVERT: G 4 ILE cc_start: 0.8294 (pp) cc_final: 0.7990 (mp) REVERT: G 21 ARG cc_start: 0.8762 (pmm-80) cc_final: 0.8472 (ptm-80) REVERT: G 71 ASN cc_start: 0.8510 (t0) cc_final: 0.8173 (t0) REVERT: H 80 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8580 (mtm180) REVERT: H 100 THR cc_start: 0.9289 (m) cc_final: 0.8917 (p) REVERT: H 106 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8266 (mm-30) REVERT: I 17 ARG cc_start: 0.5427 (tpm-80) cc_final: 0.4988 (tpp-160) REVERT: I 74 GLU cc_start: 0.8311 (tp30) cc_final: 0.7922 (tp30) REVERT: I 92 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7982 (ttm170) REVERT: J 26 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8460 (tp-100) REVERT: K 108 GLU cc_start: 0.8954 (tp30) cc_final: 0.8612 (tp30) REVERT: L 28 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8394 (mmmt) REVERT: L 38 LEU cc_start: 0.7582 (mt) cc_final: 0.6998 (mt) REVERT: L 47 ARG cc_start: 0.8768 (mtp85) cc_final: 0.8559 (mtp85) REVERT: L 63 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7541 (ptp-170) outliers start: 71 outliers final: 29 residues processed: 482 average time/residue: 0.8284 time to fit residues: 466.6683 Evaluate side-chains 441 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 405 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 276 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 367 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 171 GLN B1093 GLN D 138 ASN D 165 GLN E 179 GLN F 104 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.118801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077708 restraints weight = 56113.268| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.61 r_work: 0.3000 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33761 Z= 0.146 Angle : 0.588 12.340 45860 Z= 0.301 Chirality : 0.043 0.160 5156 Planarity : 0.004 0.066 5718 Dihedral : 13.055 169.875 5072 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 1.94 % Allowed : 16.09 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.73 (0.14), residues: 3939 helix: 1.41 (0.14), residues: 1356 sheet: -0.27 (0.20), residues: 669 loop : 0.23 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1239 TYR 0.024 0.001 TYR E 187 PHE 0.025 0.001 PHE G 79 TRP 0.029 0.001 TRP A1191 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00342 (33729) covalent geometry : angle 0.57302 (45815) hydrogen bonds : bond 0.03866 ( 1477) hydrogen bonds : angle 4.63488 ( 4083) metal coordination : bond 0.00468 ( 32) metal coordination : angle 4.19896 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 451 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8329 (mmm) cc_final: 0.7835 (mmm) REVERT: A 63 ARG cc_start: 0.7707 (tpm170) cc_final: 0.7471 (tpm170) REVERT: A 124 GLN cc_start: 0.8752 (mp10) cc_final: 0.8349 (mp10) REVERT: A 151 ASP cc_start: 0.8189 (m-30) cc_final: 0.7931 (p0) REVERT: A 175 ARG cc_start: 0.7820 (mmt90) cc_final: 0.7456 (mmt90) REVERT: A 234 MET cc_start: 0.9079 (mtm) cc_final: 0.8859 (mtp) REVERT: A 264 PHE cc_start: 0.8499 (m-80) cc_final: 0.8257 (m-10) REVERT: A 291 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8128 (pt0) REVERT: A 316 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7594 (tp-100) REVERT: A 592 ASP cc_start: 0.8751 (m-30) cc_final: 0.8534 (m-30) REVERT: A 593 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8850 (tm-30) REVERT: A 609 ASP cc_start: 0.8960 (t0) cc_final: 0.8534 (t70) REVERT: A 727 ASP cc_start: 0.8924 (m-30) cc_final: 0.8618 (m-30) REVERT: A 1144 LYS cc_start: 0.9343 (ttmt) cc_final: 0.8857 (pptt) REVERT: A 1151 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7148 (mt-10) REVERT: A 1209 MET cc_start: 0.8533 (mmm) cc_final: 0.7956 (tpp) REVERT: A 1281 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7947 (tmm160) REVERT: A 1287 TYR cc_start: 0.8232 (m-80) cc_final: 0.7921 (m-80) REVERT: A 1330 ASN cc_start: 0.8294 (m-40) cc_final: 0.8072 (m-40) REVERT: B 96 TYR cc_start: 0.8976 (m-80) cc_final: 0.8761 (m-80) REVERT: B 101 MET cc_start: 0.9004 (mtm) cc_final: 0.8673 (mtm) REVERT: B 322 PHE cc_start: 0.8632 (t80) cc_final: 0.8315 (t80) REVERT: B 336 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8352 (tpp-160) REVERT: B 358 LYS cc_start: 0.8997 (mttt) cc_final: 0.8758 (tptt) REVERT: B 391 ASP cc_start: 0.8286 (m-30) cc_final: 0.7790 (p0) REVERT: B 426 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7430 (tppt) REVERT: B 451 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7827 (tttp) REVERT: B 468 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6640 (pt0) REVERT: B 615 MET cc_start: 0.8920 (mtp) cc_final: 0.8705 (mtm) REVERT: B 789 MET cc_start: 0.8879 (mmm) cc_final: 0.8565 (mmt) REVERT: B 908 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8121 (tp30) REVERT: B 943 SER cc_start: 0.9342 (m) cc_final: 0.9009 (t) REVERT: B 959 ASP cc_start: 0.8933 (t0) cc_final: 0.8617 (t0) REVERT: B 1189 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8301 (pp) REVERT: C 16 ASP cc_start: 0.8321 (p0) cc_final: 0.8117 (p0) REVERT: C 106 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: C 125 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8357 (mmm) REVERT: C 152 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: C 217 ASP cc_start: 0.9134 (m-30) cc_final: 0.8844 (m-30) REVERT: D 56 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7481 (ttm110) REVERT: D 141 LEU cc_start: 0.8468 (mm) cc_final: 0.7646 (pp) REVERT: D 145 MET cc_start: 0.8089 (ppp) cc_final: 0.7809 (ppp) REVERT: D 158 GLU cc_start: 0.8797 (mp0) cc_final: 0.8542 (mp0) REVERT: E 3 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8614 (pm20) REVERT: E 22 MET cc_start: 0.9359 (ttm) cc_final: 0.9055 (ptm) REVERT: E 52 ARG cc_start: 0.8996 (mpt180) cc_final: 0.8610 (mpt180) REVERT: E 192 ARG cc_start: 0.8882 (ptm-80) cc_final: 0.8471 (ttp80) REVERT: E 215 MET cc_start: 0.7737 (mmt) cc_final: 0.6614 (pp-130) REVERT: F 110 ASP cc_start: 0.8290 (t0) cc_final: 0.7916 (t0) REVERT: F 118 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (tp) REVERT: F 122 MET cc_start: 0.8834 (mtm) cc_final: 0.8523 (mtp) REVERT: F 127 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8819 (pm20) REVERT: F 155 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7498 (pt) REVERT: G 1 MET cc_start: 0.7233 (tmt) cc_final: 0.6959 (ptm) REVERT: G 21 ARG cc_start: 0.8756 (pmm-80) cc_final: 0.8385 (ptm-80) REVERT: G 71 ASN cc_start: 0.8465 (t0) cc_final: 0.8133 (t0) REVERT: H 80 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8562 (mtm180) REVERT: H 100 THR cc_start: 0.9244 (m) cc_final: 0.8853 (p) REVERT: H 106 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8245 (mm-30) REVERT: H 138 GLU cc_start: 0.8190 (pt0) cc_final: 0.7917 (pm20) REVERT: I 74 GLU cc_start: 0.8318 (tp30) cc_final: 0.7956 (tp30) REVERT: J 26 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8359 (tp-100) REVERT: K 108 GLU cc_start: 0.8960 (tp30) cc_final: 0.8620 (tp30) REVERT: L 28 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8374 (mmmt) REVERT: L 38 LEU cc_start: 0.7449 (mt) cc_final: 0.6880 (mt) outliers start: 68 outliers final: 21 residues processed: 488 average time/residue: 0.7378 time to fit residues: 420.8507 Evaluate side-chains 449 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 419 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 134 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 350 optimal weight: 0.0470 chunk 135 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 333 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 114 ASN E 179 GLN F 104 ASN G 102 GLN I 90 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077078 restraints weight = 55657.879| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.63 r_work: 0.2941 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33761 Z= 0.135 Angle : 0.592 11.117 45860 Z= 0.303 Chirality : 0.042 0.159 5156 Planarity : 0.004 0.067 5718 Dihedral : 13.011 168.640 5072 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 1.88 % Allowed : 16.89 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.81 (0.14), residues: 3939 helix: 1.48 (0.14), residues: 1352 sheet: -0.21 (0.19), residues: 685 loop : 0.28 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1215 TYR 0.022 0.001 TYR E 187 PHE 0.025 0.001 PHE A 219 TRP 0.031 0.001 TRP A1191 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00314 (33729) covalent geometry : angle 0.57942 (45815) hydrogen bonds : bond 0.03722 ( 1477) hydrogen bonds : angle 4.57845 ( 4083) metal coordination : bond 0.00426 ( 32) metal coordination : angle 3.93048 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 445 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8322 (mmm) cc_final: 0.7824 (mmm) REVERT: A 63 ARG cc_start: 0.7697 (tpm170) cc_final: 0.7456 (tpm170) REVERT: A 124 GLN cc_start: 0.8699 (mp10) cc_final: 0.8269 (mp10) REVERT: A 151 ASP cc_start: 0.8255 (m-30) cc_final: 0.7966 (p0) REVERT: A 175 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7463 (mmt90) REVERT: A 234 MET cc_start: 0.8986 (mtm) cc_final: 0.8777 (mtp) REVERT: A 264 PHE cc_start: 0.8482 (m-80) cc_final: 0.8228 (m-80) REVERT: A 592 ASP cc_start: 0.8755 (m-30) cc_final: 0.8546 (m-30) REVERT: A 593 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 727 ASP cc_start: 0.8927 (m-30) cc_final: 0.8618 (m-30) REVERT: A 1144 LYS cc_start: 0.9337 (ttmt) cc_final: 0.8815 (pptt) REVERT: A 1209 MET cc_start: 0.8462 (mmm) cc_final: 0.7827 (tpp) REVERT: A 1285 MET cc_start: 0.8008 (ttm) cc_final: 0.7059 (tmm) REVERT: B 96 TYR cc_start: 0.8965 (m-80) cc_final: 0.8763 (m-80) REVERT: B 101 MET cc_start: 0.9006 (mtm) cc_final: 0.8681 (mtm) REVERT: B 322 PHE cc_start: 0.8644 (t80) cc_final: 0.8332 (t80) REVERT: B 336 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8349 (tpp-160) REVERT: B 358 LYS cc_start: 0.9003 (mttt) cc_final: 0.8727 (tptt) REVERT: B 391 ASP cc_start: 0.8280 (m-30) cc_final: 0.7765 (p0) REVERT: B 396 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: B 426 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7363 (tppt) REVERT: B 451 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7863 (tttp) REVERT: B 468 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6437 (pt0) REVERT: B 570 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 574 SER cc_start: 0.9380 (m) cc_final: 0.8951 (p) REVERT: B 615 MET cc_start: 0.8907 (mtp) cc_final: 0.8688 (mtm) REVERT: B 789 MET cc_start: 0.8820 (mmm) cc_final: 0.8587 (mmt) REVERT: B 864 LYS cc_start: 0.8500 (mmmt) cc_final: 0.7985 (tptp) REVERT: B 908 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8120 (tp30) REVERT: B 943 SER cc_start: 0.9383 (m) cc_final: 0.9048 (t) REVERT: B 959 ASP cc_start: 0.8937 (t0) cc_final: 0.8626 (t0) REVERT: C 106 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: C 125 MET cc_start: 0.8579 (mtm) cc_final: 0.8355 (mmm) REVERT: C 152 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: C 217 ASP cc_start: 0.9147 (m-30) cc_final: 0.8828 (m-30) REVERT: D 56 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7733 (ptp-170) REVERT: D 141 LEU cc_start: 0.8472 (mm) cc_final: 0.7666 (pp) REVERT: D 145 MET cc_start: 0.8070 (ppp) cc_final: 0.7664 (ppp) REVERT: D 158 GLU cc_start: 0.8907 (mp0) cc_final: 0.8663 (mp0) REVERT: E 3 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8676 (pm20) REVERT: E 22 MET cc_start: 0.9326 (ttm) cc_final: 0.9081 (ptm) REVERT: E 50 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7722 (tmm) REVERT: E 52 ARG cc_start: 0.8915 (mpt180) cc_final: 0.8701 (mmt180) REVERT: E 192 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8439 (ttp80) REVERT: E 215 MET cc_start: 0.7725 (mmt) cc_final: 0.6613 (pp-130) REVERT: F 110 ASP cc_start: 0.8277 (t0) cc_final: 0.7892 (t0) REVERT: F 122 MET cc_start: 0.8803 (mtm) cc_final: 0.8514 (mtp) REVERT: F 127 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8811 (pm20) REVERT: G 21 ARG cc_start: 0.8762 (pmm-80) cc_final: 0.8359 (ptm-80) REVERT: G 71 ASN cc_start: 0.8425 (t0) cc_final: 0.8084 (t0) REVERT: H 8 ASP cc_start: 0.8050 (t0) cc_final: 0.7624 (t0) REVERT: H 80 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8568 (mtm180) REVERT: H 100 THR cc_start: 0.9237 (m) cc_final: 0.8795 (p) REVERT: H 106 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8211 (mm-30) REVERT: H 138 GLU cc_start: 0.8227 (pt0) cc_final: 0.7899 (pm20) REVERT: I 74 GLU cc_start: 0.8324 (tp30) cc_final: 0.7933 (tp30) REVERT: J 26 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8533 (tp-100) REVERT: K 108 GLU cc_start: 0.8922 (tp30) cc_final: 0.8558 (tp30) REVERT: L 63 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7463 (ptp-170) outliers start: 66 outliers final: 22 residues processed: 478 average time/residue: 0.8147 time to fit residues: 456.5842 Evaluate side-chains 443 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 413 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 2 optimal weight: 0.4980 chunk 329 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 328 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 104 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.117885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075978 restraints weight = 55665.653| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.63 r_work: 0.2931 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33761 Z= 0.159 Angle : 0.611 12.498 45860 Z= 0.311 Chirality : 0.043 0.162 5156 Planarity : 0.004 0.067 5718 Dihedral : 12.995 167.399 5072 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.51 % Allowed : 18.05 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.79 (0.14), residues: 3939 helix: 1.45 (0.14), residues: 1351 sheet: -0.23 (0.19), residues: 687 loop : 0.28 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 7 TYR 0.025 0.001 TYR E 187 PHE 0.025 0.001 PHE A 219 TRP 0.031 0.001 TRP A1191 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00373 (33729) covalent geometry : angle 0.59775 (45815) hydrogen bonds : bond 0.03818 ( 1477) hydrogen bonds : angle 4.57613 ( 4083) metal coordination : bond 0.00524 ( 32) metal coordination : angle 4.02513 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 430 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8398 (mmm) cc_final: 0.7900 (mmm) REVERT: A 63 ARG cc_start: 0.7698 (tpm170) cc_final: 0.7459 (tpm170) REVERT: A 124 GLN cc_start: 0.8714 (mp10) cc_final: 0.8261 (mp10) REVERT: A 151 ASP cc_start: 0.8268 (m-30) cc_final: 0.8019 (p0) REVERT: A 175 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7501 (mmt90) REVERT: A 293 GLU cc_start: 0.8458 (tt0) cc_final: 0.8132 (mt-10) REVERT: A 592 ASP cc_start: 0.8787 (m-30) cc_final: 0.8551 (m-30) REVERT: A 593 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8790 (tm-30) REVERT: A 609 ASP cc_start: 0.8954 (t0) cc_final: 0.8477 (t70) REVERT: A 727 ASP cc_start: 0.8919 (m-30) cc_final: 0.8613 (m-30) REVERT: A 1144 LYS cc_start: 0.9338 (ttmt) cc_final: 0.8838 (pptt) REVERT: A 1202 MET cc_start: 0.8748 (mpp) cc_final: 0.7845 (mpp) REVERT: A 1209 MET cc_start: 0.8482 (mmm) cc_final: 0.7776 (tpp) REVERT: A 1281 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.8142 (tmm-80) REVERT: A 1285 MET cc_start: 0.7926 (ttm) cc_final: 0.7017 (tmm) REVERT: B 322 PHE cc_start: 0.8671 (t80) cc_final: 0.8365 (t80) REVERT: B 336 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8357 (tpp-160) REVERT: B 358 LYS cc_start: 0.9023 (mttt) cc_final: 0.8731 (tptt) REVERT: B 391 ASP cc_start: 0.8287 (m-30) cc_final: 0.7830 (p0) REVERT: B 396 ASP cc_start: 0.8472 (m-30) cc_final: 0.8036 (m-30) REVERT: B 426 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7417 (tppt) REVERT: B 451 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7913 (tttp) REVERT: B 468 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6539 (pt0) REVERT: B 570 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8509 (m) REVERT: B 574 SER cc_start: 0.9377 (m) cc_final: 0.8952 (p) REVERT: B 864 LYS cc_start: 0.8487 (mmmt) cc_final: 0.7901 (tptp) REVERT: B 908 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8070 (tp30) REVERT: B 943 SER cc_start: 0.9386 (m) cc_final: 0.9052 (t) REVERT: B 959 ASP cc_start: 0.8928 (t0) cc_final: 0.8617 (t0) REVERT: C 106 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: C 125 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8413 (mmm) REVERT: C 152 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: C 217 ASP cc_start: 0.9131 (m-30) cc_final: 0.8830 (m-30) REVERT: D 141 LEU cc_start: 0.8520 (mm) cc_final: 0.7740 (pp) REVERT: D 158 GLU cc_start: 0.8916 (mp0) cc_final: 0.8662 (mp0) REVERT: E 3 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8749 (pm20) REVERT: E 22 MET cc_start: 0.9314 (ttm) cc_final: 0.9037 (ptm) REVERT: E 52 ARG cc_start: 0.8881 (mpt180) cc_final: 0.8610 (mpt180) REVERT: E 192 ARG cc_start: 0.8849 (ptm-80) cc_final: 0.8440 (ttp80) REVERT: E 215 MET cc_start: 0.7742 (mmt) cc_final: 0.6693 (pp-130) REVERT: F 110 ASP cc_start: 0.8284 (t0) cc_final: 0.7892 (t0) REVERT: F 122 MET cc_start: 0.8821 (mtm) cc_final: 0.8569 (mtp) REVERT: F 127 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: F 155 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7476 (pt) REVERT: G 21 ARG cc_start: 0.8762 (pmm-80) cc_final: 0.8542 (ptm-80) REVERT: G 24 GLN cc_start: 0.8688 (tp40) cc_final: 0.8462 (tp-100) REVERT: G 69 GLU cc_start: 0.8268 (tt0) cc_final: 0.7892 (pt0) REVERT: G 71 ASN cc_start: 0.8430 (t0) cc_final: 0.8098 (t0) REVERT: H 80 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8574 (mtm180) REVERT: H 100 THR cc_start: 0.9236 (m) cc_final: 0.8833 (p) REVERT: H 106 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8202 (mm-30) REVERT: H 129 TYR cc_start: 0.8447 (p90) cc_final: 0.7451 (p90) REVERT: H 136 LYS cc_start: 0.8153 (pttm) cc_final: 0.7697 (ptpp) REVERT: H 138 GLU cc_start: 0.8231 (pt0) cc_final: 0.7811 (pm20) REVERT: I 45 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7978 (tpp80) REVERT: I 74 GLU cc_start: 0.8353 (tp30) cc_final: 0.7974 (tp30) REVERT: I 87 GLN cc_start: 0.7357 (pp30) cc_final: 0.6573 (pp30) REVERT: J 26 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8750 (tp-100) REVERT: K 108 GLU cc_start: 0.8934 (tp30) cc_final: 0.8576 (tp30) REVERT: L 28 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8203 (mmmt) REVERT: L 47 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8018 (ttt90) outliers start: 53 outliers final: 27 residues processed: 455 average time/residue: 0.7910 time to fit residues: 421.4658 Evaluate side-chains 451 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 416 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 325 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN E 5 ASN E 179 GLN F 104 ASN I 90 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075050 restraints weight = 55707.002| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.63 r_work: 0.2911 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33761 Z= 0.202 Angle : 0.642 13.455 45860 Z= 0.326 Chirality : 0.044 0.242 5156 Planarity : 0.004 0.067 5718 Dihedral : 13.017 167.264 5072 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 18.17 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.73 (0.14), residues: 3939 helix: 1.38 (0.14), residues: 1354 sheet: -0.27 (0.19), residues: 673 loop : 0.25 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1239 TYR 0.026 0.001 TYR E 187 PHE 0.026 0.002 PHE A 219 TRP 0.035 0.001 TRP A1191 HIS 0.006 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00478 (33729) covalent geometry : angle 0.62862 (45815) hydrogen bonds : bond 0.04052 ( 1477) hydrogen bonds : angle 4.64555 ( 4083) metal coordination : bond 0.00671 ( 32) metal coordination : angle 4.19023 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 416 time to evaluate : 1.354 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 41 MET cc_start: 0.8420 (mmm) cc_final: 0.7922 (mmm) REVERT: A 63 ARG cc_start: 0.7735 (tpm170) cc_final: 0.7467 (tpm170) REVERT: A 124 GLN cc_start: 0.8704 (mp10) cc_final: 0.8285 (mp10) REVERT: A 151 ASP cc_start: 0.8283 (m-30) cc_final: 0.8036 (p0) REVERT: A 175 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7524 (mmt90) REVERT: A 592 ASP cc_start: 0.8819 (m-30) cc_final: 0.8575 (m-30) REVERT: A 593 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8819 (tm-30) REVERT: A 609 ASP cc_start: 0.8943 (t0) cc_final: 0.8478 (t70) REVERT: A 727 ASP cc_start: 0.8922 (m-30) cc_final: 0.8621 (m-30) REVERT: A 1144 LYS cc_start: 0.9354 (ttmt) cc_final: 0.8871 (pptt) REVERT: A 1202 MET cc_start: 0.8754 (mpp) cc_final: 0.7860 (mpp) REVERT: A 1209 MET cc_start: 0.8452 (mmm) cc_final: 0.7742 (tpp) REVERT: A 1281 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8168 (tmm-80) REVERT: A 1285 MET cc_start: 0.7931 (ttm) cc_final: 0.7026 (tmm) REVERT: B 225 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7493 (t) REVERT: B 322 PHE cc_start: 0.8738 (t80) cc_final: 0.8449 (t80) REVERT: B 336 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8366 (tpp-160) REVERT: B 358 LYS cc_start: 0.9029 (mttt) cc_final: 0.8731 (tptt) REVERT: B 391 ASP cc_start: 0.8283 (m-30) cc_final: 0.7819 (p0) REVERT: B 396 ASP cc_start: 0.8498 (m-30) cc_final: 0.8100 (m-30) REVERT: B 426 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7431 (tppt) REVERT: B 451 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7919 (tttp) REVERT: B 570 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8593 (m) REVERT: B 574 SER cc_start: 0.9368 (m) cc_final: 0.8944 (p) REVERT: B 908 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8086 (tp30) REVERT: B 943 SER cc_start: 0.9396 (m) cc_final: 0.9074 (t) REVERT: B 959 ASP cc_start: 0.8943 (t0) cc_final: 0.8636 (t0) REVERT: C 106 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: C 125 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (mmm) REVERT: C 152 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: C 217 ASP cc_start: 0.9115 (m-30) cc_final: 0.8853 (m-30) REVERT: D 56 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8181 (ptm160) REVERT: D 141 LEU cc_start: 0.8549 (mm) cc_final: 0.7677 (pp) REVERT: D 158 GLU cc_start: 0.8903 (mp0) cc_final: 0.8660 (mp0) REVERT: E 3 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8735 (pm20) REVERT: E 48 ASP cc_start: 0.9082 (p0) cc_final: 0.8291 (p0) REVERT: E 52 ARG cc_start: 0.8881 (mpt180) cc_final: 0.8575 (mmt180) REVERT: E 192 ARG cc_start: 0.8862 (ptm-80) cc_final: 0.8459 (ttp80) REVERT: E 215 MET cc_start: 0.7722 (mmt) cc_final: 0.6633 (pp-130) REVERT: F 110 ASP cc_start: 0.8314 (t0) cc_final: 0.7891 (t0) REVERT: F 122 MET cc_start: 0.8813 (mtm) cc_final: 0.8562 (mtp) REVERT: F 127 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8826 (pm20) REVERT: G 21 ARG cc_start: 0.8807 (pmm-80) cc_final: 0.8407 (ptm-80) REVERT: G 24 GLN cc_start: 0.8717 (tp40) cc_final: 0.8490 (tp-100) REVERT: G 71 ASN cc_start: 0.8435 (t0) cc_final: 0.8090 (t0) REVERT: H 80 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8572 (mtm180) REVERT: H 100 THR cc_start: 0.9228 (m) cc_final: 0.8820 (p) REVERT: H 106 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8227 (mm-30) REVERT: I 45 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7970 (tpp80) REVERT: I 74 GLU cc_start: 0.8356 (tp30) cc_final: 0.7925 (tp30) REVERT: I 87 GLN cc_start: 0.7361 (pp30) cc_final: 0.6641 (pp30) REVERT: J 26 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8749 (tp-100) REVERT: K 108 GLU cc_start: 0.8970 (tp30) cc_final: 0.8613 (tp30) REVERT: L 28 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8068 (mmmt) REVERT: L 47 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8071 (mtt90) REVERT: L 63 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7442 (ptm160) outliers start: 53 outliers final: 31 residues processed: 443 average time/residue: 0.8228 time to fit residues: 426.2926 Evaluate side-chains 444 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 406 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 85 optimal weight: 0.9990 chunk 343 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 382 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 368 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 179 GLN F 104 ASN I 90 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076953 restraints weight = 55860.366| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.65 r_work: 0.2942 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33761 Z= 0.132 Angle : 0.622 12.237 45860 Z= 0.318 Chirality : 0.043 0.226 5156 Planarity : 0.004 0.067 5718 Dihedral : 12.995 166.956 5072 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 1.17 % Allowed : 18.68 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.79 (0.14), residues: 3939 helix: 1.45 (0.14), residues: 1356 sheet: -0.24 (0.19), residues: 685 loop : 0.29 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 7 TYR 0.024 0.001 TYR E 187 PHE 0.025 0.001 PHE A 444 TRP 0.038 0.001 TRP A1191 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00309 (33729) covalent geometry : angle 0.61018 (45815) hydrogen bonds : bond 0.03747 ( 1477) hydrogen bonds : angle 4.57845 ( 4083) metal coordination : bond 0.00409 ( 32) metal coordination : angle 3.88410 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 429 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8427 (mmm) cc_final: 0.7961 (mmm) REVERT: A 63 ARG cc_start: 0.7714 (tpm170) cc_final: 0.7483 (tpm170) REVERT: A 124 GLN cc_start: 0.8719 (mp10) cc_final: 0.8266 (mp10) REVERT: A 151 ASP cc_start: 0.8250 (m-30) cc_final: 0.8026 (p0) REVERT: A 175 ARG cc_start: 0.7857 (mmt90) cc_final: 0.7504 (mmt90) REVERT: A 293 GLU cc_start: 0.8488 (tt0) cc_final: 0.8182 (mt-10) REVERT: A 592 ASP cc_start: 0.8781 (m-30) cc_final: 0.8578 (m-30) REVERT: A 593 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8564 (pp20) REVERT: A 609 ASP cc_start: 0.8958 (t0) cc_final: 0.8566 (t70) REVERT: A 727 ASP cc_start: 0.8897 (m-30) cc_final: 0.8595 (m-30) REVERT: A 1144 LYS cc_start: 0.9349 (ttmt) cc_final: 0.8836 (pptt) REVERT: A 1202 MET cc_start: 0.8732 (mpp) cc_final: 0.7835 (mpp) REVERT: A 1209 MET cc_start: 0.8459 (mmm) cc_final: 0.7737 (tpp) REVERT: A 1278 ASN cc_start: 0.8554 (t0) cc_final: 0.7678 (t0) REVERT: A 1285 MET cc_start: 0.7889 (ttm) cc_final: 0.6991 (tmm) REVERT: A 1297 GLU cc_start: 0.8635 (mp0) cc_final: 0.8321 (mp0) REVERT: B 101 MET cc_start: 0.9304 (mtm) cc_final: 0.8808 (tpp) REVERT: B 225 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7482 (t) REVERT: B 322 PHE cc_start: 0.8745 (t80) cc_final: 0.8459 (t80) REVERT: B 336 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8357 (tpp-160) REVERT: B 358 LYS cc_start: 0.9014 (mttt) cc_final: 0.8715 (tptt) REVERT: B 391 ASP cc_start: 0.8264 (m-30) cc_final: 0.7832 (p0) REVERT: B 396 ASP cc_start: 0.8478 (m-30) cc_final: 0.8135 (m-30) REVERT: B 426 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7413 (tppt) REVERT: B 451 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7903 (tttp) REVERT: B 570 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8473 (m) REVERT: B 574 SER cc_start: 0.9352 (m) cc_final: 0.8918 (p) REVERT: B 908 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8080 (tp30) REVERT: B 943 SER cc_start: 0.9389 (m) cc_final: 0.9051 (t) REVERT: B 959 ASP cc_start: 0.8936 (t0) cc_final: 0.8627 (t0) REVERT: C 106 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: C 125 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (mmm) REVERT: C 152 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: C 217 ASP cc_start: 0.9095 (m-30) cc_final: 0.8819 (m-30) REVERT: D 141 LEU cc_start: 0.8563 (mm) cc_final: 0.7812 (pp) REVERT: D 156 ASP cc_start: 0.8142 (p0) cc_final: 0.7561 (p0) REVERT: D 158 GLU cc_start: 0.8929 (mp0) cc_final: 0.8470 (mp0) REVERT: E 3 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8791 (pm20) REVERT: E 22 MET cc_start: 0.9281 (ttm) cc_final: 0.9018 (ptm) REVERT: E 58 MET cc_start: 0.8291 (ttm) cc_final: 0.7619 (mtp) REVERT: E 192 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8448 (ttp80) REVERT: E 215 MET cc_start: 0.7700 (mmt) cc_final: 0.6646 (pp-130) REVERT: F 77 ASP cc_start: 0.8732 (p0) cc_final: 0.8506 (p0) REVERT: F 78 GLN cc_start: 0.9040 (pt0) cc_final: 0.8551 (pt0) REVERT: F 110 ASP cc_start: 0.8337 (t0) cc_final: 0.7856 (t0) REVERT: F 122 MET cc_start: 0.8764 (mtm) cc_final: 0.8522 (mtp) REVERT: F 123 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8239 (ttmt) REVERT: F 127 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8805 (pm20) REVERT: G 21 ARG cc_start: 0.8797 (pmm-80) cc_final: 0.8441 (ptm-80) REVERT: G 24 GLN cc_start: 0.8682 (tp40) cc_final: 0.8447 (tp-100) REVERT: G 71 ASN cc_start: 0.8340 (t0) cc_final: 0.7984 (t0) REVERT: G 75 ARG cc_start: 0.8290 (mmt90) cc_final: 0.8074 (mmm-85) REVERT: H 8 ASP cc_start: 0.8047 (t70) cc_final: 0.7597 (t0) REVERT: H 80 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8565 (mtm180) REVERT: H 100 THR cc_start: 0.9202 (m) cc_final: 0.8763 (p) REVERT: H 106 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8224 (mm-30) REVERT: H 138 GLU cc_start: 0.8238 (pt0) cc_final: 0.7920 (pm20) REVERT: I 45 ARG cc_start: 0.8261 (tpp80) cc_final: 0.7933 (tpp80) REVERT: I 74 GLU cc_start: 0.8381 (tp30) cc_final: 0.8044 (tp30) REVERT: I 87 GLN cc_start: 0.7328 (pp30) cc_final: 0.6548 (pp30) REVERT: K 108 GLU cc_start: 0.8953 (tp30) cc_final: 0.8586 (tp30) REVERT: L 28 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7983 (mmmt) REVERT: L 47 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8078 (mtt90) REVERT: L 63 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7457 (ptm160) outliers start: 41 outliers final: 24 residues processed: 451 average time/residue: 0.8242 time to fit residues: 435.9439 Evaluate side-chains 444 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 413 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 86 optimal weight: 0.8980 chunk 286 optimal weight: 20.0000 chunk 281 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 351 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 245 optimal weight: 0.4980 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 179 GLN F 104 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077427 restraints weight = 55579.355| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.62 r_work: 0.2954 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33761 Z= 0.134 Angle : 0.626 23.002 45860 Z= 0.317 Chirality : 0.043 0.301 5156 Planarity : 0.004 0.067 5718 Dihedral : 12.967 167.482 5072 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.31 % Rotamer: Outliers : 1.00 % Allowed : 19.02 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.83 (0.14), residues: 3939 helix: 1.47 (0.14), residues: 1355 sheet: -0.20 (0.19), residues: 687 loop : 0.30 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1239 TYR 0.026 0.001 TYR G 51 PHE 0.025 0.001 PHE A 219 TRP 0.044 0.001 TRP A1191 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00312 (33729) covalent geometry : angle 0.61565 (45815) hydrogen bonds : bond 0.03674 ( 1477) hydrogen bonds : angle 4.54196 ( 4083) metal coordination : bond 0.00416 ( 32) metal coordination : angle 3.70623 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18350.07 seconds wall clock time: 311 minutes 52.12 seconds (18712.12 seconds total)