Starting phenix.real_space_refine on Sun Aug 9 09:34:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kdn_62282/08_2026/9kdn_62282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kdn_62282/08_2026/9kdn_62282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kdn_62282/08_2026/9kdn_62282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kdn_62282/08_2026/9kdn_62282.map" model { file = "/net/cci-nas-00/data/ceres_data/9kdn_62282/08_2026/9kdn_62282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kdn_62282/08_2026/9kdn_62282.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 61 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 20634 2.51 5 N 5740 2.21 5 O 6390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33014 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11153 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1351} Chain breaks: 4 Chain: "B" Number of atoms: 9378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9378 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 5 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {'PXZ': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="PXZ M 6 " pdbres="THR M 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'PXZ:plan-1': 1, 'PXZ:plan-2': 1, 'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 84.970 76.677 132.053 1.00150.41 S ATOM 844 SG CYS A 110 86.874 73.564 132.955 1.00153.36 S ATOM 1149 SG CYS A 148 83.689 74.372 134.883 1.00159.68 S ATOM 1287 SG CYS A 167 86.809 76.482 135.358 1.00159.20 S ATOM 515 SG CYS A 67 107.469 69.305 91.117 1.00135.41 S ATOM 537 SG CYS A 70 106.949 65.647 90.211 1.00115.93 S ATOM 590 SG CYS A 77 104.073 68.167 89.874 1.00137.01 S ATOM 20037 SG CYS B1163 100.370 57.654 102.520 1.00123.10 S ATOM 20055 SG CYS B1166 98.955 60.770 104.014 1.00127.88 S ATOM 20180 SG CYS B1182 102.649 60.548 102.619 1.00117.62 S ATOM 20199 SG CYS B1185 101.557 59.127 105.984 1.00137.76 S ATOM 21178 SG CYS C 86 88.664 65.460 24.982 1.00113.84 S ATOM 21195 SG CYS C 88 90.502 68.008 27.168 1.00131.40 S ATOM 21228 SG CYS C 92 89.648 68.680 23.483 1.00115.90 S ATOM 21251 SG CYS C 95 86.877 68.551 26.189 1.00128.45 S ATOM 28918 SG CYS I 7 35.942 123.052 120.951 1.00135.47 S ATOM 28943 SG CYS I 10 39.723 123.247 120.926 1.00117.50 S ATOM 29109 SG CYS I 29 38.118 120.229 122.594 1.00142.31 S ATOM 29133 SG CYS I 32 37.774 123.769 124.083 1.00154.39 S ATOM 29460 SG CYS I 75 13.689 109.146 84.663 1.00109.32 S ATOM 29482 SG CYS I 78 12.946 112.963 84.116 1.00134.53 S ATOM 29698 SG CYS I 103 16.220 111.212 82.648 1.00100.06 S ATOM 29718 SG CYS I 106 15.585 112.007 86.230 1.00 91.89 S ATOM 29863 SG CYS J 7 59.504 79.279 36.705 1.00 89.09 S ATOM 29886 SG CYS J 10 58.992 76.892 33.732 1.00 89.41 S ATOM 30166 SG CYS J 45 56.103 77.967 35.912 1.00 90.51 S ATOM 30172 SG CYS J 46 57.801 80.331 33.352 1.00 83.51 S ATOM 31352 SG CYS L 31 90.859 107.890 47.848 1.00104.35 S ATOM 31372 SG CYS L 34 90.842 111.038 45.359 1.00 96.34 S ATOM 31476 SG CYS L 48 94.057 109.507 46.857 1.00 95.37 S ATOM 31499 SG CYS L 51 91.462 111.536 48.793 1.00107.57 S Time building chain proxies: 4.98, per 1000 atoms: 0.15 Number of scatterers: 33014 At special positions: 0 Unit cell: (156.24, 154.38, 156.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 180 16.00 P 61 15.00 Mg 1 11.99 O 6390 8.00 N 5740 7.00 C 20634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied TRANS " DVA M 2 " - " THR M 1 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA M 2 " pdb=" CB DVA M 8 " Number of C-beta restraints generated: 7498 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 51 sheets defined 38.8% alpha, 20.1% beta 21 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 4.15 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 127 removed outlier: 4.030A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.855A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.762A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.727A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.533A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.192A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix removed outlier: 3.627A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 3.848A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.967A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 4.148A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A1188 " --> pdb=" O PHE A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1188' Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.854A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 3.737A pdb=" N GLU A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.862A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.020A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 removed outlier: 3.520A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.508A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.602A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 4.333A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.432A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.551A pdb=" N GLU B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.155A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 605 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.103A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.688A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.562A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.596A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.856A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.396A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.764A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.829A pdb=" N CYS C 86 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.880A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 51 through 72 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.568A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.875A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.537A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.550A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.677A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 63 removed outlier: 4.013A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.936A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.776A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.689A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.558A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 7.849A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.388A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.604A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.115A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.390A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.810A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.817A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.165A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.165A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.763A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 242 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 252 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.501A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA B 704 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.319A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.731A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.731A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.695A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.541A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.482A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.952A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.270A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.270A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE9, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.569A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF2, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.434A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF4, first strand: chain 'I' and resid 15 through 17 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 1446 hydrogen bonds defined for protein. 3978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5521 1.31 - 1.44: 8656 1.44 - 1.57: 19138 1.57 - 1.69: 121 1.69 - 1.82: 288 Bond restraints: 33724 Sorted by residual: bond pdb=" C12 PXZ M 6 " pdb=" C4 PXZ M 6 " ideal model delta sigma weight residual 1.354 1.541 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" C1 PXZ M 6 " pdb=" C2 PXZ M 6 " ideal model delta sigma weight residual 1.372 1.520 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C2 PXZ M 6 " pdb=" N2 PXZ M 6 " ideal model delta sigma weight residual 1.344 1.467 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C11 PXZ M 6 " pdb=" N10 PXZ M 6 " ideal model delta sigma weight residual 1.297 1.418 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C13 PXZ M 6 " pdb=" O5 PXZ M 6 " ideal model delta sigma weight residual 1.353 1.471 -0.118 2.00e-02 2.50e+03 3.46e+01 ... (remaining 33719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 45316 2.32 - 4.63: 438 4.63 - 6.95: 37 6.95 - 9.27: 6 9.27 - 11.58: 3 Bond angle restraints: 45800 Sorted by residual: angle pdb=" C3' DT N 31 " pdb=" O3' DT N 31 " pdb=" P DG N 32 " ideal model delta sigma weight residual 119.70 108.12 11.58 1.20e+00 6.94e-01 9.32e+01 angle pdb=" C3' DA T 16 " pdb=" O3' DA T 16 " pdb=" P DG T 17 " ideal model delta sigma weight residual 119.70 108.36 11.34 1.20e+00 6.94e-01 8.94e+01 angle pdb=" C3' DG T 14 " pdb=" O3' DG T 14 " pdb=" P DC T 15 " ideal model delta sigma weight residual 119.70 110.40 9.30 1.20e+00 6.94e-01 6.00e+01 angle pdb=" C3' DG T 17 " pdb=" O3' DG T 17 " pdb=" P DG T 18 " ideal model delta sigma weight residual 119.70 111.03 8.67 1.20e+00 6.94e-01 5.22e+01 angle pdb=" C3' DC T 15 " pdb=" O3' DC T 15 " pdb=" P DA T 16 " ideal model delta sigma weight residual 119.70 112.06 7.64 1.20e+00 6.94e-01 4.05e+01 ... (remaining 45795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 19943 33.29 - 66.58: 534 66.58 - 99.87: 43 99.87 - 133.16: 0 133.16 - 166.44: 5 Dihedral angle restraints: 20525 sinusoidal: 8945 harmonic: 11580 Sorted by residual: dihedral pdb=" C SAR M 4 " pdb=" N SAR M 4 " pdb=" CA SAR M 4 " pdb=" CN SAR M 4 " ideal model delta sinusoidal sigma weight residual 71.89 -85.97 157.86 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C SAR M 10 " pdb=" N SAR M 10 " pdb=" CA SAR M 10 " pdb=" CN SAR M 10 " ideal model delta sinusoidal sigma weight residual 71.89 -81.69 153.58 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA GLN B 115 " pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 20522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 5110 0.129 - 0.257: 34 0.257 - 0.386: 0 0.386 - 0.515: 6 0.515 - 0.643: 3 Chirality restraints: 5153 Sorted by residual: chirality pdb=" P DC N 30 " pdb=" OP1 DC N 30 " pdb=" OP2 DC N 30 " pdb=" O5' DC N 30 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG T 14 " pdb=" OP1 DG T 14 " pdb=" OP2 DG T 14 " pdb=" O5' DG T 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" P DT N 31 " pdb=" OP1 DT N 31 " pdb=" OP2 DT N 31 " pdb=" O5' DT N 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.76e+00 ... (remaining 5150 not shown) Planarity restraints: 5727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " 0.021 2.00e-02 2.50e+03 2.74e-02 3.77e+01 pdb=" C0' PXZ M 6 " -0.008 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " -0.003 2.00e-02 2.50e+03 pdb=" C11 PXZ M 6 " 0.029 2.00e-02 2.50e+03 pdb=" C12 PXZ M 6 " 0.025 2.00e-02 2.50e+03 pdb=" C13 PXZ M 6 " 0.020 2.00e-02 2.50e+03 pdb=" C14 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C15 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ M 6 " -0.013 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " -0.018 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " -0.017 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " 0.014 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " -0.008 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " -0.029 2.00e-02 2.50e+03 pdb=" C8 PXZ M 6 " -0.043 2.00e-02 2.50e+03 pdb=" C9 PXZ M 6 " -0.020 2.00e-02 2.50e+03 pdb=" N10 PXZ M 6 " 0.054 2.00e-02 2.50e+03 pdb=" N2 PXZ M 6 " -0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ M 6 " -0.040 2.00e-02 2.50e+03 pdb=" O5 PXZ M 6 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.42e+00 pdb=" N PRO A 245 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR M 7 " -0.013 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C THR M 7 " 0.042 2.00e-02 2.50e+03 pdb=" O THR M 7 " -0.015 2.00e-02 2.50e+03 pdb=" N DVA M 8 " -0.014 2.00e-02 2.50e+03 ... (remaining 5724 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 588 2.66 - 3.22: 31527 3.22 - 3.78: 52777 3.78 - 4.34: 74306 4.34 - 4.90: 119720 Nonbonded interactions: 278918 Sorted by model distance: nonbonded pdb=" O3' A P 11 " pdb="MG MG A1803 " model vdw 2.105 2.170 nonbonded pdb=" OP1 C P 12 " pdb="MG MG A1803 " model vdw 2.108 2.170 nonbonded pdb=" OD2 ASP B 896 " pdb=" OH TYR L 29 " model vdw 2.136 3.040 nonbonded pdb=" OG SER A1115 " pdb=" OD1 ASN A1330 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASP B 837 " pdb=" NH2 ARG B1020 " model vdw 2.155 3.120 ... (remaining 278913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 32.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 33761 Z= 0.214 Angle : 0.586 11.583 45848 Z= 0.355 Chirality : 0.048 0.643 5153 Planarity : 0.004 0.084 5726 Dihedral : 15.005 166.445 13024 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3936 helix: 1.23 (0.14), residues: 1360 sheet: -0.26 (0.20), residues: 631 loop : 0.16 (0.15), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 47 TYR 0.012 0.001 TYR B1092 PHE 0.022 0.001 PHE A 444 TRP 0.013 0.001 TRP A 572 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.21 (33724) covalent geometry : angle 0.57106 / 0.35 (45800) hydrogen bonds : bond 0.14441 / 10.04 ( 1448) hydrogen bonds : angle 6.04283 / 4.38 ( 4072) metal coordination : bond 0.00567 / 0.34 ( 32) metal coordination : angle 4.22646 / 2.76 ( 45) Misc. bond : bond 0.00625 / 0.31 ( 4) link_TRANS : bond 0.00064 / 0.03 ( 1) link_TRANS : angle 0.49545 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 787 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7260 (mmm) cc_final: 0.6949 (mmm) REVERT: A 45 GLN cc_start: 0.8669 (mm110) cc_final: 0.8389 (mp10) REVERT: A 74 MET cc_start: 0.7022 (mtp) cc_final: 0.6321 (mtt) REVERT: A 147 VAL cc_start: 0.8976 (p) cc_final: 0.8695 (t) REVERT: A 268 ASP cc_start: 0.8766 (m-30) cc_final: 0.8375 (m-30) REVERT: A 281 HIS cc_start: 0.8825 (t-90) cc_final: 0.8317 (t-90) REVERT: A 592 ASP cc_start: 0.8572 (m-30) cc_final: 0.8136 (m-30) REVERT: A 593 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8045 (pp20) REVERT: A 717 ASN cc_start: 0.8183 (m-40) cc_final: 0.7958 (m-40) REVERT: A 748 MET cc_start: 0.8759 (mtm) cc_final: 0.8428 (mtp) REVERT: A 755 PHE cc_start: 0.7573 (t80) cc_final: 0.7169 (t80) REVERT: A 801 GLU cc_start: 0.8248 (pt0) cc_final: 0.7824 (pm20) REVERT: A 898 ARG cc_start: 0.6803 (tpt170) cc_final: 0.6573 (tpp-160) REVERT: A 981 LEU cc_start: 0.8640 (mt) cc_final: 0.8179 (mt) REVERT: A 1110 ASN cc_start: 0.8112 (m-40) cc_final: 0.7793 (p0) REVERT: A 1116 LEU cc_start: 0.8059 (tt) cc_final: 0.7799 (tt) REVERT: A 1209 MET cc_start: 0.5665 (mmm) cc_final: 0.5444 (mmm) REVERT: A 1228 TRP cc_start: 0.8565 (p90) cc_final: 0.8008 (p-90) REVERT: A 1312 ASN cc_start: 0.7432 (t0) cc_final: 0.6909 (t0) REVERT: A 1313 LEU cc_start: 0.8056 (tp) cc_final: 0.7705 (tp) REVERT: B 177 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8431 (tmtt) REVERT: B 315 LYS cc_start: 0.6122 (mmtt) cc_final: 0.5640 (ptpt) REVERT: B 348 ARG cc_start: 0.6285 (mmt90) cc_final: 0.5704 (mmt90) REVERT: B 367 LEU cc_start: 0.8650 (mp) cc_final: 0.8189 (mt) REVERT: B 390 LEU cc_start: 0.8552 (mt) cc_final: 0.8228 (mt) REVERT: B 418 LYS cc_start: 0.8331 (tmtt) cc_final: 0.7920 (ttpt) REVERT: B 552 MET cc_start: 0.8236 (mmp) cc_final: 0.7306 (tmm) REVERT: B 706 GLN cc_start: 0.8114 (pm20) cc_final: 0.7444 (mm-40) REVERT: B 860 MET cc_start: 0.8387 (tmm) cc_final: 0.8169 (tmm) REVERT: B 873 THR cc_start: 0.8358 (m) cc_final: 0.7971 (p) REVERT: B 908 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 939 THR cc_start: 0.8520 (m) cc_final: 0.7966 (p) REVERT: B 1125 ASP cc_start: 0.8645 (t0) cc_final: 0.8206 (t0) REVERT: B 1136 ASP cc_start: 0.8263 (m-30) cc_final: 0.7996 (m-30) REVERT: C 9 LYS cc_start: 0.8081 (tttm) cc_final: 0.7742 (tppt) REVERT: C 15 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7802 (tttt) REVERT: E 32 GLN cc_start: 0.8040 (tp40) cc_final: 0.7280 (pp30) REVERT: E 33 GLU cc_start: 0.7872 (mp0) cc_final: 0.6914 (mp0) REVERT: E 48 ASP cc_start: 0.7213 (p0) cc_final: 0.7003 (p0) REVERT: E 54 GLN cc_start: 0.7186 (pm20) cc_final: 0.6824 (pp30) REVERT: E 58 MET cc_start: 0.6110 (ttt) cc_final: 0.5283 (ttm) REVERT: E 67 GLU cc_start: 0.8321 (mp0) cc_final: 0.8032 (tp30) REVERT: E 114 ASN cc_start: 0.8521 (m110) cc_final: 0.8113 (t0) REVERT: E 140 LEU cc_start: 0.8901 (mt) cc_final: 0.8586 (mp) REVERT: F 76 LYS cc_start: 0.8723 (tttm) cc_final: 0.8509 (tttt) REVERT: F 116 ASP cc_start: 0.8635 (t0) cc_final: 0.8296 (t0) REVERT: F 122 MET cc_start: 0.8901 (mtt) cc_final: 0.8595 (mtp) REVERT: F 124 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8503 (mt-10) REVERT: F 142 SER cc_start: 0.8862 (m) cc_final: 0.8477 (m) REVERT: G 41 LYS cc_start: 0.8062 (tptp) cc_final: 0.7743 (mtpp) REVERT: G 71 ASN cc_start: 0.8905 (t0) cc_final: 0.8697 (t0) REVERT: G 119 LEU cc_start: 0.6944 (tp) cc_final: 0.6627 (mt) REVERT: G 130 TYR cc_start: 0.5523 (m-80) cc_final: 0.4665 (m-80) REVERT: G 168 LEU cc_start: 0.7535 (mm) cc_final: 0.6794 (mm) REVERT: H 35 GLN cc_start: 0.8361 (mt0) cc_final: 0.8137 (mt0) REVERT: H 53 ASP cc_start: 0.8500 (t0) cc_final: 0.8094 (t0) REVERT: H 92 ASP cc_start: 0.8637 (m-30) cc_final: 0.8391 (t0) REVERT: H 126 GLU cc_start: 0.8304 (tt0) cc_final: 0.7985 (tt0) REVERT: H 136 LYS cc_start: 0.8372 (ptpp) cc_final: 0.7896 (ptpp) REVERT: J 23 ASN cc_start: 0.8760 (t0) cc_final: 0.8070 (m110) REVERT: J 26 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8213 (tp-100) REVERT: K 11 LEU cc_start: 0.7637 (mt) cc_final: 0.7385 (mp) REVERT: K 97 LYS cc_start: 0.7223 (mttt) cc_final: 0.7004 (mttt) REVERT: K 106 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7480 (mm-30) REVERT: L 37 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7785 (ttmm) outliers start: 0 outliers final: 0 residues processed: 787 average time/residue: 0.6875 time to fit residues: 633.9768 Evaluate side-chains 430 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 71 GLN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 767 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS A1048 ASN A1078 GLN A1278 ASN B 236 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS C 252 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN G 158 HIS H 33 GLN I 90 GLN K 2 ASN K 89 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.145018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103119 restraints weight = 54838.062| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.91 r_work: 0.3344 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33761 Z= 0.222 Angle : 0.661 12.578 45848 Z= 0.340 Chirality : 0.046 0.253 5153 Planarity : 0.005 0.077 5726 Dihedral : 13.254 166.805 5050 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.22 % Allowed : 12.12 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.13), residues: 3936 helix: 1.09 (0.14), residues: 1379 sheet: -0.34 (0.19), residues: 650 loop : 0.09 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 144 TYR 0.020 0.002 TYR B1092 PHE 0.024 0.002 PHE G 18 TRP 0.010 0.001 TRP A 572 HIS 0.012 0.001 HIS A1387 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (33724) covalent geometry : angle 0.64229 / 0.34 (45800) hydrogen bonds : bond 0.04676 / 3.23 ( 1448) hydrogen bonds : angle 5.09863 / 3.66 ( 4072) metal coordination : bond 0.00705 / 0.43 ( 32) metal coordination : angle 5.04480 / 3.29 ( 45) Misc. bond : bond 0.00113 / 0.05 ( 4) link_TRANS : bond 0.00183 / 0.10 ( 1) link_TRANS : angle 0.51671 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 459 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7449 (mmm) cc_final: 0.7146 (mmm) REVERT: A 45 GLN cc_start: 0.8701 (mm110) cc_final: 0.8366 (mp10) REVERT: A 74 MET cc_start: 0.7406 (mtp) cc_final: 0.6607 (mtt) REVERT: A 268 ASP cc_start: 0.8842 (m-30) cc_final: 0.8433 (m-30) REVERT: A 281 HIS cc_start: 0.8880 (t-90) cc_final: 0.8424 (t-90) REVERT: A 487 MET cc_start: 0.8695 (mtp) cc_final: 0.8450 (mtm) REVERT: A 526 ASP cc_start: 0.8706 (m-30) cc_final: 0.8454 (t0) REVERT: A 592 ASP cc_start: 0.8423 (m-30) cc_final: 0.7930 (m-30) REVERT: A 593 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8056 (pp20) REVERT: A 894 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: A 995 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 1110 ASN cc_start: 0.8363 (m-40) cc_final: 0.7833 (p0) REVERT: A 1151 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6595 (mp0) REVERT: A 1228 TRP cc_start: 0.8490 (p90) cc_final: 0.7970 (p-90) REVERT: A 1278 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6603 (t0) REVERT: A 1312 ASN cc_start: 0.7302 (t0) cc_final: 0.6576 (t0) REVERT: A 1313 LEU cc_start: 0.7772 (tp) cc_final: 0.7507 (tp) REVERT: A 1329 THR cc_start: 0.8876 (m) cc_final: 0.8647 (m) REVERT: A 1391 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: A 1454 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.5797 (pmm) REVERT: B 177 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8423 (tmtt) REVERT: B 301 ILE cc_start: 0.8253 (mt) cc_final: 0.7876 (mm) REVERT: B 312 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8549 (tm-30) REVERT: B 315 LYS cc_start: 0.6006 (mmtt) cc_final: 0.5568 (ptpt) REVERT: B 418 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7776 (tmmt) REVERT: B 552 MET cc_start: 0.8168 (mmp) cc_final: 0.7149 (tmm) REVERT: B 564 GLU cc_start: 0.7700 (tt0) cc_final: 0.7351 (tt0) REVERT: B 570 VAL cc_start: 0.8183 (t) cc_final: 0.7978 (m) REVERT: B 589 VAL cc_start: 0.8001 (m) cc_final: 0.7243 (p) REVERT: B 706 GLN cc_start: 0.8013 (pm20) cc_final: 0.7446 (mm-40) REVERT: B 860 MET cc_start: 0.8418 (tmm) cc_final: 0.8142 (tmm) REVERT: B 873 THR cc_start: 0.8009 (m) cc_final: 0.7497 (p) REVERT: B 882 THR cc_start: 0.7170 (m) cc_final: 0.6672 (p) REVERT: B 908 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 1125 ASP cc_start: 0.8598 (t0) cc_final: 0.8195 (t0) REVERT: B 1136 ASP cc_start: 0.8072 (m-30) cc_final: 0.7767 (m-30) REVERT: C 9 LYS cc_start: 0.7594 (tttm) cc_final: 0.7104 (tppt) REVERT: C 15 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7722 (tttm) REVERT: C 16 ASP cc_start: 0.7899 (m-30) cc_final: 0.7624 (m-30) REVERT: C 53 THR cc_start: 0.6826 (m) cc_final: 0.6438 (t) REVERT: D 14 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7743 (tpp80) REVERT: D 36 LYS cc_start: 0.6100 (ptpt) cc_final: 0.5374 (ptpt) REVERT: D 54 GLU cc_start: 0.8527 (tt0) cc_final: 0.8178 (pt0) REVERT: D 121 LYS cc_start: 0.4737 (tmmt) cc_final: 0.4470 (ttpt) REVERT: D 142 LYS cc_start: 0.8274 (tptt) cc_final: 0.7970 (pptt) REVERT: D 194 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6793 (mt) REVERT: E 17 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7570 (ttm-80) REVERT: E 32 GLN cc_start: 0.7857 (tp40) cc_final: 0.7154 (tm-30) REVERT: E 33 GLU cc_start: 0.8203 (mp0) cc_final: 0.7522 (mp0) REVERT: E 46 TYR cc_start: 0.8044 (m-80) cc_final: 0.7257 (m-80) REVERT: E 48 ASP cc_start: 0.7450 (p0) cc_final: 0.7096 (p0) REVERT: E 54 GLN cc_start: 0.7087 (pm20) cc_final: 0.6690 (pp30) REVERT: E 58 MET cc_start: 0.6131 (ttt) cc_final: 0.5345 (ttm) REVERT: E 67 GLU cc_start: 0.8439 (mp0) cc_final: 0.8191 (tp30) REVERT: E 72 PHE cc_start: 0.6734 (m-80) cc_final: 0.6507 (m-80) REVERT: E 114 ASN cc_start: 0.8579 (m110) cc_final: 0.8028 (t0) REVERT: E 122 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8938 (pttt) REVERT: E 140 LEU cc_start: 0.8750 (mt) cc_final: 0.8422 (mp) REVERT: E 215 MET cc_start: 0.6264 (tpp) cc_final: 0.5302 (ppp) REVERT: F 76 LYS cc_start: 0.8354 (tttm) cc_final: 0.8135 (tttt) REVERT: F 104 ASN cc_start: 0.7863 (t0) cc_final: 0.7616 (t0) REVERT: F 116 ASP cc_start: 0.8400 (t0) cc_final: 0.8086 (t70) REVERT: F 119 ARG cc_start: 0.7408 (mtp85) cc_final: 0.7097 (mmm-85) REVERT: F 122 MET cc_start: 0.8115 (mtt) cc_final: 0.7714 (mtp) REVERT: F 124 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8181 (mt-10) REVERT: G 71 ASN cc_start: 0.8437 (t0) cc_final: 0.8119 (t0) REVERT: G 82 PHE cc_start: 0.7766 (m-10) cc_final: 0.6810 (m-10) REVERT: G 115 MET cc_start: 0.5629 (mtt) cc_final: 0.5294 (mtt) REVERT: G 119 LEU cc_start: 0.7032 (tp) cc_final: 0.6603 (mt) REVERT: G 130 TYR cc_start: 0.5403 (m-80) cc_final: 0.4477 (m-10) REVERT: H 27 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: H 126 GLU cc_start: 0.8208 (tt0) cc_final: 0.7798 (tt0) REVERT: H 136 LYS cc_start: 0.8404 (ptpp) cc_final: 0.8193 (ptpp) REVERT: I 18 GLU cc_start: 0.6595 (pm20) cc_final: 0.6249 (tp30) REVERT: I 61 ASP cc_start: 0.7371 (p0) cc_final: 0.7124 (p0) REVERT: J 23 ASN cc_start: 0.8396 (t0) cc_final: 0.7654 (m110) REVERT: K 106 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7248 (mm-30) REVERT: L 33 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7996 (tp30) REVERT: L 37 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7670 (ttmm) REVERT: L 64 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6873 (mp) outliers start: 78 outliers final: 30 residues processed: 509 average time/residue: 0.6801 time to fit residues: 408.0728 Evaluate side-chains 433 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 393 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1391 ARG Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 189 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 347 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 353 optimal weight: 0.9980 chunk 354 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS A1008 GLN B 236 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN G 96 GLN H 33 GLN J 26 GLN K 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101633 restraints weight = 54602.911| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.91 r_work: 0.3321 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 33761 Z= 0.232 Angle : 0.639 13.526 45848 Z= 0.329 Chirality : 0.045 0.242 5153 Planarity : 0.004 0.072 5726 Dihedral : 13.267 165.510 5050 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.85 % Allowed : 14.08 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 3936 helix: 1.07 (0.14), residues: 1380 sheet: -0.43 (0.19), residues: 661 loop : -0.00 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1023 TYR 0.022 0.002 TYR E 187 PHE 0.023 0.002 PHE A 219 TRP 0.010 0.001 TRP A 572 HIS 0.009 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (33724) covalent geometry : angle 0.62008 / 0.33 (45800) hydrogen bonds : bond 0.04401 / 3.01 ( 1448) hydrogen bonds : angle 4.95998 / 3.56 ( 4072) metal coordination : bond 0.00833 / 0.52 ( 32) metal coordination : angle 4.97289 / 3.25 ( 45) Misc. bond : bond 0.00044 / 0.02 ( 4) link_TRANS : bond 0.00207 / 0.11 ( 1) link_TRANS : angle 0.32392 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 415 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7638 (mmm) cc_final: 0.7262 (mmm) REVERT: A 45 GLN cc_start: 0.8714 (mm110) cc_final: 0.8337 (mp10) REVERT: A 74 MET cc_start: 0.7398 (mtp) cc_final: 0.6604 (mtt) REVERT: A 268 ASP cc_start: 0.8861 (m-30) cc_final: 0.8440 (m-30) REVERT: A 281 HIS cc_start: 0.8885 (t-90) cc_final: 0.8465 (t-90) REVERT: A 592 ASP cc_start: 0.8391 (m-30) cc_final: 0.7883 (m-30) REVERT: A 593 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8019 (pp20) REVERT: A 995 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 1110 ASN cc_start: 0.8453 (m-40) cc_final: 0.7901 (p0) REVERT: A 1151 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6609 (mp0) REVERT: A 1228 TRP cc_start: 0.8451 (p90) cc_final: 0.7976 (p-90) REVERT: A 1312 ASN cc_start: 0.7409 (t0) cc_final: 0.6632 (t0) REVERT: A 1313 LEU cc_start: 0.7749 (tp) cc_final: 0.7490 (tp) REVERT: A 1454 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.5911 (pmm) REVERT: B 135 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.7089 (mmm-85) REVERT: B 177 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8428 (tmtt) REVERT: B 301 ILE cc_start: 0.8267 (mt) cc_final: 0.7890 (mm) REVERT: B 315 LYS cc_start: 0.5963 (mmtt) cc_final: 0.5607 (tmmm) REVERT: B 418 LYS cc_start: 0.8338 (tmtt) cc_final: 0.7820 (tmmt) REVERT: B 564 GLU cc_start: 0.7728 (tt0) cc_final: 0.7417 (tt0) REVERT: B 570 VAL cc_start: 0.8220 (t) cc_final: 0.7992 (m) REVERT: B 589 VAL cc_start: 0.7898 (m) cc_final: 0.7197 (p) REVERT: B 706 GLN cc_start: 0.8084 (pm20) cc_final: 0.7431 (mm110) REVERT: B 860 MET cc_start: 0.8417 (tmm) cc_final: 0.8189 (tmm) REVERT: B 873 THR cc_start: 0.7980 (m) cc_final: 0.7453 (p) REVERT: B 882 THR cc_start: 0.7173 (m) cc_final: 0.6563 (p) REVERT: B 1136 ASP cc_start: 0.8143 (m-30) cc_final: 0.7851 (m-30) REVERT: B 1188 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8566 (mmtm) REVERT: C 9 LYS cc_start: 0.7618 (tttm) cc_final: 0.7134 (tppt) REVERT: C 53 THR cc_start: 0.6809 (m) cc_final: 0.6485 (t) REVERT: D 14 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7710 (tpp80) REVERT: D 16 LYS cc_start: 0.7643 (mppt) cc_final: 0.7397 (mppt) REVERT: D 36 LYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5679 (pmtt) REVERT: D 54 GLU cc_start: 0.8510 (tt0) cc_final: 0.8250 (pt0) REVERT: D 121 LYS cc_start: 0.4925 (tmmt) cc_final: 0.4653 (tmmt) REVERT: D 142 LYS cc_start: 0.8330 (tptt) cc_final: 0.8002 (pptt) REVERT: D 209 ARG cc_start: 0.6344 (ptm160) cc_final: 0.6132 (ptm160) REVERT: E 17 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7512 (ttm-80) REVERT: E 32 GLN cc_start: 0.7762 (tp40) cc_final: 0.7552 (pp30) REVERT: E 33 GLU cc_start: 0.8270 (mp0) cc_final: 0.7442 (mp0) REVERT: E 46 TYR cc_start: 0.7723 (m-80) cc_final: 0.7189 (m-80) REVERT: E 48 ASP cc_start: 0.7524 (p0) cc_final: 0.7162 (p0) REVERT: E 54 GLN cc_start: 0.7015 (pm20) cc_final: 0.6656 (pp30) REVERT: E 58 MET cc_start: 0.6232 (ttt) cc_final: 0.5491 (ttm) REVERT: E 67 GLU cc_start: 0.8431 (mp0) cc_final: 0.8046 (tp30) REVERT: E 114 ASN cc_start: 0.8590 (m110) cc_final: 0.8027 (t0) REVERT: E 140 LEU cc_start: 0.8736 (mt) cc_final: 0.8392 (mp) REVERT: F 103 MET cc_start: 0.8148 (mtp) cc_final: 0.7937 (mtp) REVERT: F 104 ASN cc_start: 0.7792 (t0) cc_final: 0.7474 (t0) REVERT: F 116 ASP cc_start: 0.8380 (t0) cc_final: 0.8059 (t70) REVERT: F 119 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7374 (mmm-85) REVERT: F 124 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8008 (mt-10) REVERT: G 50 ASP cc_start: 0.8136 (t70) cc_final: 0.7695 (t0) REVERT: G 57 GLN cc_start: 0.8080 (mt0) cc_final: 0.7858 (mt0) REVERT: G 69 GLU cc_start: 0.7934 (tt0) cc_final: 0.7583 (tt0) REVERT: G 71 ASN cc_start: 0.8641 (t0) cc_final: 0.7829 (t0) REVERT: G 80 LYS cc_start: 0.5372 (tptt) cc_final: 0.5159 (ttpt) REVERT: G 119 LEU cc_start: 0.7109 (tp) cc_final: 0.6685 (mt) REVERT: H 8 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7384 (t70) REVERT: H 27 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: H 126 GLU cc_start: 0.8252 (tt0) cc_final: 0.7792 (tt0) REVERT: H 138 GLU cc_start: 0.8397 (pm20) cc_final: 0.8196 (pm20) REVERT: I 8 ARG cc_start: 0.8407 (tpt90) cc_final: 0.8048 (tmm160) REVERT: I 61 ASP cc_start: 0.7234 (p0) cc_final: 0.6940 (p0) REVERT: J 23 ASN cc_start: 0.8458 (t0) cc_final: 0.7696 (m110) REVERT: K 22 ASP cc_start: 0.8325 (m-30) cc_final: 0.8120 (m-30) REVERT: K 106 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7283 (mm-30) REVERT: L 37 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7663 (ttmm) REVERT: L 64 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6857 (mp) outliers start: 100 outliers final: 41 residues processed: 478 average time/residue: 0.6826 time to fit residues: 389.0463 Evaluate side-chains 428 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 379 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 55 optimal weight: 1.9990 chunk 305 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 300 optimal weight: 0.0570 chunk 354 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A1070 GLN B 236 HIS B 357 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN G 57 GLN H 33 GLN I 108 HIS J 26 GLN K 2 ASN K 110 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.104395 restraints weight = 54238.541| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.91 r_work: 0.3368 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 33761 Z= 0.131 Angle : 0.580 12.058 45848 Z= 0.298 Chirality : 0.043 0.271 5153 Planarity : 0.004 0.072 5726 Dihedral : 13.212 164.927 5050 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.39 % Allowed : 16.25 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.13), residues: 3936 helix: 1.21 (0.14), residues: 1383 sheet: -0.39 (0.19), residues: 644 loop : 0.02 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 144 TYR 0.021 0.001 TYR I 15 PHE 0.031 0.001 PHE E 72 TRP 0.011 0.001 TRP A1044 HIS 0.010 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (33724) covalent geometry : angle 0.56403 / 0.30 (45800) hydrogen bonds : bond 0.03819 / 2.58 ( 1448) hydrogen bonds : angle 4.71987 / 3.39 ( 4072) metal coordination : bond 0.00550 / 0.34 ( 32) metal coordination : angle 4.33045 / 2.80 ( 45) Misc. bond : bond 0.00067 / 0.03 ( 4) link_TRANS : bond 0.00073 / 0.04 ( 1) link_TRANS : angle 0.26313 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 429 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7683 (mmm) cc_final: 0.7197 (mmm) REVERT: A 45 GLN cc_start: 0.8777 (mm110) cc_final: 0.8379 (mp10) REVERT: A 55 ASP cc_start: 0.8343 (t0) cc_final: 0.8112 (t0) REVERT: A 74 MET cc_start: 0.7411 (mtp) cc_final: 0.6698 (mtt) REVERT: A 268 ASP cc_start: 0.8855 (m-30) cc_final: 0.8452 (m-30) REVERT: A 281 HIS cc_start: 0.8893 (t-90) cc_final: 0.8479 (t-90) REVERT: A 592 ASP cc_start: 0.8361 (m-30) cc_final: 0.7871 (m-30) REVERT: A 593 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8069 (pp20) REVERT: A 995 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: A 1110 ASN cc_start: 0.8360 (m-40) cc_final: 0.7939 (p0) REVERT: A 1228 TRP cc_start: 0.8378 (p90) cc_final: 0.8048 (p-90) REVERT: A 1267 MET cc_start: 0.8441 (tmm) cc_final: 0.7850 (ptp) REVERT: A 1297 GLU cc_start: 0.8795 (mp0) cc_final: 0.8405 (mp0) REVERT: A 1312 ASN cc_start: 0.7343 (t0) cc_final: 0.6520 (t0) REVERT: A 1408 ILE cc_start: 0.8217 (mm) cc_final: 0.7998 (mt) REVERT: A 1454 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.5925 (ppp) REVERT: B 177 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8324 (tmtt) REVERT: B 301 ILE cc_start: 0.8261 (mt) cc_final: 0.7901 (mm) REVERT: B 315 LYS cc_start: 0.5938 (mmtt) cc_final: 0.5535 (tmmm) REVERT: B 393 LYS cc_start: 0.7392 (mtmm) cc_final: 0.6928 (mtmm) REVERT: B 418 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7808 (tmmt) REVERT: B 552 MET cc_start: 0.7967 (tpp) cc_final: 0.7710 (tpp) REVERT: B 564 GLU cc_start: 0.7651 (tt0) cc_final: 0.7327 (tt0) REVERT: B 570 VAL cc_start: 0.8150 (t) cc_final: 0.7917 (m) REVERT: B 589 VAL cc_start: 0.7781 (m) cc_final: 0.7089 (p) REVERT: B 706 GLN cc_start: 0.8041 (pm20) cc_final: 0.7422 (mm110) REVERT: B 860 MET cc_start: 0.8415 (tmm) cc_final: 0.8104 (tmm) REVERT: B 873 THR cc_start: 0.7902 (m) cc_final: 0.7378 (p) REVERT: B 882 THR cc_start: 0.7012 (m) cc_final: 0.6661 (p) REVERT: B 1136 ASP cc_start: 0.8060 (m-30) cc_final: 0.7735 (m-30) REVERT: B 1188 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (mmtm) REVERT: C 9 LYS cc_start: 0.7577 (tttm) cc_final: 0.7103 (tppt) REVERT: C 15 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7750 (tttt) REVERT: C 53 THR cc_start: 0.6867 (m) cc_final: 0.6500 (t) REVERT: C 107 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7646 (p) REVERT: D 16 LYS cc_start: 0.7550 (mppt) cc_final: 0.7201 (mppt) REVERT: D 54 GLU cc_start: 0.8444 (tt0) cc_final: 0.8097 (pt0) REVERT: D 121 LYS cc_start: 0.4730 (tmmt) cc_final: 0.4457 (tmmt) REVERT: D 142 LYS cc_start: 0.8276 (tptt) cc_final: 0.7959 (pptt) REVERT: E 17 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7568 (ttm-80) REVERT: E 33 GLU cc_start: 0.8360 (mp0) cc_final: 0.7500 (mp0) REVERT: E 41 ASP cc_start: 0.7729 (m-30) cc_final: 0.7378 (m-30) REVERT: E 45 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8830 (tttm) REVERT: E 58 MET cc_start: 0.6088 (ttt) cc_final: 0.5578 (ttm) REVERT: E 67 GLU cc_start: 0.8422 (mp0) cc_final: 0.7989 (tp30) REVERT: E 114 ASN cc_start: 0.8542 (m110) cc_final: 0.8004 (t0) REVERT: E 140 LEU cc_start: 0.8696 (mt) cc_final: 0.8354 (mp) REVERT: E 215 MET cc_start: 0.6345 (tpp) cc_final: 0.5228 (pp-130) REVERT: F 104 ASN cc_start: 0.7799 (t0) cc_final: 0.7461 (t0) REVERT: F 116 ASP cc_start: 0.8423 (t0) cc_final: 0.8095 (t70) REVERT: F 124 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8056 (mt-10) REVERT: G 29 LYS cc_start: 0.7868 (mttm) cc_final: 0.7434 (mttm) REVERT: G 33 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7111 (mm-30) REVERT: G 50 ASP cc_start: 0.8106 (t70) cc_final: 0.7671 (t0) REVERT: G 69 GLU cc_start: 0.7883 (tt0) cc_final: 0.7525 (tt0) REVERT: G 71 ASN cc_start: 0.8664 (t0) cc_final: 0.8205 (t0) REVERT: G 75 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7359 (mtp85) REVERT: G 80 LYS cc_start: 0.5466 (tptt) cc_final: 0.5196 (ttpt) REVERT: G 115 MET cc_start: 0.5865 (mtt) cc_final: 0.5590 (ptp) REVERT: G 119 LEU cc_start: 0.7090 (tp) cc_final: 0.6702 (mt) REVERT: H 8 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7270 (t70) REVERT: H 27 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: H 126 GLU cc_start: 0.8056 (tt0) cc_final: 0.7642 (tt0) REVERT: I 8 ARG cc_start: 0.8219 (tpt90) cc_final: 0.7864 (tmm160) REVERT: I 61 ASP cc_start: 0.7299 (p0) cc_final: 0.6943 (p0) REVERT: J 23 ASN cc_start: 0.8474 (t0) cc_final: 0.7703 (m110) REVERT: K 22 ASP cc_start: 0.8354 (m-30) cc_final: 0.8093 (m-30) REVERT: K 106 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7236 (mm-30) REVERT: L 37 LYS cc_start: 0.7867 (mtpp) cc_final: 0.7615 (ttmm) outliers start: 84 outliers final: 33 residues processed: 479 average time/residue: 0.6706 time to fit residues: 381.7868 Evaluate side-chains 424 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 384 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 11 optimal weight: 7.9990 chunk 352 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 109 HIS A 390 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN B 236 HIS ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100458 restraints weight = 54746.016| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.60 r_work: 0.3324 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 33761 Z= 0.283 Angle : 0.668 15.641 45848 Z= 0.342 Chirality : 0.046 0.251 5153 Planarity : 0.005 0.073 5726 Dihedral : 13.307 164.556 5050 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.19 % Allowed : 16.59 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 3936 helix: 0.99 (0.14), residues: 1385 sheet: -0.59 (0.19), residues: 645 loop : -0.13 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 144 TYR 0.023 0.002 TYR E 187 PHE 0.031 0.002 PHE A 755 TRP 0.010 0.002 TRP A 572 HIS 0.009 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.28 (33724) covalent geometry : angle 0.64912 / 0.34 (45800) hydrogen bonds : bond 0.04382 / 2.93 ( 1448) hydrogen bonds : angle 4.89716 / 3.51 ( 4072) metal coordination : bond 0.00866 / 0.50 ( 32) metal coordination : angle 5.01270 / 3.27 ( 45) Misc. bond : bond 0.00044 / 0.02 ( 4) link_TRANS : bond 0.00257 / 0.14 ( 1) link_TRANS : angle 0.17151 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 403 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7882 (mmm) cc_final: 0.7439 (mmm) REVERT: A 45 GLN cc_start: 0.8811 (mm110) cc_final: 0.8354 (mp10) REVERT: A 74 MET cc_start: 0.7623 (mtp) cc_final: 0.6925 (mtt) REVERT: A 268 ASP cc_start: 0.9033 (m-30) cc_final: 0.8634 (m-30) REVERT: A 281 HIS cc_start: 0.8931 (t-90) cc_final: 0.8724 (t70) REVERT: A 592 ASP cc_start: 0.8541 (m-30) cc_final: 0.8084 (m-30) REVERT: A 593 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8163 (pp20) REVERT: A 755 PHE cc_start: 0.7606 (t80) cc_final: 0.7153 (t80) REVERT: A 900 ASP cc_start: 0.7035 (t0) cc_final: 0.6589 (p0) REVERT: A 1110 ASN cc_start: 0.8502 (m-40) cc_final: 0.8084 (p0) REVERT: A 1151 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6036 (mm-30) REVERT: A 1202 MET cc_start: 0.6722 (tpp) cc_final: 0.6340 (tpt) REVERT: A 1228 TRP cc_start: 0.8561 (p90) cc_final: 0.8052 (OUTLIER) REVERT: A 1312 ASN cc_start: 0.7884 (t0) cc_final: 0.7096 (t0) REVERT: A 1454 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6149 (ppp) REVERT: B 138 GLU cc_start: 0.7871 (pm20) cc_final: 0.7567 (tp30) REVERT: B 177 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8584 (tmtt) REVERT: B 393 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7094 (mtmm) REVERT: B 418 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8163 (tmmt) REVERT: B 570 VAL cc_start: 0.8433 (t) cc_final: 0.8203 (m) REVERT: B 589 VAL cc_start: 0.8136 (m) cc_final: 0.7741 (p) REVERT: B 706 GLN cc_start: 0.8364 (pm20) cc_final: 0.7729 (tp40) REVERT: B 860 MET cc_start: 0.8607 (tmm) cc_final: 0.8358 (tmm) REVERT: B 873 THR cc_start: 0.8094 (m) cc_final: 0.7524 (p) REVERT: B 882 THR cc_start: 0.7294 (m) cc_final: 0.6979 (p) REVERT: B 887 HIS cc_start: 0.8426 (m90) cc_final: 0.8069 (m-70) REVERT: B 1133 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7561 (mtm) REVERT: B 1136 ASP cc_start: 0.8493 (m-30) cc_final: 0.8180 (m-30) REVERT: B 1188 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8800 (mmtm) REVERT: C 9 LYS cc_start: 0.8076 (tttm) cc_final: 0.7637 (tppt) REVERT: C 53 THR cc_start: 0.7047 (m) cc_final: 0.6803 (t) REVERT: D 16 LYS cc_start: 0.7650 (mppt) cc_final: 0.7224 (mppt) REVERT: D 36 LYS cc_start: 0.6099 (ptpt) cc_final: 0.5767 (ptpt) REVERT: D 54 GLU cc_start: 0.8534 (tt0) cc_final: 0.8257 (pt0) REVERT: D 121 LYS cc_start: 0.4945 (tmmt) cc_final: 0.4657 (ttpt) REVERT: D 142 LYS cc_start: 0.8347 (tptt) cc_final: 0.7989 (pptt) REVERT: E 17 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7684 (ttm-80) REVERT: E 58 MET cc_start: 0.6462 (ttt) cc_final: 0.6000 (ttm) REVERT: E 67 GLU cc_start: 0.8458 (mp0) cc_final: 0.8068 (tp30) REVERT: E 112 TYR cc_start: 0.7449 (p90) cc_final: 0.7225 (p90) REVERT: E 114 ASN cc_start: 0.8663 (m110) cc_final: 0.8172 (t0) REVERT: E 140 LEU cc_start: 0.8858 (mt) cc_final: 0.8539 (mp) REVERT: F 104 ASN cc_start: 0.7978 (t0) cc_final: 0.7578 (t0) REVERT: F 124 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8356 (mt-10) REVERT: G 50 ASP cc_start: 0.8206 (t70) cc_final: 0.7787 (t0) REVERT: G 69 GLU cc_start: 0.8299 (tt0) cc_final: 0.7971 (tt0) REVERT: G 71 ASN cc_start: 0.8947 (t0) cc_final: 0.8586 (t0) REVERT: G 80 LYS cc_start: 0.5557 (tptt) cc_final: 0.5313 (ttpt) REVERT: G 106 MET cc_start: 0.3560 (OUTLIER) cc_final: 0.3305 (ptp) REVERT: G 119 LEU cc_start: 0.7106 (tp) cc_final: 0.6670 (mt) REVERT: H 8 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7568 (t70) REVERT: H 27 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: H 126 GLU cc_start: 0.8506 (tt0) cc_final: 0.8102 (tt0) REVERT: I 8 ARG cc_start: 0.8308 (tpt90) cc_final: 0.8104 (tmm160) REVERT: I 13 MET cc_start: 0.3396 (pp-130) cc_final: 0.2034 (mmm) REVERT: I 89 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: J 19 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8099 (mm-30) REVERT: J 23 ASN cc_start: 0.8746 (t0) cc_final: 0.8031 (m110) REVERT: K 22 ASP cc_start: 0.8568 (m-30) cc_final: 0.8368 (m-30) REVERT: K 106 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7550 (mm-30) REVERT: L 37 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7320 (ttmm) REVERT: L 38 LEU cc_start: 0.6670 (mt) cc_final: 0.6298 (pp) outliers start: 112 outliers final: 59 residues processed: 475 average time/residue: 0.7005 time to fit residues: 394.9066 Evaluate side-chains 438 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 371 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 203 optimal weight: 5.9990 chunk 321 optimal weight: 0.3980 chunk 374 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 360 optimal weight: 4.9990 chunk 311 optimal weight: 0.6980 chunk 383 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN B 236 HIS B 306 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN D 28 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN L 53 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103683 restraints weight = 54422.988| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.60 r_work: 0.3362 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33761 Z= 0.138 Angle : 0.598 12.082 45848 Z= 0.304 Chirality : 0.044 0.337 5153 Planarity : 0.004 0.072 5726 Dihedral : 13.234 163.928 5050 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.48 % Allowed : 18.10 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3936 helix: 1.15 (0.14), residues: 1385 sheet: -0.54 (0.19), residues: 644 loop : -0.08 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 144 TYR 0.024 0.001 TYR E 187 PHE 0.024 0.001 PHE A 444 TRP 0.011 0.001 TRP A 572 HIS 0.010 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (33724) covalent geometry : angle 0.58166 / 0.30 (45800) hydrogen bonds : bond 0.03839 / 2.57 ( 1448) hydrogen bonds : angle 4.68962 / 3.37 ( 4072) metal coordination : bond 0.00572 / 0.34 ( 32) metal coordination : angle 4.49958 / 2.93 ( 45) Misc. bond : bond 0.00062 / 0.03 ( 4) link_TRANS : bond 0.00097 / 0.05 ( 1) link_TRANS : angle 0.19689 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 402 time to evaluate : 1.318 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: 0.7819 (mmm) cc_final: 0.7355 (mmm) REVERT: A 45 GLN cc_start: 0.8810 (mm110) cc_final: 0.8449 (mp10) REVERT: A 74 MET cc_start: 0.7568 (mtp) cc_final: 0.6906 (mtt) REVERT: A 268 ASP cc_start: 0.8839 (m-30) cc_final: 0.8425 (m-30) REVERT: A 281 HIS cc_start: 0.8892 (t-90) cc_final: 0.8539 (t-90) REVERT: A 592 ASP cc_start: 0.8318 (m-30) cc_final: 0.7993 (m-30) REVERT: A 593 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8094 (pp20) REVERT: A 900 ASP cc_start: 0.6910 (t0) cc_final: 0.6524 (p0) REVERT: A 1110 ASN cc_start: 0.8395 (m-40) cc_final: 0.8070 (p0) REVERT: A 1139 GLU cc_start: 0.7732 (tp30) cc_final: 0.7441 (tp30) REVERT: A 1151 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5987 (mm-30) REVERT: A 1228 TRP cc_start: 0.8549 (p90) cc_final: 0.8041 (p-90) REVERT: A 1312 ASN cc_start: 0.7683 (t0) cc_final: 0.6915 (t0) REVERT: A 1454 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6202 (ppp) REVERT: B 177 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8446 (tmtt) REVERT: B 312 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 393 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7091 (mtmm) REVERT: B 418 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8027 (tmmt) REVERT: B 570 VAL cc_start: 0.8371 (t) cc_final: 0.8125 (m) REVERT: B 589 VAL cc_start: 0.7995 (m) cc_final: 0.7649 (p) REVERT: B 706 GLN cc_start: 0.8271 (pm20) cc_final: 0.7658 (tp40) REVERT: B 860 MET cc_start: 0.8455 (tmm) cc_final: 0.8195 (tmm) REVERT: B 873 THR cc_start: 0.8122 (m) cc_final: 0.7569 (p) REVERT: B 882 THR cc_start: 0.7272 (m) cc_final: 0.6944 (p) REVERT: B 887 HIS cc_start: 0.8376 (m90) cc_final: 0.8017 (m-70) REVERT: B 925 LEU cc_start: 0.1781 (OUTLIER) cc_final: 0.1410 (mp) REVERT: B 1136 ASP cc_start: 0.8259 (m-30) cc_final: 0.7927 (m-30) REVERT: B 1188 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8764 (mmtm) REVERT: C 9 LYS cc_start: 0.7932 (tttm) cc_final: 0.7490 (tppt) REVERT: C 53 THR cc_start: 0.7025 (m) cc_final: 0.6740 (t) REVERT: C 107 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7926 (p) REVERT: D 16 LYS cc_start: 0.7554 (mppt) cc_final: 0.7342 (mppt) REVERT: D 36 LYS cc_start: 0.6186 (ptpt) cc_final: 0.5835 (ptpt) REVERT: D 54 GLU cc_start: 0.8511 (tt0) cc_final: 0.8208 (pt0) REVERT: D 59 ILE cc_start: 0.7733 (mp) cc_final: 0.7507 (mp) REVERT: D 60 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8260 (mmtt) REVERT: D 121 LYS cc_start: 0.4857 (tmmt) cc_final: 0.4534 (ttpt) REVERT: D 142 LYS cc_start: 0.8281 (tptt) cc_final: 0.7901 (pptt) REVERT: E 17 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7684 (ttm-80) REVERT: E 58 MET cc_start: 0.6113 (ttt) cc_final: 0.5719 (ttm) REVERT: E 67 GLU cc_start: 0.8391 (mp0) cc_final: 0.7999 (tp30) REVERT: E 114 ASN cc_start: 0.8590 (m110) cc_final: 0.8036 (t0) REVERT: E 140 LEU cc_start: 0.8834 (mt) cc_final: 0.8505 (mp) REVERT: E 215 MET cc_start: 0.6944 (tpp) cc_final: 0.5960 (pp-130) REVERT: F 104 ASN cc_start: 0.7852 (t0) cc_final: 0.7429 (t0) REVERT: F 124 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8317 (mt-10) REVERT: G 33 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7316 (mm-30) REVERT: G 34 VAL cc_start: 0.7019 (OUTLIER) cc_final: 0.6338 (t) REVERT: G 50 ASP cc_start: 0.8184 (t70) cc_final: 0.7737 (t0) REVERT: G 69 GLU cc_start: 0.8105 (tt0) cc_final: 0.7711 (tt0) REVERT: G 71 ASN cc_start: 0.8797 (t0) cc_final: 0.8443 (t0) REVERT: G 119 LEU cc_start: 0.7048 (tp) cc_final: 0.6679 (mt) REVERT: H 8 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7475 (t70) REVERT: H 126 GLU cc_start: 0.8316 (tt0) cc_final: 0.7844 (tt0) REVERT: I 13 MET cc_start: 0.3405 (pp-130) cc_final: 0.2090 (mmm) REVERT: I 15 TYR cc_start: 0.6578 (t80) cc_final: 0.5991 (t80) REVERT: I 61 ASP cc_start: 0.7336 (p0) cc_final: 0.6916 (p0) REVERT: J 19 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7722 (mm-30) REVERT: J 23 ASN cc_start: 0.8702 (t0) cc_final: 0.7990 (m110) REVERT: K 22 ASP cc_start: 0.8433 (m-30) cc_final: 0.8200 (m-30) REVERT: K 106 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7469 (mm-30) REVERT: L 37 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7525 (ttmm) REVERT: L 38 LEU cc_start: 0.6636 (mt) cc_final: 0.6223 (pp) REVERT: L 58 LYS cc_start: 0.8218 (tttp) cc_final: 0.7996 (tttp) outliers start: 87 outliers final: 36 residues processed: 459 average time/residue: 0.7394 time to fit residues: 403.6175 Evaluate side-chains 420 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 376 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 141 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 390 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 89 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.144106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103971 restraints weight = 54435.146| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.60 r_work: 0.3369 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33761 Z= 0.142 Angle : 0.590 11.767 45848 Z= 0.300 Chirality : 0.043 0.255 5153 Planarity : 0.004 0.073 5726 Dihedral : 13.127 163.748 5050 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 18.73 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 3936 helix: 1.22 (0.14), residues: 1383 sheet: -0.54 (0.19), residues: 637 loop : -0.02 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 144 TYR 0.021 0.001 TYR E 187 PHE 0.023 0.001 PHE A 444 TRP 0.011 0.001 TRP A 572 HIS 0.010 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (33724) covalent geometry : angle 0.57588 / 0.30 (45800) hydrogen bonds : bond 0.03721 / 2.48 ( 1448) hydrogen bonds : angle 4.61090 / 3.31 ( 4072) metal coordination : bond 0.00538 / 0.33 ( 32) metal coordination : angle 4.14314 / 2.68 ( 45) Misc. bond : bond 0.00066 / 0.03 ( 4) link_TRANS : bond 0.00111 / 0.06 ( 1) link_TRANS : angle 0.17325 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 393 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7841 (mmm) cc_final: 0.7319 (mmm) REVERT: A 45 GLN cc_start: 0.8811 (mm110) cc_final: 0.8383 (mp10) REVERT: A 74 MET cc_start: 0.7593 (mtp) cc_final: 0.6936 (mtt) REVERT: A 268 ASP cc_start: 0.8871 (m-30) cc_final: 0.8452 (m-30) REVERT: A 281 HIS cc_start: 0.8911 (t-90) cc_final: 0.8538 (t-90) REVERT: A 592 ASP cc_start: 0.8300 (m-30) cc_final: 0.7975 (m-30) REVERT: A 593 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8023 (pp20) REVERT: A 900 ASP cc_start: 0.6893 (t0) cc_final: 0.6570 (p0) REVERT: A 1110 ASN cc_start: 0.8379 (m-40) cc_final: 0.8045 (p0) REVERT: A 1139 GLU cc_start: 0.7803 (tp30) cc_final: 0.7557 (tp30) REVERT: A 1151 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5956 (mm-30) REVERT: A 1202 MET cc_start: 0.6658 (tpp) cc_final: 0.6225 (tpt) REVERT: A 1228 TRP cc_start: 0.8568 (p90) cc_final: 0.8003 (OUTLIER) REVERT: A 1290 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7660 (mmmm) REVERT: A 1297 GLU cc_start: 0.8877 (mp0) cc_final: 0.8528 (mp0) REVERT: A 1312 ASN cc_start: 0.7678 (t0) cc_final: 0.6903 (t0) REVERT: A 1454 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6295 (ppp) REVERT: B 177 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8445 (tmtt) REVERT: B 355 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 393 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7162 (mtmm) REVERT: B 418 LYS cc_start: 0.8507 (tmtt) cc_final: 0.8046 (tmmt) REVERT: B 570 VAL cc_start: 0.8374 (t) cc_final: 0.8123 (m) REVERT: B 589 VAL cc_start: 0.8037 (m) cc_final: 0.7705 (p) REVERT: B 691 GLU cc_start: 0.7715 (tt0) cc_final: 0.7459 (tt0) REVERT: B 706 GLN cc_start: 0.8295 (pm20) cc_final: 0.7642 (tp40) REVERT: B 860 MET cc_start: 0.8476 (tmm) cc_final: 0.8143 (tmm) REVERT: B 873 THR cc_start: 0.8089 (m) cc_final: 0.7569 (p) REVERT: B 882 THR cc_start: 0.7255 (m) cc_final: 0.6944 (p) REVERT: B 887 HIS cc_start: 0.8393 (m90) cc_final: 0.8022 (m-70) REVERT: B 925 LEU cc_start: 0.1546 (OUTLIER) cc_final: 0.1187 (mp) REVERT: B 1136 ASP cc_start: 0.8247 (m-30) cc_final: 0.7912 (m-30) REVERT: C 9 LYS cc_start: 0.7952 (tttm) cc_final: 0.7498 (tppt) REVERT: C 53 THR cc_start: 0.6996 (m) cc_final: 0.6728 (t) REVERT: C 107 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7903 (p) REVERT: C 148 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: D 36 LYS cc_start: 0.6193 (ptpt) cc_final: 0.5853 (ptpt) REVERT: D 54 GLU cc_start: 0.8508 (tt0) cc_final: 0.8218 (pt0) REVERT: D 59 ILE cc_start: 0.7798 (mp) cc_final: 0.7575 (mp) REVERT: D 60 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8305 (mptt) REVERT: D 121 LYS cc_start: 0.4884 (tmmt) cc_final: 0.4560 (ttpt) REVERT: D 142 LYS cc_start: 0.8312 (tptt) cc_final: 0.7937 (pptt) REVERT: E 17 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7682 (ttm-80) REVERT: E 32 GLN cc_start: 0.7316 (pm20) cc_final: 0.7106 (pp30) REVERT: E 67 GLU cc_start: 0.8388 (mp0) cc_final: 0.8009 (tp30) REVERT: E 140 LEU cc_start: 0.8829 (mt) cc_final: 0.8505 (mp) REVERT: E 215 MET cc_start: 0.6883 (tpp) cc_final: 0.6034 (pp-130) REVERT: F 104 ASN cc_start: 0.7811 (t0) cc_final: 0.7389 (t0) REVERT: F 116 ASP cc_start: 0.8423 (t0) cc_final: 0.8195 (t70) REVERT: F 124 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8304 (mt-10) REVERT: G 25 TYR cc_start: 0.7076 (m-80) cc_final: 0.6700 (m-80) REVERT: G 33 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7259 (mm-30) REVERT: G 34 VAL cc_start: 0.6961 (OUTLIER) cc_final: 0.6306 (t) REVERT: G 50 ASP cc_start: 0.8177 (t70) cc_final: 0.7811 (t0) REVERT: G 57 GLN cc_start: 0.8260 (mt0) cc_final: 0.7737 (mt0) REVERT: G 69 GLU cc_start: 0.8101 (tt0) cc_final: 0.7714 (tt0) REVERT: G 71 ASN cc_start: 0.8799 (t0) cc_final: 0.7939 (t0) REVERT: G 106 MET cc_start: 0.3553 (ptm) cc_final: 0.3104 (ptp) REVERT: G 119 LEU cc_start: 0.7028 (tp) cc_final: 0.6639 (mt) REVERT: H 8 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7455 (t70) REVERT: H 126 GLU cc_start: 0.8257 (tt0) cc_final: 0.7795 (tt0) REVERT: I 5 ARG cc_start: 0.6322 (mmm160) cc_final: 0.6060 (tpp80) REVERT: I 8 ARG cc_start: 0.8084 (tpt90) cc_final: 0.7824 (tmm160) REVERT: I 13 MET cc_start: 0.3408 (pp-130) cc_final: 0.2042 (mmm) REVERT: I 15 TYR cc_start: 0.6811 (t80) cc_final: 0.6259 (t80) REVERT: I 61 ASP cc_start: 0.7313 (p0) cc_final: 0.6926 (p0) REVERT: I 89 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: J 23 ASN cc_start: 0.8682 (t0) cc_final: 0.7958 (m110) REVERT: K 106 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7449 (mm-30) REVERT: L 37 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7508 (ttmm) REVERT: L 38 LEU cc_start: 0.6733 (mt) cc_final: 0.6408 (pp) outliers start: 85 outliers final: 43 residues processed: 451 average time/residue: 0.7348 time to fit residues: 394.6985 Evaluate side-chains 432 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 252 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 291 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS B 306 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 114 ASN I 89 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.142699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102653 restraints weight = 54728.714| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.61 r_work: 0.3345 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33761 Z= 0.199 Angle : 0.624 12.635 45848 Z= 0.316 Chirality : 0.044 0.256 5153 Planarity : 0.004 0.073 5726 Dihedral : 13.117 163.780 5050 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.45 % Allowed : 19.01 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 3936 helix: 1.16 (0.14), residues: 1383 sheet: -0.54 (0.19), residues: 637 loop : -0.06 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 144 TYR 0.024 0.001 TYR E 112 PHE 0.025 0.002 PHE A 755 TRP 0.009 0.001 TRP A 572 HIS 0.010 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (33724) covalent geometry : angle 0.61005 / 0.32 (45800) hydrogen bonds : bond 0.03856 / 2.56 ( 1448) hydrogen bonds : angle 4.64569 / 3.33 ( 4072) metal coordination : bond 0.00686 / 0.43 ( 32) metal coordination : angle 4.30199 / 2.80 ( 45) Misc. bond : bond 0.00062 / 0.03 ( 4) link_TRANS : bond 0.00165 / 0.09 ( 1) link_TRANS : angle 0.15465 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 388 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7777 (mmm) cc_final: 0.7254 (mmm) REVERT: A 45 GLN cc_start: 0.8804 (mm110) cc_final: 0.8374 (mp10) REVERT: A 74 MET cc_start: 0.7594 (mtp) cc_final: 0.6935 (mtt) REVERT: A 268 ASP cc_start: 0.8882 (m-30) cc_final: 0.8441 (m-30) REVERT: A 281 HIS cc_start: 0.8916 (t-90) cc_final: 0.8543 (t-90) REVERT: A 592 ASP cc_start: 0.8316 (m-30) cc_final: 0.7989 (m-30) REVERT: A 593 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8031 (pp20) REVERT: A 900 ASP cc_start: 0.6873 (t0) cc_final: 0.6463 (p0) REVERT: A 1110 ASN cc_start: 0.8409 (m-40) cc_final: 0.8008 (p0) REVERT: A 1151 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5987 (mm-30) REVERT: A 1228 TRP cc_start: 0.8599 (p90) cc_final: 0.7988 (p-90) REVERT: A 1278 ASN cc_start: 0.7119 (t0) cc_final: 0.6758 (t0) REVERT: A 1290 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7636 (mmmm) REVERT: A 1312 ASN cc_start: 0.7735 (t0) cc_final: 0.6960 (t0) REVERT: A 1454 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6175 (ppp) REVERT: B 177 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8458 (tmtt) REVERT: B 239 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: B 355 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8257 (tp) REVERT: B 393 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7202 (mtmm) REVERT: B 418 LYS cc_start: 0.8507 (tmtt) cc_final: 0.8038 (tmmt) REVERT: B 570 VAL cc_start: 0.8393 (t) cc_final: 0.8162 (m) REVERT: B 589 VAL cc_start: 0.8088 (m) cc_final: 0.7741 (p) REVERT: B 691 GLU cc_start: 0.7729 (tt0) cc_final: 0.7498 (tt0) REVERT: B 706 GLN cc_start: 0.8212 (pm20) cc_final: 0.7640 (tp40) REVERT: B 860 MET cc_start: 0.8514 (tmm) cc_final: 0.8172 (tmm) REVERT: B 873 THR cc_start: 0.8099 (m) cc_final: 0.7543 (p) REVERT: B 882 THR cc_start: 0.7265 (m) cc_final: 0.7016 (p) REVERT: B 887 HIS cc_start: 0.8486 (m90) cc_final: 0.8114 (m-70) REVERT: B 925 LEU cc_start: 0.1514 (OUTLIER) cc_final: 0.1184 (mp) REVERT: B 1136 ASP cc_start: 0.8311 (m-30) cc_final: 0.7963 (m-30) REVERT: C 9 LYS cc_start: 0.7954 (tttm) cc_final: 0.7510 (tppt) REVERT: C 53 THR cc_start: 0.7058 (m) cc_final: 0.6781 (t) REVERT: C 148 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7188 (ttm-80) REVERT: D 36 LYS cc_start: 0.6194 (ptpt) cc_final: 0.5858 (ptpt) REVERT: D 54 GLU cc_start: 0.8549 (tt0) cc_final: 0.8249 (pt0) REVERT: D 59 ILE cc_start: 0.7813 (mp) cc_final: 0.7613 (mp) REVERT: D 60 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8338 (mptt) REVERT: D 121 LYS cc_start: 0.5026 (tmmt) cc_final: 0.4684 (ttpt) REVERT: D 142 LYS cc_start: 0.8310 (tptt) cc_final: 0.7929 (pptt) REVERT: E 17 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7737 (ttm-80) REVERT: E 67 GLU cc_start: 0.8385 (mp0) cc_final: 0.8010 (tp30) REVERT: E 215 MET cc_start: 0.7024 (tpp) cc_final: 0.6096 (pp-130) REVERT: F 104 ASN cc_start: 0.7800 (t0) cc_final: 0.7347 (t0) REVERT: F 124 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8341 (mt-10) REVERT: G 25 TYR cc_start: 0.7047 (m-80) cc_final: 0.6643 (m-80) REVERT: G 49 LEU cc_start: 0.8555 (mt) cc_final: 0.8147 (pp) REVERT: G 50 ASP cc_start: 0.8194 (t70) cc_final: 0.7855 (t0) REVERT: G 57 GLN cc_start: 0.8305 (mt0) cc_final: 0.7817 (mt0) REVERT: G 69 GLU cc_start: 0.8109 (tt0) cc_final: 0.7710 (tt0) REVERT: G 71 ASN cc_start: 0.8814 (t0) cc_final: 0.8024 (t0) REVERT: G 106 MET cc_start: 0.3606 (ptm) cc_final: 0.3182 (ptp) REVERT: G 119 LEU cc_start: 0.7030 (tp) cc_final: 0.6630 (mt) REVERT: H 8 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7473 (t70) REVERT: H 126 GLU cc_start: 0.8306 (tt0) cc_final: 0.7887 (tt0) REVERT: I 13 MET cc_start: 0.3532 (pp-130) cc_final: 0.2032 (mmm) REVERT: J 1 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7155 (mpp) REVERT: J 23 ASN cc_start: 0.8703 (t0) cc_final: 0.7991 (m110) REVERT: K 106 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7480 (mm-30) REVERT: L 37 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7572 (ttmm) REVERT: L 38 LEU cc_start: 0.6750 (mt) cc_final: 0.6356 (pp) outliers start: 86 outliers final: 51 residues processed: 438 average time/residue: 0.7409 time to fit residues: 386.2869 Evaluate side-chains 438 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 378 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 193 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 369 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.144041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104034 restraints weight = 54336.045| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.61 r_work: 0.3372 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33761 Z= 0.142 Angle : 0.611 13.268 45848 Z= 0.310 Chirality : 0.043 0.269 5153 Planarity : 0.004 0.072 5726 Dihedral : 13.072 163.519 5050 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.08 % Allowed : 19.90 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 3936 helix: 1.19 (0.14), residues: 1384 sheet: -0.54 (0.19), residues: 639 loop : -0.03 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 144 TYR 0.020 0.001 TYR E 112 PHE 0.022 0.001 PHE A 219 TRP 0.011 0.001 TRP A 572 HIS 0.011 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (33724) covalent geometry : angle 0.59810 / 0.31 (45800) hydrogen bonds : bond 0.03675 / 2.45 ( 1448) hydrogen bonds : angle 4.56641 / 3.28 ( 4072) metal coordination : bond 0.00563 / 0.35 ( 32) metal coordination : angle 4.10351 / 2.66 ( 45) Misc. bond : bond 0.00072 / 0.04 ( 4) link_TRANS : bond 0.00108 / 0.06 ( 1) link_TRANS : angle 0.17472 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7783 (mmm) cc_final: 0.7266 (mmm) REVERT: A 45 GLN cc_start: 0.8818 (mm110) cc_final: 0.8430 (mp10) REVERT: A 74 MET cc_start: 0.7544 (mtp) cc_final: 0.6876 (mtt) REVERT: A 173 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7576 (p) REVERT: A 218 ASP cc_start: 0.8238 (t0) cc_final: 0.8015 (t0) REVERT: A 268 ASP cc_start: 0.8886 (m-30) cc_final: 0.8454 (m-30) REVERT: A 281 HIS cc_start: 0.8920 (t-90) cc_final: 0.8547 (t-90) REVERT: A 592 ASP cc_start: 0.8300 (m-30) cc_final: 0.7972 (m-30) REVERT: A 593 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8024 (pp20) REVERT: A 755 PHE cc_start: 0.7133 (t80) cc_final: 0.6890 (t80) REVERT: A 900 ASP cc_start: 0.6845 (t0) cc_final: 0.6436 (p0) REVERT: A 1110 ASN cc_start: 0.8322 (m-40) cc_final: 0.7938 (p0) REVERT: A 1151 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5973 (mm-30) REVERT: A 1202 MET cc_start: 0.6650 (tpp) cc_final: 0.6351 (tpt) REVERT: A 1228 TRP cc_start: 0.8567 (p90) cc_final: 0.8019 (OUTLIER) REVERT: A 1278 ASN cc_start: 0.7136 (t0) cc_final: 0.6777 (t0) REVERT: A 1290 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7648 (mmmm) REVERT: A 1312 ASN cc_start: 0.7635 (t0) cc_final: 0.6894 (t0) REVERT: A 1454 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6195 (ppp) REVERT: B 177 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8446 (tmtt) REVERT: B 418 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8027 (tmmt) REVERT: B 570 VAL cc_start: 0.8369 (t) cc_final: 0.8128 (m) REVERT: B 589 VAL cc_start: 0.8049 (m) cc_final: 0.7691 (p) REVERT: B 691 GLU cc_start: 0.7708 (tt0) cc_final: 0.7479 (tt0) REVERT: B 705 MET cc_start: 0.8871 (tpp) cc_final: 0.8575 (mmm) REVERT: B 706 GLN cc_start: 0.8205 (pm20) cc_final: 0.7652 (tp40) REVERT: B 860 MET cc_start: 0.8490 (tmm) cc_final: 0.8155 (tmm) REVERT: B 873 THR cc_start: 0.8103 (m) cc_final: 0.7611 (p) REVERT: B 887 HIS cc_start: 0.8536 (m90) cc_final: 0.8316 (m-70) REVERT: B 925 LEU cc_start: 0.1491 (OUTLIER) cc_final: 0.1166 (mp) REVERT: B 1136 ASP cc_start: 0.8286 (m-30) cc_final: 0.7923 (m-30) REVERT: B 1181 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: B 1208 MET cc_start: 0.8828 (mtt) cc_final: 0.8600 (mtp) REVERT: C 9 LYS cc_start: 0.7930 (tttm) cc_final: 0.7488 (tppt) REVERT: C 53 THR cc_start: 0.7015 (m) cc_final: 0.6745 (t) REVERT: C 107 SER cc_start: 0.8186 (m) cc_final: 0.7886 (p) REVERT: D 12 ARG cc_start: 0.4350 (mmp-170) cc_final: 0.4141 (mmp-170) REVERT: D 36 LYS cc_start: 0.6197 (ptpt) cc_final: 0.5960 (ptpt) REVERT: D 54 GLU cc_start: 0.8542 (tt0) cc_final: 0.8179 (pt0) REVERT: D 142 LYS cc_start: 0.8306 (tptt) cc_final: 0.7916 (pptt) REVERT: E 17 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7721 (ttm-80) REVERT: E 58 MET cc_start: 0.5867 (mtp) cc_final: 0.5179 (mtp) REVERT: E 67 GLU cc_start: 0.8385 (mp0) cc_final: 0.8004 (tp30) REVERT: E 140 LEU cc_start: 0.8811 (mt) cc_final: 0.8538 (mp) REVERT: E 215 MET cc_start: 0.7013 (tpp) cc_final: 0.6147 (pp-130) REVERT: F 104 ASN cc_start: 0.7622 (t0) cc_final: 0.7201 (t0) REVERT: F 124 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8329 (mt-10) REVERT: G 25 TYR cc_start: 0.7171 (m-80) cc_final: 0.6745 (m-80) REVERT: G 33 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7173 (mm-30) REVERT: G 49 LEU cc_start: 0.8532 (mt) cc_final: 0.8217 (pt) REVERT: G 50 ASP cc_start: 0.8183 (t70) cc_final: 0.7842 (t0) REVERT: G 57 GLN cc_start: 0.8297 (mt0) cc_final: 0.7838 (mt0) REVERT: G 69 GLU cc_start: 0.8048 (tt0) cc_final: 0.7662 (tt0) REVERT: G 71 ASN cc_start: 0.8789 (t0) cc_final: 0.7795 (t0) REVERT: G 106 MET cc_start: 0.3795 (ptm) cc_final: 0.3371 (ptp) REVERT: G 115 MET cc_start: 0.5624 (ptt) cc_final: 0.5360 (pmt) REVERT: G 119 LEU cc_start: 0.7048 (tp) cc_final: 0.6710 (mt) REVERT: H 8 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7492 (t70) REVERT: H 126 GLU cc_start: 0.8239 (tt0) cc_final: 0.7782 (tt0) REVERT: I 5 ARG cc_start: 0.6323 (mmm160) cc_final: 0.6122 (tpp80) REVERT: I 13 MET cc_start: 0.3596 (pp-130) cc_final: 0.2081 (mmm) REVERT: I 15 TYR cc_start: 0.6591 (t80) cc_final: 0.6035 (t80) REVERT: I 61 ASP cc_start: 0.7376 (p0) cc_final: 0.7100 (p0) REVERT: J 1 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7312 (mpp) REVERT: J 23 ASN cc_start: 0.8692 (t0) cc_final: 0.7967 (m110) REVERT: K 54 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8230 (tpp-160) REVERT: K 106 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7466 (mm-30) REVERT: L 37 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7584 (ttmm) REVERT: L 38 LEU cc_start: 0.6815 (mt) cc_final: 0.6436 (pp) outliers start: 73 outliers final: 41 residues processed: 438 average time/residue: 0.6786 time to fit residues: 354.5109 Evaluate side-chains 421 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 21 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 389 optimal weight: 6.9990 chunk 281 optimal weight: 0.0030 chunk 84 optimal weight: 3.9990 chunk 269 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 overall best weight: 2.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 760 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN B 236 HIS B 306 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100973 restraints weight = 55091.208| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.61 r_work: 0.3316 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 33761 Z= 0.237 Angle : 0.674 15.106 45848 Z= 0.341 Chirality : 0.046 0.261 5153 Planarity : 0.004 0.073 5726 Dihedral : 13.129 163.655 5050 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.80 % Allowed : 20.50 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 3936 helix: 1.03 (0.14), residues: 1386 sheet: -0.55 (0.19), residues: 641 loop : -0.12 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 144 TYR 0.019 0.002 TYR C 114 PHE 0.024 0.002 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.009 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (33724) covalent geometry : angle 0.65912 / 0.34 (45800) hydrogen bonds : bond 0.04079 / 2.71 ( 1448) hydrogen bonds : angle 4.72856 / 3.40 ( 4072) metal coordination : bond 0.00794 / 0.48 ( 32) metal coordination : angle 4.59082 / 2.98 ( 45) Misc. bond : bond 0.00060 / 0.03 ( 4) link_TRANS : bond 0.00186 / 0.10 ( 1) link_TRANS : angle 0.15418 / 0.09 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 379 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7685 (mmm) cc_final: 0.7110 (mmm) REVERT: A 45 GLN cc_start: 0.8791 (mm110) cc_final: 0.8401 (mp10) REVERT: A 74 MET cc_start: 0.7569 (mtp) cc_final: 0.6901 (mtt) REVERT: A 173 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7689 (p) REVERT: A 268 ASP cc_start: 0.8915 (m-30) cc_final: 0.8469 (m-30) REVERT: A 281 HIS cc_start: 0.8903 (t-90) cc_final: 0.8540 (t-90) REVERT: A 592 ASP cc_start: 0.8293 (m-30) cc_final: 0.7938 (m-30) REVERT: A 593 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8021 (pp20) REVERT: A 900 ASP cc_start: 0.6880 (t0) cc_final: 0.6420 (p0) REVERT: A 1110 ASN cc_start: 0.8375 (m-40) cc_final: 0.7930 (p0) REVERT: A 1151 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6076 (mm-30) REVERT: A 1202 MET cc_start: 0.6663 (tpp) cc_final: 0.6173 (tpt) REVERT: A 1228 TRP cc_start: 0.8596 (p90) cc_final: 0.8031 (p-90) REVERT: A 1278 ASN cc_start: 0.7200 (t0) cc_final: 0.6817 (t0) REVERT: A 1290 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7545 (mmmm) REVERT: A 1312 ASN cc_start: 0.7869 (t0) cc_final: 0.7068 (t0) REVERT: A 1454 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6213 (ppp) REVERT: B 177 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8485 (tmtt) REVERT: B 355 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8175 (tp) REVERT: B 418 LYS cc_start: 0.8521 (tmtt) cc_final: 0.8042 (tmmt) REVERT: B 564 GLU cc_start: 0.8146 (tt0) cc_final: 0.7840 (tt0) REVERT: B 570 VAL cc_start: 0.8348 (t) cc_final: 0.8088 (m) REVERT: B 589 VAL cc_start: 0.8101 (m) cc_final: 0.7527 (p) REVERT: B 705 MET cc_start: 0.8900 (tpp) cc_final: 0.8592 (mmm) REVERT: B 706 GLN cc_start: 0.8152 (pm20) cc_final: 0.7676 (tp40) REVERT: B 773 MET cc_start: 0.8612 (ttm) cc_final: 0.8309 (mtt) REVERT: B 860 MET cc_start: 0.8518 (tmm) cc_final: 0.8239 (tmm) REVERT: B 873 THR cc_start: 0.8154 (m) cc_final: 0.7588 (p) REVERT: B 887 HIS cc_start: 0.8669 (m90) cc_final: 0.8422 (m-70) REVERT: B 925 LEU cc_start: 0.1564 (OUTLIER) cc_final: 0.1238 (mp) REVERT: B 1136 ASP cc_start: 0.8407 (m-30) cc_final: 0.8059 (m-30) REVERT: B 1181 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7124 (tp30) REVERT: C 9 LYS cc_start: 0.8004 (tttm) cc_final: 0.7574 (tppt) REVERT: C 53 THR cc_start: 0.7061 (m) cc_final: 0.6782 (t) REVERT: D 36 LYS cc_start: 0.6246 (ptpt) cc_final: 0.6005 (ptpt) REVERT: D 54 GLU cc_start: 0.8558 (tt0) cc_final: 0.8210 (pt0) REVERT: D 60 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8419 (mmtt) REVERT: D 142 LYS cc_start: 0.8331 (tptt) cc_final: 0.7933 (pptt) REVERT: E 17 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7682 (ttm-80) REVERT: E 58 MET cc_start: 0.5921 (mtp) cc_final: 0.5137 (mtp) REVERT: E 67 GLU cc_start: 0.8391 (mp0) cc_final: 0.8004 (tp30) REVERT: E 140 LEU cc_start: 0.8801 (mt) cc_final: 0.8520 (mp) REVERT: F 103 MET cc_start: 0.9102 (ptp) cc_final: 0.8898 (ptp) REVERT: F 104 ASN cc_start: 0.7767 (t0) cc_final: 0.7356 (t0) REVERT: G 25 TYR cc_start: 0.7168 (m-80) cc_final: 0.6749 (m-80) REVERT: G 33 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7372 (mm-30) REVERT: G 49 LEU cc_start: 0.8469 (mt) cc_final: 0.8114 (pp) REVERT: G 50 ASP cc_start: 0.8198 (t70) cc_final: 0.7856 (t0) REVERT: G 57 GLN cc_start: 0.8332 (mt0) cc_final: 0.7772 (mt0) REVERT: G 69 GLU cc_start: 0.8105 (tt0) cc_final: 0.7748 (tt0) REVERT: G 71 ASN cc_start: 0.8757 (t0) cc_final: 0.7950 (t0) REVERT: G 106 MET cc_start: 0.3699 (ptm) cc_final: 0.3271 (ptp) REVERT: G 119 LEU cc_start: 0.7071 (tp) cc_final: 0.6635 (mt) REVERT: H 8 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7579 (t70) REVERT: H 126 GLU cc_start: 0.8381 (tt0) cc_final: 0.7972 (tt0) REVERT: I 5 ARG cc_start: 0.6485 (mmm160) cc_final: 0.6223 (tpp80) REVERT: I 13 MET cc_start: 0.3495 (pp-130) cc_final: 0.1969 (mmm) REVERT: I 15 TYR cc_start: 0.6506 (t80) cc_final: 0.5910 (t80) REVERT: J 1 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7310 (mpp) REVERT: J 23 ASN cc_start: 0.8705 (t0) cc_final: 0.7987 (m110) REVERT: K 54 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8373 (tpp-160) REVERT: K 106 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7533 (mm-30) REVERT: L 37 LYS cc_start: 0.7787 (mtpp) cc_final: 0.7320 (ttmm) REVERT: L 38 LEU cc_start: 0.6644 (mt) cc_final: 0.6230 (pp) outliers start: 63 outliers final: 41 residues processed: 417 average time/residue: 0.7344 time to fit residues: 364.5371 Evaluate side-chains 407 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 220 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 293 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 316 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.141419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101132 restraints weight = 54694.231| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.60 r_work: 0.3320 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.462 33761 Z= 0.278 Angle : 0.843 65.556 45848 Z= 0.438 Chirality : 0.045 0.321 5153 Planarity : 0.005 0.213 5726 Dihedral : 13.130 163.650 5050 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.65 % Allowed : 20.81 % Favored : 77.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3936 helix: 1.04 (0.14), residues: 1386 sheet: -0.56 (0.19), residues: 641 loop : -0.13 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 144 TYR 0.016 0.001 TYR C 114 PHE 0.023 0.002 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.008 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.28 (33724) covalent geometry : angle 0.83072 / 0.44 (45800) hydrogen bonds : bond 0.04036 / 2.68 ( 1448) hydrogen bonds : angle 4.72909 / 3.40 ( 4072) metal coordination : bond 0.00744 / 0.45 ( 32) metal coordination : angle 4.59370 / 2.98 ( 45) Misc. bond : bond 0.00061 / 0.03 ( 4) link_TRANS : bond 0.00179 / 0.09 ( 1) link_TRANS : angle 0.18140 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11281.36 seconds wall clock time: 192 minutes 52.45 seconds (11572.45 seconds total)