Starting phenix.real_space_refine on Sat Feb 24 20:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0w_34416/02_2024/8h0w_34416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0w_34416/02_2024/8h0w_34416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0w_34416/02_2024/8h0w_34416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0w_34416/02_2024/8h0w_34416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0w_34416/02_2024/8h0w_34416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0w_34416/02_2024/8h0w_34416.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 415 5.49 5 Mg 1 5.21 5 S 204 5.16 5 C 27898 2.51 5 N 8260 2.21 5 O 9578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46364 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11120 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 9261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9261 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 52, 'TRANS': 1108} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} 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: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 4212 Classifications: {'DNA': 205} Link IDs: {'rna3p': 204} Chain: "N" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 4007 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain breaks: 1 Chain: "a" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "u" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 525 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} 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 527 SG CYS A 67 118.464 61.782 157.206 1.00212.06 S ATOM 549 SG CYS A 70 121.929 60.692 156.366 1.00223.37 S ATOM 594 SG CYS A 77 121.344 64.287 157.497 1.00212.07 S ATOM 829 SG CYS A 107 104.946 85.153 117.143 1.00197.61 S ATOM 851 SG CYS A 110 105.336 81.557 115.837 1.00175.27 S ATOM 1157 SG CYS A 148 106.374 84.456 113.740 1.00197.34 S ATOM 1245 SG CYS A 168 102.607 84.066 114.516 1.00178.82 S ATOM 19913 SG CYS B1163 125.068 62.071 140.171 1.00275.71 S ATOM 19931 SG CYS B1166 123.189 65.340 140.300 1.00265.90 S ATOM 20054 SG CYS B1182 121.788 62.067 141.940 1.00264.26 S ATOM 20077 SG CYS B1185 121.976 62.488 138.119 1.00247.82 S ATOM 21022 SG CYS C 85 158.527 74.281 212.082 1.00259.18 S ATOM 21035 SG CYS C 87 154.791 74.287 211.418 1.00265.68 S ATOM 21070 SG CYS C 91 155.751 75.537 214.557 1.00232.29 S ATOM 21093 SG CYS C 94 156.474 77.645 211.585 1.00240.43 S ATOM 29179 SG CYS I 75 130.709 164.090 158.725 1.00771.26 S ATOM 29201 SG CYS I 78 128.811 166.433 161.695 1.00825.26 S ATOM 29417 SG CYS I 103 129.118 162.539 161.405 1.00739.64 S ATOM 29439 SG CYS I 106 126.933 164.950 158.693 1.00793.90 S ATOM 28631 SG CYS I 7 93.740 149.080 134.907 1.00467.38 S ATOM 28817 SG CYS I 29 94.070 145.456 132.156 1.00436.91 S ATOM 28842 SG CYS I 32 91.913 147.503 132.155 1.00474.88 S ATOM 29558 SG CYS J 7 154.966 108.107 201.314 1.00163.87 S ATOM 29581 SG CYS J 10 158.598 107.292 202.363 1.00156.45 S ATOM 29857 SG CYS J 44 157.863 110.335 200.049 1.00141.00 S ATOM 29863 SG CYS J 45 157.137 110.053 203.806 1.00146.86 S ATOM 31025 SG CYS L 33 113.953 93.818 207.874 1.00221.54 S ATOM 31040 SG CYS L 36 113.087 93.902 211.311 1.00228.85 S ATOM 31150 SG CYS L 50 112.107 90.947 208.224 1.00216.72 S ATOM 31174 SG CYS L 53 110.274 94.003 209.955 1.00209.29 S Time building chain proxies: 23.22, per 1000 atoms: 0.50 Number of scatterers: 46364 At special positions: 0 Unit cell: (220.52, 177.31, 238.4, 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 204 16.00 P 415 15.00 Mg 1 11.99 O 9578 8.00 N 8260 7.00 C 27898 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 - 3.50 Amino acid : False - 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: 19.34 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " 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 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " Number of angles added : 39 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8928 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 62 sheets defined 44.2% alpha, 16.2% beta 194 base pairs and 370 stacking pairs defined. Time for finding SS restraints: 18.21 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 126 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.091A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.771A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.615A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.976A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.633A pdb=" N THR A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.706A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.716A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.603A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 810 through 847 removed outlier: 3.964A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.642A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 4.119A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'A' and resid 1006 through 1017 Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.924A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.762A pdb=" N ASP A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.515A pdb=" N ALA A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1149 Processing helix chain 'A' and resid 1168 through 1174 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.904A pdb=" N LYS A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.798A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1274 Processing helix chain 'A' and resid 1315 through 1322 removed outlier: 3.537A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.519A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.057A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1406 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.901A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.999A pdb=" N ALA A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 53 removed outlier: 5.487A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.528A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.732A pdb=" N LYS B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.571A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.738A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.947A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 429 removed outlier: 4.343A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.729A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.516A pdb=" N ALA B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.312A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.552A pdb=" N GLY B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.738A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.885A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.593A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.537A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.578A pdb=" N LEU B 707 " --> pdb=" O PRO B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.554A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.921A 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 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 79 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 206 through 210 Processing helix chain 'C' and resid 239 through 264 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.905A pdb=" N LEU D 28 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.578A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 4.030A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 4.013A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.612A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.598A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.616A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.287A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.675A pdb=" N GLU J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.710A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.604A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 45 through 72 removed outlier: 4.403A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.876A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.668A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.850A pdb=" N GLN f 93 " --> pdb=" O ALA f 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing helix chain 'u' and resid 39 through 51 removed outlier: 3.531A pdb=" N LEU u 43 " --> pdb=" O PRO u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 59 through 69 Processing helix chain 'u' and resid 76 through 90 Processing helix chain 'u' and resid 99 through 102 removed outlier: 3.755A pdb=" N SER u 102 " --> pdb=" O THR u 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 99 through 102' Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.107A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 4.270A pdb=" N LEU A 182 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.859A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 259 " --> pdb=" O ILE A 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.628A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.721A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.621A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.162A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR H 56 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.838A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.723A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 880 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.179A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1306 " --> pdb=" O HIS A1290 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 6.859A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 3.856A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.197A pdb=" N LEU B 56 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 77 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 60 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 73 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET B 119 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 155 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.572A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.649A pdb=" N LEU B 249 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL B 228 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 247 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.849A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.358A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.570A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.570A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.053A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.513A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.565A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.513A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.907A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.575A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.438A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 5 through 6 removed outlier: 4.126A pdb=" N THR D 5 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL G 77 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 46 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE6, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.236A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 79 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.944A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.546A pdb=" N LEU G 11 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE G 70 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.525A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.525A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AF4, first strand: chain 'I' and resid 15 through 18 removed outlier: 3.579A pdb=" N LYS I 17 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF7, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.828A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF9, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AG1, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.248A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG3, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.006A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.762A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG6, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.352A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AG8, first strand: chain 'u' and resid 57 through 58 removed outlier: 6.368A pdb=" N SER u 104 " --> pdb=" O THR u 96 " (cutoff:3.500A) 1765 hydrogen bonds defined for protein. 4932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 487 hydrogen bonds 970 hydrogen bond angles 0 basepair planarities 194 basepair parallelities 370 stacking parallelities Total time for adding SS restraints: 37.30 Time building geometry restraints manager: 20.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13879 1.34 - 1.47: 13339 1.47 - 1.60: 20100 1.60 - 1.73: 402 1.73 - 1.86: 331 Bond restraints: 48051 Sorted by residual: bond pdb=" C1' G P 4 " pdb=" N9 G P 4 " ideal model delta sigma weight residual 1.475 1.375 0.100 1.50e-02 4.44e+03 4.45e+01 bond pdb=" C1' G P 3 " pdb=" N9 G P 3 " ideal model delta sigma weight residual 1.475 1.381 0.094 1.50e-02 4.44e+03 3.93e+01 bond pdb=" C1' U P 1 " pdb=" N1 U P 1 " ideal model delta sigma weight residual 1.480 1.564 -0.084 1.50e-02 4.44e+03 3.10e+01 bond pdb=" C1' A P 5 " pdb=" N9 A P 5 " ideal model delta sigma weight residual 1.475 1.393 0.082 1.50e-02 4.44e+03 2.96e+01 bond pdb=" C1' U P 8 " pdb=" N1 U P 8 " ideal model delta sigma weight residual 1.480 1.559 -0.079 1.50e-02 4.44e+03 2.80e+01 ... (remaining 48046 not shown) Histogram of bond angle deviations from ideal: 94.87 - 102.89: 1057 102.89 - 110.92: 19324 110.92 - 118.94: 21136 118.94 - 126.96: 23775 126.96 - 134.99: 1378 Bond angle restraints: 66670 Sorted by residual: angle pdb=" N CYS I 78 " pdb=" CA CYS I 78 " pdb=" CB CYS I 78 " ideal model delta sigma weight residual 111.20 101.10 10.10 1.65e+00 3.67e-01 3.75e+01 angle pdb=" CA CYS I 103 " pdb=" CB CYS I 103 " pdb=" SG CYS I 103 " ideal model delta sigma weight residual 114.40 127.92 -13.52 2.30e+00 1.89e-01 3.46e+01 angle pdb=" CA CYS I 78 " pdb=" CB CYS I 78 " pdb=" SG CYS I 78 " ideal model delta sigma weight residual 114.40 127.17 -12.77 2.30e+00 1.89e-01 3.08e+01 angle pdb=" N CYS I 106 " pdb=" CA CYS I 106 " pdb=" CB CYS I 106 " ideal model delta sigma weight residual 110.53 102.29 8.24 1.49e+00 4.50e-01 3.06e+01 angle pdb=" CA CYS I 106 " pdb=" CB CYS I 106 " pdb=" SG CYS I 106 " ideal model delta sigma weight residual 114.40 126.12 -11.72 2.30e+00 1.89e-01 2.60e+01 ... (remaining 66665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 25735 33.89 - 67.79: 2414 67.79 - 101.68: 93 101.68 - 135.58: 4 135.58 - 169.47: 3 Dihedral angle restraints: 28249 sinusoidal: 14432 harmonic: 13817 Sorted by residual: dihedral pdb=" CA VAL A 525 " pdb=" C VAL A 525 " pdb=" N GLN A 526 " pdb=" CA GLN A 526 " ideal model delta harmonic sigma weight residual 180.00 140.25 39.75 0 5.00e+00 4.00e-02 6.32e+01 dihedral pdb=" CA PRO A 959 " pdb=" C PRO A 959 " pdb=" N VAL A 960 " pdb=" CA VAL A 960 " ideal model delta harmonic sigma weight residual 180.00 -145.63 -34.37 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA ASP C 89 " pdb=" C ASP C 89 " pdb=" N TYR C 90 " pdb=" CA TYR C 90 " ideal model delta harmonic sigma weight residual -180.00 -147.17 -32.83 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 28246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6230 0.064 - 0.127: 1152 0.127 - 0.191: 101 0.191 - 0.255: 15 0.255 - 0.318: 2 Chirality restraints: 7500 Sorted by residual: chirality pdb=" CG LEU F 99 " pdb=" CB LEU F 99 " pdb=" CD1 LEU F 99 " pdb=" CD2 LEU F 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE G 45 " pdb=" CA ILE G 45 " pdb=" CG1 ILE G 45 " pdb=" CG2 ILE G 45 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA CYS I 75 " pdb=" N CYS I 75 " pdb=" C CYS I 75 " pdb=" CB CYS I 75 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 7497 not shown) Planarity restraints: 7138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N -81 " 0.150 2.00e-02 2.50e+03 7.69e-02 1.48e+02 pdb=" N1 DT N -81 " -0.009 2.00e-02 2.50e+03 pdb=" C2 DT N -81 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DT N -81 " -0.105 2.00e-02 2.50e+03 pdb=" N3 DT N -81 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DT N -81 " 0.028 2.00e-02 2.50e+03 pdb=" O4 DT N -81 " 0.123 2.00e-02 2.50e+03 pdb=" C5 DT N -81 " -0.031 2.00e-02 2.50e+03 pdb=" C7 DT N -81 " -0.076 2.00e-02 2.50e+03 pdb=" C6 DT N -81 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -77 " 0.140 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" N9 DG N -77 " -0.013 2.00e-02 2.50e+03 pdb=" C8 DG N -77 " -0.040 2.00e-02 2.50e+03 pdb=" N7 DG N -77 " -0.058 2.00e-02 2.50e+03 pdb=" C5 DG N -77 " -0.042 2.00e-02 2.50e+03 pdb=" C6 DG N -77 " 0.009 2.00e-02 2.50e+03 pdb=" O6 DG N -77 " 0.125 2.00e-02 2.50e+03 pdb=" N1 DG N -77 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DG N -77 " -0.037 2.00e-02 2.50e+03 pdb=" N2 DG N -77 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG N -77 " -0.040 2.00e-02 2.50e+03 pdb=" C4 DG N -77 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N -80 " 0.139 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" N1 DT N -80 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT N -80 " -0.036 2.00e-02 2.50e+03 pdb=" O2 DT N -80 " -0.062 2.00e-02 2.50e+03 pdb=" N3 DT N -80 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DT N -80 " 0.017 2.00e-02 2.50e+03 pdb=" O4 DT N -80 " 0.110 2.00e-02 2.50e+03 pdb=" C5 DT N -80 " -0.026 2.00e-02 2.50e+03 pdb=" C7 DT N -80 " -0.044 2.00e-02 2.50e+03 pdb=" C6 DT N -80 " -0.047 2.00e-02 2.50e+03 ... (remaining 7135 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 241 2.54 - 3.13: 34724 3.13 - 3.72: 75229 3.72 - 4.31: 108080 4.31 - 4.90: 169096 Nonbonded interactions: 387370 Sorted by model distance: nonbonded pdb=" OD1 ASP A 486 " pdb=" O2' A P 10 " model vdw 1.953 2.440 nonbonded pdb=" O ARG A1003 " pdb=" OG1 THR F 80 " model vdw 2.095 2.440 nonbonded pdb=" OE1 GLU A1064 " pdb=" OH TYR F 88 " model vdw 2.107 2.440 nonbonded pdb=" O LEU A1145 " pdb=" OG1 THR A1149 " model vdw 2.114 2.440 nonbonded pdb=" OD1 ASN H 17 " pdb=" OG SER H 24 " model vdw 2.115 2.440 ... (remaining 387365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } 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 group one per residue 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.000 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 154.470 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.260 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 48051 Z= 0.340 Angle : 0.818 13.521 66670 Z= 0.468 Chirality : 0.049 0.318 7500 Planarity : 0.006 0.145 7138 Dihedral : 21.424 169.474 19321 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 0.02 % Allowed : 0.58 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4700 helix: 0.60 (0.12), residues: 1843 sheet: -1.23 (0.19), residues: 656 loop : -0.90 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 183 HIS 0.013 0.001 HIS A 660 PHE 0.028 0.002 PHE C 260 TYR 0.029 0.002 TYR B1192 ARG 0.015 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 485 time to evaluate : 5.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.7981 (mt) cc_final: 0.7534 (mt) REVERT: A 74 MET cc_start: 0.4829 (tpt) cc_final: 0.4506 (tpt) REVERT: A 84 MET cc_start: 0.9031 (tmm) cc_final: 0.8681 (ppp) REVERT: A 103 CYS cc_start: 0.6983 (t) cc_final: 0.6758 (t) REVERT: A 122 MET cc_start: -0.1855 (ttt) cc_final: -0.2082 (ttt) REVERT: A 305 MET cc_start: 0.7987 (mtt) cc_final: 0.7421 (mtm) REVERT: A 340 ASN cc_start: 0.5262 (m110) cc_final: 0.5034 (m110) REVERT: A 522 MET cc_start: 0.3807 (mtt) cc_final: 0.3482 (mtt) REVERT: A 546 GLN cc_start: 0.8855 (tt0) cc_final: 0.8562 (tp40) REVERT: A 608 ILE cc_start: 0.8618 (mt) cc_final: 0.8320 (mm) REVERT: A 631 ILE cc_start: 0.8570 (mt) cc_final: 0.8346 (tp) REVERT: A 747 MET cc_start: 0.8134 (mtm) cc_final: 0.7857 (mtm) REVERT: A 819 MET cc_start: 0.7992 (mtt) cc_final: 0.7754 (mmm) REVERT: A 839 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8221 (pp30) REVERT: A 1000 PHE cc_start: 0.6846 (m-80) cc_final: 0.6502 (m-80) REVERT: B 105 ARG cc_start: 0.8638 (mtt90) cc_final: 0.7378 (ptm-80) REVERT: B 164 MET cc_start: 0.2608 (ttm) cc_final: 0.1656 (ttm) REVERT: B 302 MET cc_start: -0.3587 (ttm) cc_final: -0.3940 (ptm) REVERT: B 998 ASP cc_start: 0.5619 (m-30) cc_final: 0.5281 (m-30) REVERT: B 1021 MET cc_start: 0.7395 (mtm) cc_final: 0.7116 (mtp) REVERT: B 1100 ASP cc_start: 0.8591 (m-30) cc_final: 0.8250 (t0) REVERT: G 52 MET cc_start: 0.3035 (tpt) cc_final: 0.2382 (pmm) REVERT: H 57 VAL cc_start: 0.8118 (t) cc_final: 0.7885 (t) REVERT: H 109 ASP cc_start: 0.7033 (t0) cc_final: 0.6541 (t70) REVERT: J 3 ILE cc_start: 0.8444 (tp) cc_final: 0.8038 (pt) REVERT: J 8 PHE cc_start: 0.5449 (m-10) cc_final: 0.5083 (m-80) REVERT: J 51 THR cc_start: 0.7210 (p) cc_final: 0.6851 (p) REVERT: K 59 VAL cc_start: 0.8538 (p) cc_final: 0.7733 (p) REVERT: K 73 MET cc_start: 0.9178 (ttm) cc_final: 0.8735 (tmm) REVERT: K 91 CYS cc_start: 0.7074 (m) cc_final: 0.6730 (t) REVERT: d 59 MET cc_start: 0.9300 (mmm) cc_final: 0.8834 (mmm) REVERT: d 86 ILE cc_start: 0.6540 (tt) cc_final: 0.6328 (mm) outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.6256 time to fit residues: 494.4474 Evaluate side-chains 267 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 428 optimal weight: 30.0000 chunk 385 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 205 optimal weight: 30.0000 chunk 398 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 242 optimal weight: 0.9990 chunk 296 optimal weight: 0.1980 chunk 461 optimal weight: 30.0000 overall best weight: 4.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN A 651 GLN A 882 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS E 100 GLN F 104 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 HIS ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN d 79 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 48051 Z= 0.251 Angle : 0.665 17.431 66670 Z= 0.362 Chirality : 0.042 0.220 7500 Planarity : 0.005 0.076 7138 Dihedral : 23.949 177.451 9818 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 0.12 % Allowed : 3.93 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4700 helix: 1.04 (0.12), residues: 1897 sheet: -0.71 (0.20), residues: 643 loop : -0.56 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 956 HIS 0.014 0.002 HIS A 660 PHE 0.026 0.002 PHE B1204 TYR 0.029 0.002 TYR B 75 ARG 0.008 0.001 ARG A 881 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 312 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8097 (mt) cc_final: 0.7509 (mt) REVERT: A 74 MET cc_start: 0.5968 (tpt) cc_final: 0.5461 (tpt) REVERT: A 84 MET cc_start: 0.9029 (tmm) cc_final: 0.8587 (ppp) REVERT: A 103 CYS cc_start: 0.6894 (t) cc_final: 0.6513 (t) REVERT: A 133 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8727 (tppt) REVERT: A 305 MET cc_start: 0.8237 (mtt) cc_final: 0.7668 (mtm) REVERT: A 522 MET cc_start: 0.4482 (mtt) cc_final: 0.3951 (mtp) REVERT: A 609 VAL cc_start: 0.8831 (t) cc_final: 0.8570 (m) REVERT: A 819 MET cc_start: 0.8182 (mtt) cc_final: 0.7488 (mmm) REVERT: A 839 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 847 GLU cc_start: 0.7541 (pt0) cc_final: 0.6905 (pt0) REVERT: A 928 LYS cc_start: 0.8581 (pptt) cc_final: 0.8363 (pptt) REVERT: A 1000 PHE cc_start: 0.6375 (m-80) cc_final: 0.6036 (m-80) REVERT: A 1065 MET cc_start: 0.7914 (mmp) cc_final: 0.7455 (mmt) REVERT: B 302 MET cc_start: -0.2558 (ttm) cc_final: -0.3738 (ptm) REVERT: B 436 ASN cc_start: 0.8608 (m-40) cc_final: 0.8111 (p0) REVERT: B 593 MET cc_start: 0.7389 (mmp) cc_final: 0.7099 (mmm) REVERT: B 730 MET cc_start: -0.4585 (mmm) cc_final: -0.4854 (mmm) REVERT: B 836 GLU cc_start: 0.6242 (mp0) cc_final: 0.5843 (mp0) REVERT: B 972 LYS cc_start: 0.8539 (ptpt) cc_final: 0.8220 (ptpp) REVERT: B 1021 MET cc_start: 0.7489 (mtm) cc_final: 0.7178 (mtp) REVERT: B 1100 ASP cc_start: 0.7812 (m-30) cc_final: 0.7580 (t0) REVERT: B 1132 GLU cc_start: 0.7953 (pm20) cc_final: 0.7598 (pm20) REVERT: B 1169 MET cc_start: 0.6746 (mtt) cc_final: 0.6253 (tpp) REVERT: B 1211 ASN cc_start: 0.6718 (t0) cc_final: 0.6216 (t0) REVERT: G 52 MET cc_start: 0.2939 (tpt) cc_final: 0.2307 (pmm) REVERT: H 109 ASP cc_start: 0.7505 (t0) cc_final: 0.6746 (t70) REVERT: H 121 LEU cc_start: 0.7303 (mt) cc_final: 0.6870 (mt) REVERT: J 3 ILE cc_start: 0.8720 (tp) cc_final: 0.8289 (pt) REVERT: K 1 MET cc_start: 0.2931 (ptm) cc_final: 0.2136 (ptm) REVERT: K 59 VAL cc_start: 0.8890 (p) cc_final: 0.8557 (p) REVERT: K 73 MET cc_start: 0.9175 (ttm) cc_final: 0.8670 (tmm) REVERT: K 91 CYS cc_start: 0.7096 (m) cc_final: 0.6833 (t) REVERT: d 59 MET cc_start: 0.9267 (mmm) cc_final: 0.8701 (mmm) outliers start: 5 outliers final: 1 residues processed: 317 average time/residue: 0.5902 time to fit residues: 309.6840 Evaluate side-chains 233 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 256 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 383 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 462 optimal weight: 0.6980 chunk 499 optimal weight: 0.0970 chunk 411 optimal weight: 30.0000 chunk 458 optimal weight: 50.0000 chunk 157 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 769 GLN A 961 ASN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 506 GLN B 843 GLN B 932 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 48051 Z= 0.174 Angle : 0.570 14.284 66670 Z= 0.313 Chirality : 0.040 0.243 7500 Planarity : 0.004 0.057 7138 Dihedral : 23.856 178.657 9818 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.12), residues: 4700 helix: 1.41 (0.12), residues: 1893 sheet: -0.55 (0.20), residues: 635 loop : -0.46 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 554 HIS 0.009 0.001 HIS A 660 PHE 0.019 0.001 PHE K 10 TYR 0.013 0.001 TYR g 50 ARG 0.014 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 4.705 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 22 LEU cc_start: 0.8044 (mt) cc_final: 0.7472 (mt) REVERT: A 74 MET cc_start: 0.6194 (tpt) cc_final: 0.5736 (tpt) REVERT: A 84 MET cc_start: 0.8466 (tmm) cc_final: 0.8124 (tmm) REVERT: A 128 ILE cc_start: 0.7385 (mm) cc_final: 0.7176 (mm) REVERT: A 133 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8715 (tppt) REVERT: A 208 ILE cc_start: 0.7426 (mm) cc_final: 0.7225 (mm) REVERT: A 305 MET cc_start: 0.8229 (mtt) cc_final: 0.7700 (mtm) REVERT: A 456 MET cc_start: 0.7930 (ttm) cc_final: 0.7697 (tpp) REVERT: A 522 MET cc_start: 0.4467 (mtt) cc_final: 0.3766 (mtp) REVERT: A 609 VAL cc_start: 0.8883 (t) cc_final: 0.8609 (m) REVERT: A 631 ILE cc_start: 0.8559 (mp) cc_final: 0.8347 (pt) REVERT: A 736 MET cc_start: 0.8439 (ptp) cc_final: 0.8225 (ppp) REVERT: A 819 MET cc_start: 0.8143 (mtt) cc_final: 0.7416 (mmm) REVERT: A 839 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 843 VAL cc_start: 0.8800 (p) cc_final: 0.8488 (p) REVERT: A 847 GLU cc_start: 0.7629 (pt0) cc_final: 0.6827 (pt0) REVERT: A 928 LYS cc_start: 0.8490 (pptt) cc_final: 0.8266 (pptt) REVERT: A 1000 PHE cc_start: 0.6495 (m-80) cc_final: 0.6106 (m-80) REVERT: A 1038 ARG cc_start: 0.6711 (ptt180) cc_final: 0.6202 (ptt180) REVERT: B 105 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7835 (mtt-85) REVERT: B 164 MET cc_start: 0.2111 (ttm) cc_final: 0.1730 (tpp) REVERT: B 302 MET cc_start: -0.2600 (ttm) cc_final: -0.2885 (ttp) REVERT: B 436 ASN cc_start: 0.8388 (m-40) cc_final: 0.7981 (p0) REVERT: B 466 MET cc_start: 0.3691 (pmm) cc_final: 0.3376 (ptp) REVERT: B 836 GLU cc_start: 0.6192 (mp0) cc_final: 0.5802 (mp0) REVERT: B 1021 MET cc_start: 0.7204 (mtm) cc_final: 0.6887 (mtp) REVERT: B 1169 MET cc_start: 0.6466 (mtt) cc_final: 0.6051 (mmt) REVERT: B 1211 ASN cc_start: 0.6871 (t0) cc_final: 0.6445 (t0) REVERT: C 230 MET cc_start: 0.1813 (ttm) cc_final: 0.1547 (ttm) REVERT: D 51 LEU cc_start: 0.4373 (mt) cc_final: 0.4155 (tt) REVERT: D 171 LEU cc_start: 0.6044 (pp) cc_final: 0.5524 (mm) REVERT: E 178 GLN cc_start: 0.8003 (pm20) cc_final: 0.7570 (pm20) REVERT: F 127 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: G 52 MET cc_start: 0.2911 (tpt) cc_final: 0.2286 (pmm) REVERT: H 109 ASP cc_start: 0.7767 (t0) cc_final: 0.7080 (t70) REVERT: J 3 ILE cc_start: 0.8688 (tp) cc_final: 0.8283 (pt) REVERT: K 1 MET cc_start: 0.3174 (ptm) cc_final: 0.2565 (ptm) REVERT: K 59 VAL cc_start: 0.9051 (p) cc_final: 0.8116 (p) REVERT: K 73 MET cc_start: 0.9134 (ttm) cc_final: 0.8682 (tmm) REVERT: K 91 CYS cc_start: 0.7083 (m) cc_final: 0.6800 (t) REVERT: d 59 MET cc_start: 0.9266 (mmm) cc_final: 0.8708 (mmm) outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 0.5976 time to fit residues: 290.4153 Evaluate side-chains 231 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 456 optimal weight: 30.0000 chunk 347 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 463 optimal weight: 5.9990 chunk 491 optimal weight: 4.9990 chunk 242 optimal weight: 0.4980 chunk 439 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 HIS B 47 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 744 HIS B 986 GLN B1104 HIS ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 106 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 48051 Z= 0.265 Angle : 0.641 15.205 66670 Z= 0.349 Chirality : 0.041 0.225 7500 Planarity : 0.005 0.064 7138 Dihedral : 23.861 179.686 9818 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 0.02 % Allowed : 3.40 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 4700 helix: 1.20 (0.12), residues: 1902 sheet: -0.67 (0.19), residues: 659 loop : -0.51 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 554 HIS 0.007 0.001 HIS C 64 PHE 0.050 0.002 PHE J 59 TYR 0.037 0.002 TYR I 44 ARG 0.008 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 4.793 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: A 22 LEU cc_start: 0.8241 (mt) cc_final: 0.7710 (mt) REVERT: A 84 MET cc_start: 0.8461 (tmm) cc_final: 0.8063 (tmm) REVERT: A 103 CYS cc_start: 0.7056 (t) cc_final: 0.6830 (t) REVERT: A 122 MET cc_start: -0.1168 (mtt) cc_final: -0.1422 (ttm) REVERT: A 128 ILE cc_start: 0.7088 (mm) cc_final: 0.6847 (mm) REVERT: A 305 MET cc_start: 0.8408 (mtt) cc_final: 0.7521 (mtp) REVERT: A 456 MET cc_start: 0.8019 (ttm) cc_final: 0.7777 (tpp) REVERT: A 464 MET cc_start: 0.8004 (mtp) cc_final: 0.7801 (mtp) REVERT: A 522 MET cc_start: 0.4658 (mtt) cc_final: 0.3890 (mtp) REVERT: A 578 LEU cc_start: 0.8519 (mm) cc_final: 0.8293 (mm) REVERT: A 819 MET cc_start: 0.8466 (mtt) cc_final: 0.7394 (mmm) REVERT: A 839 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 928 LYS cc_start: 0.8504 (pptt) cc_final: 0.8288 (pptt) REVERT: A 1038 ARG cc_start: 0.7216 (ptt180) cc_final: 0.6892 (ptt180) REVERT: A 1065 MET cc_start: 0.7402 (mmm) cc_final: 0.6739 (mmm) REVERT: A 1371 MET cc_start: 0.5379 (mtp) cc_final: 0.5102 (mtt) REVERT: A 1432 MET cc_start: 0.7497 (mtm) cc_final: 0.7158 (mtt) REVERT: B 436 ASN cc_start: 0.8514 (m-40) cc_final: 0.8044 (p0) REVERT: B 836 GLU cc_start: 0.6108 (mp0) cc_final: 0.5671 (mp0) REVERT: B 1021 MET cc_start: 0.7141 (mtm) cc_final: 0.6866 (mtp) REVERT: B 1211 ASN cc_start: 0.7261 (t0) cc_final: 0.6726 (t0) REVERT: C 79 MET cc_start: 0.4911 (mpp) cc_final: 0.4128 (mpp) REVERT: C 142 ILE cc_start: 0.6854 (mt) cc_final: 0.6383 (tt) REVERT: D 171 LEU cc_start: 0.6337 (pp) cc_final: 0.5707 (mm) REVERT: E 122 MET cc_start: 0.0645 (ppp) cc_final: 0.0159 (ppp) REVERT: G 52 MET cc_start: 0.3390 (tpt) cc_final: 0.2876 (pmm) REVERT: H 109 ASP cc_start: 0.7631 (t0) cc_final: 0.6975 (t70) REVERT: I 52 ILE cc_start: 0.3372 (mt) cc_final: 0.3148 (mt) REVERT: K 1 MET cc_start: 0.3734 (ptm) cc_final: 0.3169 (ptm) REVERT: K 91 CYS cc_start: 0.7193 (m) cc_final: 0.6925 (t) REVERT: d 59 MET cc_start: 0.9268 (mmm) cc_final: 0.8743 (mmm) outliers start: 1 outliers final: 1 residues processed: 264 average time/residue: 0.5764 time to fit residues: 258.7578 Evaluate side-chains 218 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 408 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 7 optimal weight: 40.0000 chunk 365 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 419 optimal weight: 10.0000 chunk 339 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 250 optimal weight: 20.0000 chunk 440 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS B 767 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 48051 Z= 0.364 Angle : 0.772 18.164 66670 Z= 0.417 Chirality : 0.046 0.393 7500 Planarity : 0.006 0.074 7138 Dihedral : 24.441 176.911 9818 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 4700 helix: 0.34 (0.11), residues: 1911 sheet: -0.86 (0.19), residues: 652 loop : -0.88 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.004 TRP B 554 HIS 0.012 0.002 HIS B 508 PHE 0.045 0.003 PHE B1087 TYR 0.038 0.003 TYR K 61 ARG 0.015 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8635 (m-80) cc_final: 0.8424 (m-80) REVERT: A 84 MET cc_start: 0.8485 (tmm) cc_final: 0.8226 (tmm) REVERT: A 235 MET cc_start: 0.6177 (ptt) cc_final: 0.5603 (ptt) REVERT: A 305 MET cc_start: 0.7752 (mtt) cc_final: 0.7128 (mtp) REVERT: A 456 MET cc_start: 0.8381 (ttm) cc_final: 0.7797 (tpp) REVERT: A 522 MET cc_start: 0.4373 (mtt) cc_final: 0.3760 (mtp) REVERT: A 819 MET cc_start: 0.8020 (mtt) cc_final: 0.7485 (mmm) REVERT: A 839 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 928 LYS cc_start: 0.8569 (pptt) cc_final: 0.8289 (pptt) REVERT: A 983 LEU cc_start: 0.7914 (tp) cc_final: 0.7415 (tp) REVERT: A 1032 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.7598 (ttm-80) REVERT: A 1065 MET cc_start: 0.7469 (mmm) cc_final: 0.7127 (mmm) REVERT: B 836 GLU cc_start: 0.5642 (mp0) cc_final: 0.5207 (mp0) REVERT: B 972 LYS cc_start: 0.8814 (pttt) cc_final: 0.8605 (pttp) REVERT: B 1021 MET cc_start: 0.6993 (mtm) cc_final: 0.6735 (mtp) REVERT: B 1082 MET cc_start: 0.7679 (mmm) cc_final: 0.7198 (mmm) REVERT: B 1169 MET cc_start: 0.6965 (tpp) cc_final: 0.6282 (mmt) REVERT: C 79 MET cc_start: 0.5151 (mpp) cc_final: 0.4549 (mpp) REVERT: C 142 ILE cc_start: 0.7143 (mt) cc_final: 0.6628 (tp) REVERT: D 171 LEU cc_start: 0.6358 (pp) cc_final: 0.5752 (mm) REVERT: E 122 MET cc_start: 0.0772 (ppp) cc_final: 0.0476 (ppp) REVERT: G 52 MET cc_start: 0.3387 (tpt) cc_final: 0.2938 (pmm) REVERT: K 1 MET cc_start: 0.5358 (ptm) cc_final: 0.5082 (ptm) REVERT: d 59 MET cc_start: 0.9208 (mmm) cc_final: 0.8537 (mmm) REVERT: e 120 MET cc_start: 0.8976 (tpp) cc_final: 0.8732 (tpp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.5881 time to fit residues: 237.6535 Evaluate side-chains 204 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 5.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 165 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 97 optimal weight: 0.0670 chunk 288 optimal weight: 30.0000 chunk 121 optimal weight: 9.9990 chunk 491 optimal weight: 8.9990 chunk 408 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 40.0000 chunk 258 optimal weight: 4.9990 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN d 44 GLN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 48051 Z= 0.244 Angle : 0.637 12.858 66670 Z= 0.347 Chirality : 0.042 0.251 7500 Planarity : 0.005 0.061 7138 Dihedral : 24.372 178.028 9818 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4700 helix: 0.76 (0.12), residues: 1910 sheet: -0.84 (0.19), residues: 669 loop : -0.77 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 554 HIS 0.012 0.001 HIS A 990 PHE 0.029 0.002 PHE a 104 TYR 0.022 0.002 TYR A 466 ARG 0.008 0.001 ARG J 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 4.287 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: A 37 TYR cc_start: 0.8783 (m-80) cc_final: 0.8537 (m-80) REVERT: A 74 MET cc_start: 0.6135 (tpt) cc_final: 0.5903 (tpt) REVERT: A 84 MET cc_start: 0.8462 (tmm) cc_final: 0.7991 (tmm) REVERT: A 103 CYS cc_start: 0.7488 (t) cc_final: 0.7202 (t) REVERT: A 235 MET cc_start: 0.5703 (ptt) cc_final: 0.4226 (ptt) REVERT: A 305 MET cc_start: 0.7979 (mtt) cc_final: 0.7622 (mtp) REVERT: A 522 MET cc_start: 0.4666 (mtt) cc_final: 0.3825 (mtp) REVERT: A 578 LEU cc_start: 0.8738 (mm) cc_final: 0.8532 (mm) REVERT: A 589 LEU cc_start: 0.8525 (tt) cc_final: 0.8309 (tt) REVERT: A 839 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 928 LYS cc_start: 0.8522 (pptt) cc_final: 0.8243 (pptt) REVERT: A 1065 MET cc_start: 0.7594 (mmm) cc_final: 0.7373 (mmm) REVERT: A 1371 MET cc_start: 0.5001 (mtp) cc_final: 0.4445 (mtt) REVERT: A 1432 MET cc_start: 0.7330 (mtm) cc_final: 0.6849 (mtm) REVERT: B 785 TYR cc_start: 0.8236 (p90) cc_final: 0.7893 (p90) REVERT: B 836 GLU cc_start: 0.5760 (mp0) cc_final: 0.5369 (mp0) REVERT: B 972 LYS cc_start: 0.8823 (pttt) cc_final: 0.8561 (pttp) REVERT: B 1072 MET cc_start: 0.5015 (ptm) cc_final: 0.4646 (ttp) REVERT: B 1082 MET cc_start: 0.7753 (mmm) cc_final: 0.7257 (mmm) REVERT: C 79 MET cc_start: 0.5322 (mpp) cc_final: 0.4647 (mpp) REVERT: C 142 ILE cc_start: 0.7092 (mt) cc_final: 0.6588 (tp) REVERT: D 51 LEU cc_start: 0.3650 (mt) cc_final: 0.3350 (pp) REVERT: D 171 LEU cc_start: 0.6006 (pp) cc_final: 0.5495 (mm) REVERT: E 122 MET cc_start: 0.1754 (ppp) cc_final: 0.1165 (ppp) REVERT: G 52 MET cc_start: 0.3435 (tpt) cc_final: 0.2999 (pmm) REVERT: H 45 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7338 (tm-30) REVERT: H 104 GLU cc_start: 0.6214 (pp20) cc_final: 0.5635 (pp20) REVERT: I 13 MET cc_start: -0.2358 (pmm) cc_final: -0.3022 (ptp) REVERT: K 1 MET cc_start: 0.5151 (ptm) cc_final: 0.4865 (ptm) REVERT: d 59 MET cc_start: 0.9228 (mmm) cc_final: 0.8628 (mmm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.6371 time to fit residues: 257.9636 Evaluate side-chains 203 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 473 optimal weight: 20.0000 chunk 55 optimal weight: 0.0070 chunk 280 optimal weight: 9.9990 chunk 358 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 413 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 489 optimal weight: 20.0000 chunk 306 optimal weight: 30.0000 chunk 298 optimal weight: 50.0000 chunk 226 optimal weight: 3.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 312 GLN A 317 GLN A 516 GLN ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 48051 Z= 0.209 Angle : 0.599 10.979 66670 Z= 0.329 Chirality : 0.041 0.249 7500 Planarity : 0.004 0.069 7138 Dihedral : 24.227 176.911 9818 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.02 % Allowed : 1.30 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 4700 helix: 1.04 (0.12), residues: 1898 sheet: -0.72 (0.19), residues: 675 loop : -0.72 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 170 HIS 0.010 0.001 HIS C 167 PHE 0.025 0.002 PHE a 104 TYR 0.019 0.001 TYR K 61 ARG 0.006 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 4.692 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 37 TYR cc_start: 0.8784 (m-80) cc_final: 0.8514 (m-80) REVERT: A 41 MET cc_start: 0.7905 (tpp) cc_final: 0.7704 (tpp) REVERT: A 84 MET cc_start: 0.8486 (tmm) cc_final: 0.8014 (tmm) REVERT: A 103 CYS cc_start: 0.7359 (t) cc_final: 0.7057 (t) REVERT: A 235 MET cc_start: 0.5538 (ptt) cc_final: 0.3995 (ptt) REVERT: A 305 MET cc_start: 0.7875 (mtt) cc_final: 0.7487 (mtp) REVERT: A 522 MET cc_start: 0.4212 (mtt) cc_final: 0.3995 (mtp) REVERT: A 545 GLU cc_start: 0.8498 (mp0) cc_final: 0.8276 (tp30) REVERT: A 578 LEU cc_start: 0.8655 (mm) cc_final: 0.8439 (mm) REVERT: A 839 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 928 LYS cc_start: 0.8546 (pptt) cc_final: 0.8256 (pptt) REVERT: A 1065 MET cc_start: 0.7228 (mmm) cc_final: 0.7013 (mmm) REVERT: A 1371 MET cc_start: 0.5151 (mtp) cc_final: 0.4826 (ttm) REVERT: B 836 GLU cc_start: 0.5825 (mp0) cc_final: 0.5382 (mp0) REVERT: B 972 LYS cc_start: 0.8948 (pttt) cc_final: 0.8637 (pttp) REVERT: B 1021 MET cc_start: 0.6664 (mtm) cc_final: 0.6302 (mtp) REVERT: B 1072 MET cc_start: 0.5126 (ptm) cc_final: 0.4748 (ttp) REVERT: B 1082 MET cc_start: 0.7747 (mmm) cc_final: 0.7272 (mmm) REVERT: C 79 MET cc_start: 0.5707 (mpp) cc_final: 0.5023 (mpp) REVERT: C 142 ILE cc_start: 0.7109 (mt) cc_final: 0.6655 (tp) REVERT: C 169 LYS cc_start: 0.8199 (pttt) cc_final: 0.7995 (pptt) REVERT: D 171 LEU cc_start: 0.5852 (pp) cc_final: 0.5299 (mm) REVERT: E 122 MET cc_start: 0.1201 (ppp) cc_final: 0.0694 (ppp) REVERT: G 52 MET cc_start: 0.3437 (tpt) cc_final: 0.3024 (pmm) REVERT: H 104 GLU cc_start: 0.4797 (pp20) cc_final: 0.4564 (pp20) REVERT: I 13 MET cc_start: -0.2960 (pmm) cc_final: -0.3468 (ptp) REVERT: I 52 ILE cc_start: 0.3620 (mt) cc_final: 0.3410 (mt) REVERT: K 73 MET cc_start: 0.9082 (mmp) cc_final: 0.8816 (mmm) REVERT: d 59 MET cc_start: 0.9237 (mmm) cc_final: 0.8637 (mmm) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.5913 time to fit residues: 240.6997 Evaluate side-chains 208 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 302 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 292 optimal weight: 50.0000 chunk 147 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 311 optimal weight: 0.7980 chunk 333 optimal weight: 0.5980 chunk 242 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 48051 Z= 0.189 Angle : 0.585 10.357 66670 Z= 0.321 Chirality : 0.040 0.289 7500 Planarity : 0.004 0.057 7138 Dihedral : 24.101 177.189 9818 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 4700 helix: 1.21 (0.12), residues: 1906 sheet: -0.63 (0.19), residues: 663 loop : -0.64 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 554 HIS 0.008 0.001 HIS A 660 PHE 0.025 0.002 PHE A 445 TYR 0.029 0.001 TYR f 72 ARG 0.007 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 4.940 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: A 37 TYR cc_start: 0.8754 (m-80) cc_final: 0.8513 (m-80) REVERT: A 41 MET cc_start: 0.8072 (tpp) cc_final: 0.7812 (tpp) REVERT: A 84 MET cc_start: 0.8462 (tmm) cc_final: 0.7981 (tmm) REVERT: A 103 CYS cc_start: 0.7383 (t) cc_final: 0.7083 (t) REVERT: A 235 MET cc_start: 0.5404 (ptt) cc_final: 0.3912 (ptt) REVERT: A 305 MET cc_start: 0.7882 (mtt) cc_final: 0.7335 (mtp) REVERT: A 522 MET cc_start: 0.4362 (mtt) cc_final: 0.4016 (mtp) REVERT: A 545 GLU cc_start: 0.8650 (mp0) cc_final: 0.8127 (tp30) REVERT: A 578 LEU cc_start: 0.8623 (mm) cc_final: 0.8394 (mm) REVERT: A 839 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8281 (pp30) REVERT: A 928 LYS cc_start: 0.8572 (pptt) cc_final: 0.8282 (pptt) REVERT: A 1065 MET cc_start: 0.7892 (mmm) cc_final: 0.7203 (mmt) REVERT: A 1371 MET cc_start: 0.5340 (mtp) cc_final: 0.4985 (ttm) REVERT: B 836 GLU cc_start: 0.5972 (mp0) cc_final: 0.5577 (mp0) REVERT: B 972 LYS cc_start: 0.8817 (pttt) cc_final: 0.8521 (pttp) REVERT: B 1072 MET cc_start: 0.5150 (ptm) cc_final: 0.4260 (ttp) REVERT: B 1082 MET cc_start: 0.7708 (mmm) cc_final: 0.7231 (mmm) REVERT: C 142 ILE cc_start: 0.7025 (mt) cc_final: 0.6572 (tp) REVERT: C 221 TYR cc_start: 0.8987 (p90) cc_final: 0.8707 (p90) REVERT: D 171 LEU cc_start: 0.5849 (pp) cc_final: 0.5306 (mm) REVERT: E 121 LYS cc_start: 0.9201 (tptp) cc_final: 0.8968 (pttp) REVERT: E 122 MET cc_start: 0.2429 (ppp) cc_final: 0.2171 (ppp) REVERT: G 52 MET cc_start: 0.3243 (tpt) cc_final: 0.2878 (pmm) REVERT: H 104 GLU cc_start: 0.4883 (pp20) cc_final: 0.4680 (pp20) REVERT: I 13 MET cc_start: -0.2747 (pmm) cc_final: -0.3459 (ptp) REVERT: d 59 MET cc_start: 0.9225 (mmm) cc_final: 0.8581 (mtt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.6004 time to fit residues: 245.5962 Evaluate side-chains 210 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 4.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 445 optimal weight: 50.0000 chunk 469 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 456 optimal weight: 50.0000 chunk 468 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 358 optimal weight: 0.0040 chunk 140 optimal weight: 20.0000 chunk 412 optimal weight: 10.0000 chunk 431 optimal weight: 6.9990 overall best weight: 6.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 48051 Z= 0.273 Angle : 0.660 18.348 66670 Z= 0.358 Chirality : 0.042 0.228 7500 Planarity : 0.005 0.075 7138 Dihedral : 24.226 178.386 9818 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4700 helix: 0.90 (0.12), residues: 1912 sheet: -0.74 (0.19), residues: 649 loop : -0.86 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 956 HIS 0.007 0.001 HIS A 491 PHE 0.028 0.002 PHE C 61 TYR 0.020 0.002 TYR A 544 ARG 0.007 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8184 (tpp) cc_final: 0.7959 (tpp) REVERT: A 84 MET cc_start: 0.8491 (tmm) cc_final: 0.8053 (tmm) REVERT: A 103 CYS cc_start: 0.7338 (t) cc_final: 0.7070 (t) REVERT: A 305 MET cc_start: 0.7910 (mtt) cc_final: 0.7535 (mtp) REVERT: A 456 MET cc_start: 0.8308 (ttm) cc_final: 0.7440 (tpp) REVERT: A 464 MET cc_start: 0.7774 (ptm) cc_final: 0.7483 (ptm) REVERT: A 522 MET cc_start: 0.4301 (mtt) cc_final: 0.3820 (mtp) REVERT: A 578 LEU cc_start: 0.8812 (mm) cc_final: 0.8553 (mm) REVERT: A 839 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 928 LYS cc_start: 0.8684 (pptt) cc_final: 0.8451 (pptt) REVERT: A 1065 MET cc_start: 0.7491 (mmm) cc_final: 0.7108 (mmm) REVERT: A 1371 MET cc_start: 0.5301 (mtp) cc_final: 0.4903 (ttm) REVERT: B 190 MET cc_start: 0.3206 (mtp) cc_final: 0.2853 (ttm) REVERT: B 836 GLU cc_start: 0.5440 (mp0) cc_final: 0.5041 (mp0) REVERT: B 972 LYS cc_start: 0.8880 (pttt) cc_final: 0.8572 (pttp) REVERT: B 1072 MET cc_start: 0.5509 (ptm) cc_final: 0.5004 (ttp) REVERT: B 1082 MET cc_start: 0.7711 (mmm) cc_final: 0.7354 (mmm) REVERT: C 142 ILE cc_start: 0.7248 (mt) cc_final: 0.6828 (tp) REVERT: C 221 TYR cc_start: 0.9031 (p90) cc_final: 0.8680 (p90) REVERT: D 171 LEU cc_start: 0.5845 (pp) cc_final: 0.5301 (mm) REVERT: E 34 MET cc_start: 0.8092 (mmp) cc_final: 0.7890 (mmp) REVERT: E 122 MET cc_start: 0.2450 (ppp) cc_final: 0.1772 (ppp) REVERT: G 52 MET cc_start: 0.3271 (tpt) cc_final: 0.2906 (pmm) REVERT: H 104 GLU cc_start: 0.4967 (pp20) cc_final: 0.4610 (pp20) REVERT: I 13 MET cc_start: -0.3292 (pmm) cc_final: -0.3855 (ptp) REVERT: d 59 MET cc_start: 0.9221 (mmm) cc_final: 0.8493 (mtm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.5996 time to fit residues: 241.1384 Evaluate side-chains 209 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 454 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 482 optimal weight: 50.0000 chunk 294 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 506 optimal weight: 8.9990 chunk 465 optimal weight: 40.0000 chunk 403 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 301 GLN ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 48051 Z= 0.290 Angle : 0.674 12.844 66670 Z= 0.367 Chirality : 0.043 0.231 7500 Planarity : 0.005 0.069 7138 Dihedral : 24.410 178.816 9818 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4700 helix: 0.75 (0.12), residues: 1906 sheet: -0.81 (0.19), residues: 636 loop : -1.00 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 554 HIS 0.008 0.002 HIS B 356 PHE 0.025 0.002 PHE a 104 TYR 0.020 0.002 TYR H 101 ARG 0.008 0.001 ARG J 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 6.874 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: 0.8106 (tpp) cc_final: 0.7812 (tpp) REVERT: A 74 MET cc_start: 0.7052 (tpt) cc_final: 0.6761 (tpt) REVERT: A 84 MET cc_start: 0.8471 (tmm) cc_final: 0.8023 (tmm) REVERT: A 305 MET cc_start: 0.7891 (mtt) cc_final: 0.7286 (mtp) REVERT: A 308 ASP cc_start: 0.7903 (t0) cc_final: 0.7612 (m-30) REVERT: A 438 MET cc_start: 0.1238 (mmt) cc_final: 0.0956 (mmt) REVERT: A 464 MET cc_start: 0.7649 (ptm) cc_final: 0.7421 (ptm) REVERT: A 488 MET cc_start: 0.5860 (ttt) cc_final: 0.5628 (ttm) REVERT: A 522 MET cc_start: 0.4153 (mtt) cc_final: 0.3715 (mtp) REVERT: A 578 LEU cc_start: 0.8969 (mm) cc_final: 0.8735 (mm) REVERT: A 819 MET cc_start: 0.8433 (mtt) cc_final: 0.8007 (mmt) REVERT: A 839 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 1065 MET cc_start: 0.7002 (mmm) cc_final: 0.6772 (mmm) REVERT: A 1371 MET cc_start: 0.5157 (mtp) cc_final: 0.4748 (ttm) REVERT: B 164 MET cc_start: 0.2003 (mtt) cc_final: 0.1764 (mtt) REVERT: B 190 MET cc_start: 0.3273 (mtp) cc_final: 0.2013 (ttm) REVERT: B 836 GLU cc_start: 0.6069 (mp0) cc_final: 0.5537 (mp0) REVERT: B 839 MET cc_start: 0.6724 (mtm) cc_final: 0.6443 (mtm) REVERT: B 987 LYS cc_start: 0.7741 (pttt) cc_final: 0.6668 (mtmt) REVERT: B 1072 MET cc_start: 0.5411 (ptm) cc_final: 0.4961 (ttp) REVERT: B 1082 MET cc_start: 0.7835 (mmm) cc_final: 0.7466 (mmm) REVERT: C 142 ILE cc_start: 0.7294 (mt) cc_final: 0.6891 (tp) REVERT: C 221 TYR cc_start: 0.8823 (p90) cc_final: 0.8495 (p90) REVERT: D 171 LEU cc_start: 0.5880 (pp) cc_final: 0.5339 (mm) REVERT: E 49 MET cc_start: 0.3539 (ppp) cc_final: 0.3312 (ppp) REVERT: E 122 MET cc_start: 0.2350 (ppp) cc_final: 0.1655 (ppp) REVERT: G 52 MET cc_start: 0.3317 (tpt) cc_final: 0.2970 (pmm) REVERT: H 104 GLU cc_start: 0.4886 (pp20) cc_final: 0.4562 (pp20) REVERT: a 90 MET cc_start: 0.8340 (mpp) cc_final: 0.8027 (mpp) REVERT: d 59 MET cc_start: 0.9215 (mmm) cc_final: 0.8543 (mtt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.5965 time to fit residues: 233.4747 Evaluate side-chains 206 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 247 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 429 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 371 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 403 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 414 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** 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 = 0.4132 r_free = 0.4132 target = 0.067932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.053328 restraints weight = 588204.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.053232 restraints weight = 461670.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.053655 restraints weight = 372674.819| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 48051 Z= 0.215 Angle : 0.615 16.805 66670 Z= 0.336 Chirality : 0.041 0.212 7500 Planarity : 0.004 0.063 7138 Dihedral : 24.308 178.530 9818 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 4700 helix: 1.01 (0.12), residues: 1910 sheet: -0.78 (0.20), residues: 634 loop : -0.90 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 554 HIS 0.008 0.001 HIS K 40 PHE 0.037 0.002 PHE K 71 TYR 0.025 0.002 TYR K 61 ARG 0.011 0.000 ARG K 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7773.92 seconds wall clock time: 144 minutes 52.85 seconds (8692.85 seconds total)