Starting phenix.real_space_refine on Sun Aug 9 09:04:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kdo_62283/08_2026/9kdo_62283_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kdo_62283/08_2026/9kdo_62283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kdo_62283/08_2026/9kdo_62283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kdo_62283/08_2026/9kdo_62283.map" model { file = "/net/cci-nas-00/data/ceres_data/9kdo_62283/08_2026/9kdo_62283_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kdo_62283/08_2026/9kdo_62283_neut.cif" } resolution = 2.92 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 57 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 20685 2.51 5 N 5749 2.21 5 O 6391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 33071 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: 9427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9427 Classifications: {'peptide': 1183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1130} Chain breaks: 4 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: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} 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: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} 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 70.627 79.449 133.650 1.00 76.92 S ATOM 844 SG CYS A 110 68.860 82.743 134.193 1.00 68.55 S ATOM 1149 SG CYS A 148 72.215 82.239 135.850 1.00 73.57 S ATOM 1287 SG CYS A 167 69.300 80.222 137.076 1.00 60.45 S ATOM 515 SG CYS A 67 45.067 81.191 94.264 1.00 71.81 S ATOM 537 SG CYS A 70 45.664 84.657 92.786 1.00 73.77 S ATOM 590 SG CYS A 77 48.403 81.967 92.577 1.00 93.28 S ATOM 20086 SG CYS B1163 53.360 94.215 102.964 1.00 76.29 S ATOM 20104 SG CYS B1166 54.765 91.279 104.706 1.00 63.30 S ATOM 20229 SG CYS B1182 50.952 91.437 103.672 1.00 54.89 S ATOM 20248 SG CYS B1185 52.439 93.334 106.656 1.00 66.42 S ATOM 21227 SG CYS C 86 58.259 73.665 27.264 1.00 64.78 S ATOM 21244 SG CYS C 88 56.585 71.604 30.005 1.00103.12 S ATOM 21277 SG CYS C 92 57.139 70.230 26.473 1.00 67.19 S ATOM 21300 SG CYS C 95 60.082 70.741 28.944 1.00 92.23 S ATOM 28967 SG CYS I 7 117.320 29.802 126.330 1.00145.89 S ATOM 28992 SG CYS I 10 113.530 29.844 126.534 1.00153.30 S ATOM 29158 SG CYS I 29 115.350 33.062 127.378 1.00136.79 S ATOM 29182 SG CYS I 32 115.664 30.004 129.643 1.00156.73 S ATOM 29509 SG CYS I 75 136.797 37.082 86.920 1.00 88.81 S ATOM 29531 SG CYS I 78 137.514 33.193 87.008 1.00123.13 S ATOM 29747 SG CYS I 103 134.210 34.683 85.354 1.00111.42 S ATOM 29767 SG CYS I 106 134.872 34.551 88.929 1.00 91.74 S ATOM 29912 SG CYS J 7 87.904 60.814 38.583 1.00 65.31 S ATOM 29935 SG CYS J 10 88.263 62.652 35.197 1.00 57.50 S ATOM 30215 SG CYS J 45 91.247 61.762 37.394 1.00 66.62 S ATOM 30221 SG CYS J 46 89.275 59.127 35.350 1.00 60.00 S ATOM 31401 SG CYS L 31 57.186 35.640 56.745 1.00 99.28 S ATOM 31421 SG CYS L 34 56.764 32.080 54.928 1.00 90.61 S ATOM 31525 SG CYS L 48 53.852 34.053 56.660 1.00 69.79 S ATOM 31548 SG CYS L 51 56.702 32.269 58.438 1.00 75.93 S Restraints were copied for chains: O Time building chain proxies: 7.85, per 1000 atoms: 0.24 Number of scatterers: 33071 At special positions: 0 Unit cell: (155.31, 151.59, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 180 16.00 P 57 15.00 Mg 1 11.99 O 6391 8.00 N 5749 7.00 C 20685 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=8, symmetry=0 Links applied TRANS " DVA M 2 " - " THR M 1 " " DVA O 2 " - " THR O 1 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " 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 B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 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 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 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 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 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 " pdb=" CB DVA O 2 " pdb=" CB DVA O 8 " Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 49 sheets defined 38.4% alpha, 19.9% beta 21 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.82 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: 3.625A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 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 removed outlier: 3.507A pdb=" N LEU A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) 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: 3.592A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.509A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.669A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.105A 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 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: 3.715A 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 Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.133A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.787A pdb=" N ALA A1125 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.891A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.676A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.533A 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 1255 through 1269 removed outlier: 3.758A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 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: 3.979A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 removed outlier: 3.731A pdb=" N SER A1392 " --> pdb=" O PHE A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.558A 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 Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.635A 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: 5.512A 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 removed outlier: 3.569A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 4.473A pdb=" N ILE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.534A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.329A 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 562 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 699 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.508A pdb=" N LEU B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.519A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.990A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.514A pdb=" N MET B 809 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 806 through 811' Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.227A pdb=" N THR B 882 " --> pdb=" O ARG B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.798A 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 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.702A pdb=" N ASP C 117 " --> pdb=" O TYR C 114 " (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: 3.615A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.503A 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 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.726A 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: 3.746A 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 removed outlier: 3.586A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.555A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.508A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.633A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.925A 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: 10.641A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.604A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.775A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.040A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.150A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.502A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.752A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.833A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.075A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.075A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.202A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.768A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.815A pdb=" N ALA B 704 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.427A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.721A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.721A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.854A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.498A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.784A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 51 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.927A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.409A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE7, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.214A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AE9, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.624A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER G 141 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.542A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 14 through 17 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 1444 hydrogen bonds defined for protein. 3981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 4.39 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: 5538 1.31 - 1.44: 8631 1.44 - 1.57: 19200 1.57 - 1.69: 116 1.69 - 1.82: 288 Bond restraints: 33773 Sorted by residual: bond pdb=" C12 PXZ M 6 " pdb=" C4 PXZ M 6 " ideal model delta sigma weight residual 1.354 1.542 -0.188 2.00e-02 2.50e+03 8.87e+01 bond pdb=" C12 PXZ O 6 " pdb=" C4 PXZ O 6 " ideal model delta sigma weight residual 1.354 1.542 -0.188 2.00e-02 2.50e+03 8.82e+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 5.47e+01 bond pdb=" C1 PXZ O 6 " pdb=" C2 PXZ O 6 " ideal model delta sigma weight residual 1.372 1.520 -0.148 2.00e-02 2.50e+03 5.45e+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 3.78e+01 ... (remaining 33768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 45115 2.13 - 4.26: 619 4.26 - 6.40: 101 6.40 - 8.53: 18 8.53 - 10.66: 1 Bond angle restraints: 45854 Sorted by residual: angle pdb=" O4' DG T 20 " pdb=" C4' DG T 20 " pdb=" C3' DG T 20 " ideal model delta sigma weight residual 106.00 102.46 3.54 6.00e-01 2.78e+00 3.47e+01 angle pdb=" C GLY B 503 " pdb=" N ARG B 504 " pdb=" CA ARG B 504 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 angle pdb=" CA MVA O 11 " pdb=" C MVA O 11 " pdb=" O MVA O 11 " ideal model delta sigma weight residual 120.80 112.98 7.82 1.70e+00 3.46e-01 2.12e+01 angle pdb=" CA MVA M 11 " pdb=" C MVA M 11 " pdb=" O MVA M 11 " ideal model delta sigma weight residual 120.80 113.01 7.79 1.70e+00 3.46e-01 2.10e+01 angle pdb=" C4' DT N 37 " pdb=" O4' DT N 37 " pdb=" C1' DT N 37 " ideal model delta sigma weight residual 110.10 105.55 4.55 1.00e+00 1.00e+00 2.07e+01 ... (remaining 45849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 20021 34.44 - 68.87: 482 68.87 - 103.31: 40 103.31 - 137.75: 0 137.75 - 172.18: 5 Dihedral angle restraints: 20548 sinusoidal: 8930 harmonic: 11618 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 -86.01 157.90 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C SAR O 4 " pdb=" N SAR O 4 " pdb=" CA SAR O 4 " pdb=" CN SAR O 4 " ideal model delta sinusoidal sigma weight residual 71.89 -85.91 157.80 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 ... (remaining 20545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 5102 0.131 - 0.261: 23 0.261 - 0.392: 0 0.392 - 0.523: 17 0.523 - 0.654: 13 Chirality restraints: 5155 Sorted by residual: chirality pdb=" P DT T 10 " pdb=" OP1 DT T 10 " pdb=" OP2 DT T 10 " pdb=" O5' DT T 10 " both_signs ideal model delta sigma weight residual True 2.34 2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DC 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 -2.96 -0.62 2.00e-01 2.50e+01 9.69e+00 chirality pdb=" P DA T 33 " pdb=" OP1 DA T 33 " pdb=" OP2 DA T 33 " pdb=" O5' DA T 33 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 5152 not shown) Planarity restraints: 5748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " 0.021 2.00e-02 2.50e+03 2.75e-02 3.77e+01 pdb=" C0' PXZ M 6 " -0.008 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " -0.002 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 " -0.012 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " -0.018 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " -0.016 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " 0.014 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " -0.009 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " -0.028 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 " -0.039 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=" C0 PXZ O 6 " 0.021 2.00e-02 2.50e+03 2.74e-02 3.75e+01 pdb=" C0' PXZ O 6 " -0.008 2.00e-02 2.50e+03 pdb=" C1 PXZ O 6 " -0.003 2.00e-02 2.50e+03 pdb=" C11 PXZ O 6 " 0.029 2.00e-02 2.50e+03 pdb=" C12 PXZ O 6 " 0.024 2.00e-02 2.50e+03 pdb=" C13 PXZ O 6 " 0.021 2.00e-02 2.50e+03 pdb=" C14 PXZ O 6 " 0.009 2.00e-02 2.50e+03 pdb=" C15 PXZ O 6 " 0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ O 6 " -0.013 2.00e-02 2.50e+03 pdb=" C2 PXZ O 6 " -0.017 2.00e-02 2.50e+03 pdb=" C3 PXZ O 6 " -0.017 2.00e-02 2.50e+03 pdb=" C4 PXZ O 6 " 0.015 2.00e-02 2.50e+03 pdb=" C6 PXZ O 6 " -0.010 2.00e-02 2.50e+03 pdb=" C7 PXZ O 6 " -0.028 2.00e-02 2.50e+03 pdb=" C8 PXZ O 6 " -0.043 2.00e-02 2.50e+03 pdb=" C9 PXZ O 6 " -0.019 2.00e-02 2.50e+03 pdb=" N10 PXZ O 6 " 0.053 2.00e-02 2.50e+03 pdb=" N2 PXZ O 6 " -0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ O 6 " -0.040 2.00e-02 2.50e+03 pdb=" O5 PXZ O 6 " 0.052 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 7.32e-02 8.57e+00 pdb=" N PRO A 245 " 0.127 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 ... (remaining 5745 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 519 2.65 - 3.21: 30979 3.21 - 3.78: 53006 3.78 - 4.34: 75550 4.34 - 4.90: 121380 Nonbonded interactions: 281434 Sorted by model distance: nonbonded pdb=" NZ LYS B 979 " pdb=" OP1 A P 11 " model vdw 2.091 3.120 nonbonded pdb=" OG SER A1115 " pdb=" OD1 ASN A1330 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP B 837 " pdb=" NH2 ARG B1020 " model vdw 2.163 3.120 nonbonded pdb=" N GLY G 84 " pdb=" O ILE G 147 " model vdw 2.166 3.120 nonbonded pdb=" NH1 ARG B 996 " pdb=" O ALA C 174 " model vdw 2.176 3.120 ... (remaining 281429 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 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.050 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 45.940 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.005 0.188 33815 Z= 0.242 Angle : 0.640 11.222 45905 Z= 0.356 Chirality : 0.059 0.654 5155 Planarity : 0.004 0.073 5746 Dihedral : 14.993 172.184 13022 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.66 (0.13), residues: 3945 helix: 1.10 (0.14), residues: 1356 sheet: -0.08 (0.19), residues: 683 loop : 0.31 (0.15), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 840 TYR 0.014 0.001 TYR B1092 PHE 0.029 0.001 PHE A 444 TRP 0.011 0.001 TRP A1044 HIS 0.004 0.001 HIS A1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.24 (33773) covalent geometry : angle 0.62503 / 0.35 (45854) hydrogen bonds : bond 0.13954 / 9.45 ( 1449) hydrogen bonds : angle 6.12403 / 4.46 ( 4075) metal coordination : bond 0.00517 / 0.33 ( 32) metal coordination : angle 4.37432 / 3.02 ( 45) Misc. bond : bond 0.00603 / 0.35 ( 8) link_TRANS : bond 0.00111 / 0.06 ( 2) link_TRANS : angle 0.49146 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 901 time to evaluate : 1.280 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: A 735 VAL cc_start: 0.8871 (t) cc_final: 0.8625 (m) REVERT: A 792 TYR cc_start: 0.8002 (m-80) cc_final: 0.7652 (m-80) REVERT: A 833 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 969 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 1209 MET cc_start: 0.5869 (mmm) cc_final: 0.5406 (mpp) REVERT: A 1333 ILE cc_start: 0.8637 (mt) cc_final: 0.8397 (mp) REVERT: B 193 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8396 (mtmt) REVERT: B 572 HIS cc_start: 0.7221 (m90) cc_final: 0.7002 (m-70) REVERT: B 686 ASN cc_start: 0.7750 (m-40) cc_final: 0.7201 (t0) REVERT: B 706 GLN cc_start: 0.8359 (pm20) cc_final: 0.8052 (mt0) REVERT: B 739 THR cc_start: 0.8558 (p) cc_final: 0.8333 (p) REVERT: C 81 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7138 (mm-30) REVERT: E 32 GLN cc_start: 0.8031 (tp40) cc_final: 0.7753 (mm-40) REVERT: E 215 MET cc_start: 0.6568 (mmt) cc_final: 0.5773 (ptt) REVERT: G 152 SER cc_start: 0.8197 (m) cc_final: 0.7623 (p) REVERT: G 160 ILE cc_start: 0.8063 (mm) cc_final: 0.7727 (pp) REVERT: I 12 ASN cc_start: 0.6447 (m-40) cc_final: 0.6121 (m110) REVERT: I 30 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6651 (mtt-85) REVERT: I 31 THR cc_start: 0.8678 (t) cc_final: 0.8425 (p) REVERT: K 9 LEU cc_start: 0.8716 (mt) cc_final: 0.8428 (mt) REVERT: L 38 LEU cc_start: 0.8298 (mt) cc_final: 0.8097 (pp) outliers start: 0 outliers final: 6 residues processed: 901 average time/residue: 0.7737 time to fit residues: 819.0705 Evaluate side-chains 534 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 528 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 92 HIS A 118 HIS A 213 HIS A 390 GLN A 394 ASN A 427 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 ASN A1330 ASN B 395 GLN B 538 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 214 ASN C 252 GLN D 179 GLN E 63 ASN E 104 ASN E 174 GLN G 10 ASN H 11 GLN H 128 ASN H 139 ASN I 90 GLN I 116 ASN K 89 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.153721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112367 restraints weight = 48100.235| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.49 r_work: 0.3329 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 33815 Z= 0.253 Angle : 0.686 13.744 45905 Z= 0.350 Chirality : 0.047 0.237 5155 Planarity : 0.005 0.073 5746 Dihedral : 13.398 179.520 5040 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.41 % Allowed : 12.63 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.51 (0.13), residues: 3945 helix: 0.94 (0.14), residues: 1385 sheet: -0.19 (0.19), residues: 667 loop : 0.24 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1094 TYR 0.022 0.002 TYR G 167 PHE 0.027 0.002 PHE D 154 TRP 0.016 0.002 TRP A1191 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (33773) covalent geometry : angle 0.66661 / 0.35 (45854) hydrogen bonds : bond 0.04794 / 3.22 ( 1449) hydrogen bonds : angle 5.03497 / 3.64 ( 4075) metal coordination : bond 0.01081 / 0.73 ( 32) metal coordination : angle 5.16300 / 3.54 ( 45) Misc. bond : bond 0.00078 / 0.04 ( 8) link_TRANS : bond 0.00080 / 0.04 ( 2) link_TRANS : angle 0.63175 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 573 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8539 (ptp-170) REVERT: A 146 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6512 (mmm) REVERT: A 260 ASP cc_start: 0.7681 (t0) cc_final: 0.7228 (t0) REVERT: A 329 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 710 LEU cc_start: 0.8451 (mt) cc_final: 0.8211 (tp) REVERT: A 712 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8140 (mm-30) REVERT: A 735 VAL cc_start: 0.8607 (t) cc_final: 0.8232 (m) REVERT: A 833 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 840 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8110 (mtp180) REVERT: A 874 ASP cc_start: 0.8507 (t0) cc_final: 0.8290 (t0) REVERT: A 969 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 1151 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: A 1193 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8178 (tm) REVERT: A 1194 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5659 (ttm-80) REVERT: A 1209 MET cc_start: 0.5545 (mmm) cc_final: 0.4649 (mpp) REVERT: A 1274 ARG cc_start: 0.5982 (ptp90) cc_final: 0.5699 (ptt180) REVERT: A 1278 ASN cc_start: 0.8415 (m-40) cc_final: 0.8101 (m110) REVERT: A 1448 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 1454 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5437 (pp-130) REVERT: B 89 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7050 (pp20) REVERT: B 258 LEU cc_start: 0.8435 (tt) cc_final: 0.7975 (tt) REVERT: B 359 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: B 434 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7429 (ttp80) REVERT: B 445 LYS cc_start: 0.8136 (mttm) cc_final: 0.7899 (mppt) REVERT: B 561 TRP cc_start: 0.7983 (m-90) cc_final: 0.7764 (m-90) REVERT: B 686 ASN cc_start: 0.7745 (m-40) cc_final: 0.6791 (t0) REVERT: B 694 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7960 (p0) REVERT: B 699 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7897 (mm-30) REVERT: B 706 GLN cc_start: 0.8492 (pm20) cc_final: 0.7770 (mt0) REVERT: B 739 THR cc_start: 0.9028 (p) cc_final: 0.8751 (p) REVERT: B 878 GLN cc_start: 0.7570 (mt0) cc_final: 0.7151 (mt0) REVERT: B 908 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7201 (tm-30) REVERT: B 935 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7317 (ttm-80) REVERT: B 1222 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8141 (ttp-110) REVERT: C 16 ASP cc_start: 0.7784 (m-30) cc_final: 0.7472 (t0) REVERT: C 81 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7048 (mt-10) REVERT: C 107 SER cc_start: 0.8385 (t) cc_final: 0.7928 (p) REVERT: C 111 THR cc_start: 0.8575 (m) cc_final: 0.8126 (p) REVERT: D 16 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7566 (tmmt) REVERT: D 29 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7408 (mt) REVERT: D 141 LEU cc_start: 0.8469 (tp) cc_final: 0.8088 (pp) REVERT: E 17 ARG cc_start: 0.7066 (ttt90) cc_final: 0.6645 (ttm-80) REVERT: E 25 ASP cc_start: 0.7860 (m-30) cc_final: 0.7566 (m-30) REVERT: E 32 GLN cc_start: 0.8134 (tp40) cc_final: 0.7776 (mm-40) REVERT: E 36 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: E 57 MET cc_start: 0.7600 (tmm) cc_final: 0.6666 (tpt) REVERT: E 94 LYS cc_start: 0.8942 (tppp) cc_final: 0.8543 (ttpp) REVERT: E 96 PHE cc_start: 0.8583 (t80) cc_final: 0.8353 (t80) REVERT: E 137 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7430 (mt-10) REVERT: E 215 MET cc_start: 0.6086 (mmt) cc_final: 0.5160 (ptt) REVERT: F 149 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8171 (pp20) REVERT: G 22 MET cc_start: 0.7888 (ttp) cc_final: 0.7446 (ttm) REVERT: G 29 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7684 (mmtp) REVERT: G 152 SER cc_start: 0.8212 (m) cc_final: 0.7904 (p) REVERT: G 164 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7749 (mmtm) REVERT: H 8 ASP cc_start: 0.8110 (t0) cc_final: 0.7774 (t70) REVERT: H 16 ASP cc_start: 0.8532 (t0) cc_final: 0.8275 (t0) REVERT: H 91 ASP cc_start: 0.8600 (m-30) cc_final: 0.8244 (m-30) REVERT: I 4 PHE cc_start: 0.7427 (m-80) cc_final: 0.7062 (m-10) REVERT: I 30 ARG cc_start: 0.7438 (mtp180) cc_final: 0.6572 (mtt-85) REVERT: I 45 ARG cc_start: 0.6941 (tpp80) cc_final: 0.6558 (tpp80) REVERT: I 91 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7220 (mpt180) REVERT: K 9 LEU cc_start: 0.8126 (mt) cc_final: 0.7797 (mt) REVERT: K 38 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8376 (mm-30) REVERT: L 38 LEU cc_start: 0.7886 (mt) cc_final: 0.7423 (pp) REVERT: L 44 ASP cc_start: 0.8072 (t0) cc_final: 0.7716 (t0) REVERT: L 54 ARG cc_start: 0.8627 (mtt-85) cc_final: 0.8390 (mtp85) outliers start: 120 outliers final: 34 residues processed: 631 average time/residue: 0.7483 time to fit residues: 558.3792 Evaluate side-chains 547 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 496 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain K residue 26 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 285 optimal weight: 9.9990 chunk 308 optimal weight: 7.9990 chunk 337 optimal weight: 0.9980 chunk 349 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 114 ASN G 10 ASN H 128 ASN H 139 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110990 restraints weight = 48217.408| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.29 r_work: 0.3304 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 33815 Z= 0.249 Angle : 0.664 15.014 45905 Z= 0.338 Chirality : 0.047 0.208 5155 Planarity : 0.005 0.073 5746 Dihedral : 13.190 175.511 5030 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 3.47 % Allowed : 15.30 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 3945 helix: 0.88 (0.14), residues: 1380 sheet: -0.33 (0.19), residues: 669 loop : 0.12 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 17 TYR 0.027 0.002 TYR G 167 PHE 0.037 0.002 PHE A1402 TRP 0.016 0.001 TRP A1191 HIS 0.009 0.001 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (33773) covalent geometry : angle 0.64063 / 0.34 (45854) hydrogen bonds : bond 0.04571 / 3.09 ( 1449) hydrogen bonds : angle 4.93325 / 3.56 ( 4075) metal coordination : bond 0.01427 / 0.99 ( 32) metal coordination : angle 5.61715 / 3.72 ( 45) Misc. bond : bond 0.00042 / 0.02 ( 8) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.38813 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 529 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7349 (mtm110) cc_final: 0.7135 (mtm110) REVERT: A 63 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8514 (ptp-170) REVERT: A 346 ASP cc_start: 0.8030 (m-30) cc_final: 0.7788 (m-30) REVERT: A 453 MET cc_start: 0.8824 (mpp) cc_final: 0.8154 (mpp) REVERT: A 487 MET cc_start: 0.8963 (mtp) cc_final: 0.8596 (mtp) REVERT: A 542 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: A 618 GLU cc_start: 0.7617 (pt0) cc_final: 0.7322 (pm20) REVERT: A 710 LEU cc_start: 0.8499 (mt) cc_final: 0.8262 (tp) REVERT: A 712 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8122 (mm-30) REVERT: A 735 VAL cc_start: 0.8594 (t) cc_final: 0.8197 (m) REVERT: A 833 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 874 ASP cc_start: 0.8474 (t0) cc_final: 0.8221 (t0) REVERT: A 969 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 1151 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: A 1209 MET cc_start: 0.5537 (mmm) cc_final: 0.4742 (mpp) REVERT: A 1258 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7829 (t-90) REVERT: A 1262 LYS cc_start: 0.8902 (tppt) cc_final: 0.8669 (tppt) REVERT: A 1274 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5673 (ptt180) REVERT: A 1278 ASN cc_start: 0.8274 (m110) cc_final: 0.7943 (m110) REVERT: A 1448 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 135 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6781 (mpt-90) REVERT: B 258 LEU cc_start: 0.8394 (tt) cc_final: 0.7980 (tt) REVERT: B 310 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7830 (mtp) REVERT: B 564 GLU cc_start: 0.7872 (tt0) cc_final: 0.7327 (mp0) REVERT: B 592 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7728 (t0) REVERT: B 595 ARG cc_start: 0.6662 (ttm170) cc_final: 0.6176 (ttp-110) REVERT: B 686 ASN cc_start: 0.7758 (m-40) cc_final: 0.6874 (t0) REVERT: B 694 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7927 (p0) REVERT: B 699 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 706 GLN cc_start: 0.8448 (pm20) cc_final: 0.7548 (mt0) REVERT: B 739 THR cc_start: 0.9003 (p) cc_final: 0.8764 (p) REVERT: B 894 ASP cc_start: 0.7352 (p0) cc_final: 0.7020 (p0) REVERT: B 908 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7195 (tm-30) REVERT: B 916 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7117 (m) REVERT: B 1222 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8095 (ttp-110) REVERT: C 16 ASP cc_start: 0.7882 (m-30) cc_final: 0.7587 (t0) REVERT: C 81 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7029 (mt-10) REVERT: C 111 THR cc_start: 0.8541 (m) cc_final: 0.8119 (p) REVERT: D 141 LEU cc_start: 0.8497 (tp) cc_final: 0.8138 (pp) REVERT: D 213 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: E 25 ASP cc_start: 0.7797 (m-30) cc_final: 0.7428 (m-30) REVERT: E 32 GLN cc_start: 0.7969 (tp40) cc_final: 0.6680 (mm-40) REVERT: E 36 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: E 57 MET cc_start: 0.7746 (tmm) cc_final: 0.6679 (tpt) REVERT: E 93 MET cc_start: 0.8841 (tpp) cc_final: 0.8357 (tmt) REVERT: E 123 LEU cc_start: 0.8548 (tm) cc_final: 0.8238 (tm) REVERT: E 137 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7447 (mt-10) REVERT: E 215 MET cc_start: 0.6101 (mmt) cc_final: 0.5131 (ptt) REVERT: F 149 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8442 (pp20) REVERT: G 22 MET cc_start: 0.7948 (ttp) cc_final: 0.7399 (ttm) REVERT: G 25 TYR cc_start: 0.6591 (t80) cc_final: 0.6177 (t80) REVERT: G 29 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7648 (mmtp) REVERT: G 140 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6439 (tmmt) REVERT: G 152 SER cc_start: 0.8073 (m) cc_final: 0.7851 (p) REVERT: H 8 ASP cc_start: 0.8046 (t0) cc_final: 0.7548 (t70) REVERT: H 16 ASP cc_start: 0.8502 (t0) cc_final: 0.8157 (t0) REVERT: H 62 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8207 (p) REVERT: H 109 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8410 (ttmt) REVERT: H 126 GLU cc_start: 0.8580 (tt0) cc_final: 0.8141 (tt0) REVERT: I 19 ASP cc_start: 0.7269 (t70) cc_final: 0.7067 (t70) REVERT: I 30 ARG cc_start: 0.7398 (mtp180) cc_final: 0.6701 (mtt-85) REVERT: I 36 GLU cc_start: 0.7982 (pp20) cc_final: 0.7732 (pp20) REVERT: I 45 ARG cc_start: 0.7056 (tpp80) cc_final: 0.6617 (tpp80) REVERT: I 91 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7330 (mpt180) REVERT: J 27 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8151 (mm-30) REVERT: K 9 LEU cc_start: 0.8125 (mt) cc_final: 0.7796 (mt) REVERT: K 29 ASN cc_start: 0.8022 (t0) cc_final: 0.7659 (t0) REVERT: K 38 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8477 (mm-30) REVERT: K 64 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7842 (mt-10) REVERT: L 38 LEU cc_start: 0.7850 (mt) cc_final: 0.7385 (pp) REVERT: L 44 ASP cc_start: 0.8089 (t0) cc_final: 0.7668 (t0) REVERT: L 63 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7708 (ptm160) outliers start: 122 outliers final: 42 residues processed: 605 average time/residue: 0.7664 time to fit residues: 548.9294 Evaluate side-chains 536 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 474 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 63 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 288 optimal weight: 20.0000 chunk 356 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 262 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 104 ASN E 114 ASN G 10 ASN H 128 ASN H 139 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111439 restraints weight = 47759.571| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.28 r_work: 0.3317 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33815 Z= 0.200 Angle : 0.624 11.549 45905 Z= 0.318 Chirality : 0.045 0.195 5155 Planarity : 0.004 0.072 5746 Dihedral : 13.122 174.597 5030 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 3.75 % Allowed : 16.92 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 3945 helix: 0.94 (0.14), residues: 1381 sheet: -0.33 (0.20), residues: 652 loop : 0.07 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 17 TYR 0.022 0.002 TYR G 167 PHE 0.031 0.002 PHE A1402 TRP 0.015 0.001 TRP A1191 HIS 0.005 0.001 HIS C 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (33773) covalent geometry : angle 0.60486 / 0.32 (45854) hydrogen bonds : bond 0.04260 / 2.88 ( 1449) hydrogen bonds : angle 4.83074 / 3.48 ( 4075) metal coordination : bond 0.00788 / 0.53 ( 32) metal coordination : angle 4.91221 / 3.32 ( 45) Misc. bond : bond 0.00047 / 0.03 ( 8) link_TRANS : bond 0.00073 / 0.04 ( 2) link_TRANS : angle 0.29955 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 505 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7423 (mtm110) cc_final: 0.7103 (mtm110) REVERT: A 55 ASP cc_start: 0.8680 (t0) cc_final: 0.8457 (t0) REVERT: A 63 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8472 (ptp-170) REVERT: A 260 ASP cc_start: 0.7654 (t70) cc_final: 0.7060 (t0) REVERT: A 287 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7497 (t-90) REVERT: A 346 ASP cc_start: 0.8018 (m-30) cc_final: 0.7756 (m-30) REVERT: A 453 MET cc_start: 0.8820 (mpp) cc_final: 0.8157 (mpp) REVERT: A 618 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: A 710 LEU cc_start: 0.8510 (mt) cc_final: 0.8293 (tp) REVERT: A 712 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8114 (mm-30) REVERT: A 735 VAL cc_start: 0.8594 (t) cc_final: 0.8193 (m) REVERT: A 833 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 874 ASP cc_start: 0.8405 (t0) cc_final: 0.8161 (t0) REVERT: A 1151 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6896 (mp0) REVERT: A 1209 MET cc_start: 0.5517 (mmm) cc_final: 0.4764 (mpp) REVERT: A 1258 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7642 (t-170) REVERT: A 1262 LYS cc_start: 0.8809 (tppt) cc_final: 0.8528 (tppt) REVERT: A 1274 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5640 (ptt180) REVERT: A 1278 ASN cc_start: 0.8235 (m110) cc_final: 0.7864 (m110) REVERT: A 1280 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 1281 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6905 (ttp-110) REVERT: A 1448 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 1454 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5809 (pp-130) REVERT: B 89 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: B 135 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6765 (mpt-90) REVERT: B 258 LEU cc_start: 0.8338 (tt) cc_final: 0.7992 (tt) REVERT: B 310 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: B 368 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: B 434 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6986 (ttp80) REVERT: B 529 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: B 564 GLU cc_start: 0.7913 (tt0) cc_final: 0.7312 (mp0) REVERT: B 592 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 595 ARG cc_start: 0.6703 (ttm170) cc_final: 0.6221 (ttp80) REVERT: B 686 ASN cc_start: 0.7712 (m-40) cc_final: 0.6916 (t0) REVERT: B 694 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 706 GLN cc_start: 0.8420 (pm20) cc_final: 0.7615 (mt0) REVERT: B 739 THR cc_start: 0.9023 (p) cc_final: 0.8779 (p) REVERT: B 894 ASP cc_start: 0.7236 (p0) cc_final: 0.7025 (p0) REVERT: B 908 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7170 (tm-30) REVERT: B 963 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8285 (p90) REVERT: B 1133 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8263 (ptm) REVERT: B 1206 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: B 1222 ARG cc_start: 0.8463 (mtp-110) cc_final: 0.8078 (ttp-110) REVERT: C 16 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7568 (t0) REVERT: C 81 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7070 (mt-10) REVERT: C 111 THR cc_start: 0.8514 (m) cc_final: 0.8098 (p) REVERT: C 195 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8041 (mp-120) REVERT: C 230 MET cc_start: 0.8616 (mtp) cc_final: 0.8398 (mtp) REVERT: D 56 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7074 (ppp-140) REVERT: D 141 LEU cc_start: 0.8464 (tp) cc_final: 0.8107 (pp) REVERT: D 145 MET cc_start: 0.8773 (mmm) cc_final: 0.8562 (mmm) REVERT: D 213 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: E 25 ASP cc_start: 0.7759 (m-30) cc_final: 0.7391 (m-30) REVERT: E 32 GLN cc_start: 0.7948 (tp40) cc_final: 0.6607 (mm-40) REVERT: E 36 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: E 57 MET cc_start: 0.7807 (tmm) cc_final: 0.6697 (tpt) REVERT: E 93 MET cc_start: 0.8859 (tpp) cc_final: 0.8385 (tmt) REVERT: E 94 LYS cc_start: 0.8806 (tppp) cc_final: 0.8510 (ttpp) REVERT: E 123 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8289 (tm) REVERT: E 137 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7403 (mt-10) REVERT: E 215 MET cc_start: 0.6034 (mmt) cc_final: 0.5199 (ptt) REVERT: G 29 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7655 (mmtp) REVERT: G 140 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6487 (tmmt) REVERT: H 8 ASP cc_start: 0.8106 (t0) cc_final: 0.7508 (t70) REVERT: H 16 ASP cc_start: 0.8499 (t0) cc_final: 0.8122 (t0) REVERT: H 62 SER cc_start: 0.8933 (t) cc_final: 0.8177 (p) REVERT: H 109 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8490 (ttmt) REVERT: H 126 GLU cc_start: 0.8415 (tt0) cc_final: 0.8204 (tt0) REVERT: I 24 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7620 (ptp90) REVERT: I 30 ARG cc_start: 0.7483 (mtp180) cc_final: 0.7052 (mtt-85) REVERT: I 36 GLU cc_start: 0.8010 (pp20) cc_final: 0.7788 (pp20) REVERT: J 19 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: J 27 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8160 (mm-30) REVERT: K 5 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: K 9 LEU cc_start: 0.8079 (mt) cc_final: 0.7729 (mt) REVERT: K 29 ASN cc_start: 0.7966 (t0) cc_final: 0.7731 (t0) REVERT: K 38 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8477 (mm-30) REVERT: K 64 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7815 (mt-10) REVERT: L 38 LEU cc_start: 0.7842 (mt) cc_final: 0.7397 (pp) REVERT: L 42 ARG cc_start: 0.8426 (mtp85) cc_final: 0.7806 (mmt90) REVERT: L 44 ASP cc_start: 0.8136 (t0) cc_final: 0.7700 (t0) REVERT: L 63 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7753 (ptm160) outliers start: 132 outliers final: 51 residues processed: 590 average time/residue: 0.6965 time to fit residues: 486.1318 Evaluate side-chains 543 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 463 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 63 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 263 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 325 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS E 114 ASN G 10 ASN H 128 ASN H 139 ASN K 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113850 restraints weight = 47885.678| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.28 r_work: 0.3350 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33815 Z= 0.139 Angle : 0.589 11.620 45905 Z= 0.301 Chirality : 0.044 0.175 5155 Planarity : 0.004 0.072 5746 Dihedral : 13.033 174.386 5030 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.75 % Allowed : 17.97 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 3945 helix: 1.09 (0.14), residues: 1382 sheet: -0.29 (0.20), residues: 650 loop : 0.11 (0.15), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 155 TYR 0.018 0.001 TYR G 167 PHE 0.034 0.002 PHE A1402 TRP 0.016 0.001 TRP A1191 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (33773) covalent geometry : angle 0.57232 / 0.30 (45854) hydrogen bonds : bond 0.03929 / 2.67 ( 1449) hydrogen bonds : angle 4.68222 / 3.37 ( 4075) metal coordination : bond 0.00632 / 0.43 ( 32) metal coordination : angle 4.55024 / 3.06 ( 45) Misc. bond : bond 0.00063 / 0.04 ( 8) link_TRANS : bond 0.00037 / 0.02 ( 2) link_TRANS : angle 0.27558 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 503 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8690 (t0) cc_final: 0.8480 (t0) REVERT: A 260 ASP cc_start: 0.7666 (t70) cc_final: 0.7082 (t0) REVERT: A 287 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7460 (t-90) REVERT: A 346 ASP cc_start: 0.8024 (m-30) cc_final: 0.7777 (m-30) REVERT: A 398 GLU cc_start: 0.7785 (pt0) cc_final: 0.7243 (pp20) REVERT: A 453 MET cc_start: 0.8765 (mpp) cc_final: 0.8153 (mpp) REVERT: A 618 GLU cc_start: 0.7592 (pt0) cc_final: 0.7307 (pm20) REVERT: A 710 LEU cc_start: 0.8486 (mt) cc_final: 0.8272 (tp) REVERT: A 712 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8101 (mm-30) REVERT: A 720 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7231 (ttm-80) REVERT: A 735 VAL cc_start: 0.8570 (t) cc_final: 0.8176 (m) REVERT: A 833 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 874 ASP cc_start: 0.8362 (t0) cc_final: 0.8110 (t0) REVERT: A 1121 GLU cc_start: 0.8542 (tt0) cc_final: 0.8027 (tm-30) REVERT: A 1151 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: A 1209 MET cc_start: 0.5484 (mmm) cc_final: 0.4936 (mpp) REVERT: A 1262 LYS cc_start: 0.8708 (tppt) cc_final: 0.8393 (tppt) REVERT: A 1278 ASN cc_start: 0.8168 (m110) cc_final: 0.7787 (m110) REVERT: A 1280 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6748 (tm-30) REVERT: A 1281 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6835 (ttp-110) REVERT: A 1284 MET cc_start: 0.8377 (mtp) cc_final: 0.8159 (ttp) REVERT: A 1398 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (ptp) REVERT: A 1448 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 89 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: B 258 LEU cc_start: 0.8274 (tt) cc_final: 0.7699 (tt) REVERT: B 310 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7817 (mtp) REVERT: B 368 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: B 434 ARG cc_start: 0.7313 (ttp80) cc_final: 0.6956 (ttp80) REVERT: B 529 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 564 GLU cc_start: 0.7929 (tt0) cc_final: 0.7296 (mp0) REVERT: B 592 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7588 (t0) REVERT: B 595 ARG cc_start: 0.6738 (ttm170) cc_final: 0.6296 (ttp-110) REVERT: B 686 ASN cc_start: 0.7763 (m-40) cc_final: 0.6909 (t0) REVERT: B 694 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7959 (p0) REVERT: B 706 GLN cc_start: 0.8365 (pm20) cc_final: 0.7707 (mt0) REVERT: B 739 THR cc_start: 0.9035 (p) cc_final: 0.8785 (p) REVERT: B 860 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: B 872 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6319 (mm-30) REVERT: B 894 ASP cc_start: 0.7141 (p0) cc_final: 0.6922 (p0) REVERT: B 908 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7090 (tm-30) REVERT: B 1004 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: B 1132 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6906 (tt0) REVERT: B 1133 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8035 (ptm) REVERT: B 1136 ASP cc_start: 0.7916 (m-30) cc_final: 0.7714 (m-30) REVERT: B 1222 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8059 (ttp-110) REVERT: C 16 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7487 (t0) REVERT: C 81 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7020 (mt-10) REVERT: C 111 THR cc_start: 0.8543 (m) cc_final: 0.8186 (p) REVERT: C 230 MET cc_start: 0.8597 (mtp) cc_final: 0.8320 (mtp) REVERT: D 213 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: E 25 ASP cc_start: 0.7753 (m-30) cc_final: 0.7361 (m-30) REVERT: E 36 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: E 93 MET cc_start: 0.8880 (tpp) cc_final: 0.8439 (tmt) REVERT: E 94 LYS cc_start: 0.8842 (tppp) cc_final: 0.8546 (ttpp) REVERT: E 137 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 215 MET cc_start: 0.6038 (mmt) cc_final: 0.5154 (ptt) REVERT: G 140 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6463 (tmmt) REVERT: G 168 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6185 (tp) REVERT: H 8 ASP cc_start: 0.8151 (t0) cc_final: 0.7480 (t70) REVERT: H 16 ASP cc_start: 0.8506 (t0) cc_final: 0.8074 (t0) REVERT: H 62 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8171 (p) REVERT: H 109 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8447 (ttmt) REVERT: H 126 GLU cc_start: 0.8345 (tt0) cc_final: 0.8127 (tt0) REVERT: I 13 MET cc_start: 0.5587 (mmm) cc_final: 0.5182 (mmm) REVERT: I 30 ARG cc_start: 0.7551 (mtp180) cc_final: 0.7075 (mtt-85) REVERT: I 36 GLU cc_start: 0.7966 (pp20) cc_final: 0.7650 (pp20) REVERT: I 45 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5458 (ttm-80) REVERT: I 91 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7329 (mpt180) REVERT: J 19 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: J 27 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8197 (mm-30) REVERT: K 9 LEU cc_start: 0.8070 (mt) cc_final: 0.7713 (mt) REVERT: K 29 ASN cc_start: 0.7992 (t0) cc_final: 0.7628 (t0) REVERT: K 64 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7806 (mt-10) REVERT: L 38 LEU cc_start: 0.7892 (mt) cc_final: 0.7423 (pp) REVERT: L 42 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7838 (mmt90) REVERT: L 44 ASP cc_start: 0.8122 (t0) cc_final: 0.7666 (t0) REVERT: L 63 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7731 (ptm160) outliers start: 132 outliers final: 46 residues processed: 587 average time/residue: 0.7128 time to fit residues: 497.7407 Evaluate side-chains 525 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 454 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 63 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 334 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 372 optimal weight: 0.6980 chunk 379 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS A1004 ASN A1070 GLN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 104 ASN E 114 ASN G 10 ASN H 139 ASN L 53 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112936 restraints weight = 47918.704| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.28 r_work: 0.3340 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33815 Z= 0.158 Angle : 0.602 15.018 45905 Z= 0.305 Chirality : 0.044 0.244 5155 Planarity : 0.004 0.072 5746 Dihedral : 12.982 173.727 5030 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 3.50 % Allowed : 19.17 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.49 (0.13), residues: 3945 helix: 1.10 (0.14), residues: 1384 sheet: -0.29 (0.20), residues: 647 loop : 0.11 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 155 TYR 0.025 0.001 TYR G 167 PHE 0.038 0.002 PHE A1402 TRP 0.018 0.001 TRP A1191 HIS 0.018 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (33773) covalent geometry : angle 0.58783 / 0.30 (45854) hydrogen bonds : bond 0.03915 / 2.66 ( 1449) hydrogen bonds : angle 4.64276 / 3.34 ( 4075) metal coordination : bond 0.00541 / 0.36 ( 32) metal coordination : angle 4.24614 / 2.87 ( 45) Misc. bond : bond 0.00057 / 0.03 ( 8) link_TRANS : bond 0.00058 / 0.03 ( 2) link_TRANS : angle 0.23681 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 487 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7435 (mtm110) cc_final: 0.7229 (mtm110) REVERT: A 260 ASP cc_start: 0.7722 (t70) cc_final: 0.7139 (t0) REVERT: A 287 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7525 (t-90) REVERT: A 398 GLU cc_start: 0.7756 (pt0) cc_final: 0.7319 (pp20) REVERT: A 453 MET cc_start: 0.8778 (mpp) cc_final: 0.8166 (mpp) REVERT: A 618 GLU cc_start: 0.7654 (pt0) cc_final: 0.7349 (pm20) REVERT: A 710 LEU cc_start: 0.8491 (mt) cc_final: 0.8263 (tp) REVERT: A 712 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8102 (mm-30) REVERT: A 720 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7171 (ttm-80) REVERT: A 801 GLU cc_start: 0.8167 (pm20) cc_final: 0.7771 (pm20) REVERT: A 833 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 874 ASP cc_start: 0.8377 (t0) cc_final: 0.8136 (t0) REVERT: A 1004 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8287 (p0) REVERT: A 1116 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7706 (tt) REVERT: A 1121 GLU cc_start: 0.8537 (tt0) cc_final: 0.8012 (tm-30) REVERT: A 1151 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 1209 MET cc_start: 0.5725 (mmm) cc_final: 0.4971 (mpt) REVERT: A 1258 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7635 (t-170) REVERT: A 1262 LYS cc_start: 0.8784 (tppt) cc_final: 0.8437 (tppt) REVERT: A 1278 ASN cc_start: 0.8188 (m110) cc_final: 0.7806 (m110) REVERT: A 1398 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8214 (ptp) REVERT: A 1448 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 1454 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6148 (pp-130) REVERT: B 89 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: B 135 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6530 (mpt-90) REVERT: B 258 LEU cc_start: 0.8327 (tt) cc_final: 0.7973 (tt) REVERT: B 310 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7869 (mtp) REVERT: B 368 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: B 434 ARG cc_start: 0.7366 (ttp80) cc_final: 0.6753 (ttp80) REVERT: B 529 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 564 GLU cc_start: 0.7917 (tt0) cc_final: 0.7283 (mp0) REVERT: B 592 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7619 (t0) REVERT: B 595 ARG cc_start: 0.6757 (ttm170) cc_final: 0.6362 (ttp-170) REVERT: B 620 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7315 (tpp-160) REVERT: B 686 ASN cc_start: 0.7770 (m-40) cc_final: 0.6922 (t0) REVERT: B 694 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 706 GLN cc_start: 0.8349 (pm20) cc_final: 0.7731 (mt0) REVERT: B 739 THR cc_start: 0.9037 (p) cc_final: 0.8783 (p) REVERT: B 773 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: B 860 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (tmm) REVERT: B 872 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6300 (mm-30) REVERT: B 873 THR cc_start: 0.8022 (m) cc_final: 0.7724 (t) REVERT: B 879 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6601 (mmm160) REVERT: B 894 ASP cc_start: 0.7152 (p0) cc_final: 0.6940 (p0) REVERT: B 908 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7086 (tm-30) REVERT: B 935 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7292 (ttm-80) REVERT: B 987 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8575 (ptpt) REVERT: B 1004 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: B 1132 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6946 (tt0) REVERT: B 1133 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8005 (ptm) REVERT: B 1222 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8048 (ttp-110) REVERT: C 16 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7550 (t0) REVERT: C 29 MET cc_start: 0.9069 (ttm) cc_final: 0.8721 (ttp) REVERT: C 81 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7040 (mt-10) REVERT: C 111 THR cc_start: 0.8486 (m) cc_final: 0.8165 (p) REVERT: C 230 MET cc_start: 0.8635 (mtp) cc_final: 0.8326 (mtp) REVERT: D 67 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7630 (ttm-80) REVERT: D 131 GLU cc_start: 0.6443 (mm-30) cc_final: 0.5873 (tp30) REVERT: D 141 LEU cc_start: 0.8368 (tp) cc_final: 0.8076 (pp) REVERT: D 155 ARG cc_start: 0.7719 (mmm160) cc_final: 0.7206 (tpp-160) REVERT: D 213 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: E 25 ASP cc_start: 0.7799 (m-30) cc_final: 0.7423 (m-30) REVERT: E 93 MET cc_start: 0.8827 (tpp) cc_final: 0.8377 (tmt) REVERT: E 123 LEU cc_start: 0.8367 (tm) cc_final: 0.8132 (tm) REVERT: E 137 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7378 (mt-10) REVERT: E 215 MET cc_start: 0.6061 (mmt) cc_final: 0.5147 (ptt) REVERT: G 1 MET cc_start: 0.6449 (mpp) cc_final: 0.6104 (mpp) REVERT: G 22 MET cc_start: 0.7844 (ttp) cc_final: 0.7184 (ttm) REVERT: G 50 ASP cc_start: 0.7434 (t0) cc_final: 0.7152 (t0) REVERT: G 69 GLU cc_start: 0.7996 (tt0) cc_final: 0.7332 (pt0) REVERT: G 140 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6551 (tmmt) REVERT: G 167 TYR cc_start: 0.6888 (t80) cc_final: 0.6516 (t80) REVERT: G 168 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6174 (tp) REVERT: H 8 ASP cc_start: 0.8161 (t0) cc_final: 0.7484 (t70) REVERT: H 62 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8198 (p) REVERT: H 109 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (ttmt) REVERT: H 126 GLU cc_start: 0.8348 (tt0) cc_final: 0.8090 (tt0) REVERT: I 13 MET cc_start: 0.5507 (mmm) cc_final: 0.5040 (mmm) REVERT: I 23 ASN cc_start: 0.6023 (p0) cc_final: 0.5782 (p0) REVERT: I 30 ARG cc_start: 0.7523 (mtp180) cc_final: 0.7058 (mtt-85) REVERT: I 64 SER cc_start: 0.8532 (m) cc_final: 0.8223 (t) REVERT: J 19 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: J 27 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8198 (mm-30) REVERT: K 5 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: K 9 LEU cc_start: 0.8058 (mt) cc_final: 0.7702 (mt) REVERT: K 29 ASN cc_start: 0.7990 (t0) cc_final: 0.7655 (t0) REVERT: K 64 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7825 (mt-10) REVERT: L 38 LEU cc_start: 0.7893 (mt) cc_final: 0.7425 (pp) REVERT: L 42 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7843 (mmt90) REVERT: L 44 ASP cc_start: 0.8149 (t0) cc_final: 0.7730 (t0) outliers start: 123 outliers final: 47 residues processed: 565 average time/residue: 0.7288 time to fit residues: 490.6278 Evaluate side-chains 536 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 460 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 62 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 336 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 376 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 114 ASN G 10 ASN H 139 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110925 restraints weight = 48035.188| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.47 r_work: 0.3318 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 33815 Z= 0.196 Angle : 0.625 12.125 45905 Z= 0.316 Chirality : 0.045 0.212 5155 Planarity : 0.004 0.073 5746 Dihedral : 12.974 173.141 5030 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.41 % Allowed : 19.94 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.44 (0.13), residues: 3945 helix: 1.05 (0.14), residues: 1383 sheet: -0.35 (0.20), residues: 664 loop : 0.11 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 155 TYR 0.020 0.001 TYR G 167 PHE 0.041 0.002 PHE A1402 TRP 0.020 0.001 TRP A1191 HIS 0.004 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (33773) covalent geometry : angle 0.61079 / 0.32 (45854) hydrogen bonds : bond 0.04004 / 2.71 ( 1449) hydrogen bonds : angle 4.66206 / 3.35 ( 4075) metal coordination : bond 0.00579 / 0.37 ( 32) metal coordination : angle 4.25498 / 2.89 ( 45) Misc. bond : bond 0.00054 / 0.03 ( 8) link_TRANS : bond 0.00086 / 0.04 ( 2) link_TRANS : angle 0.20706 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 473 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7188 (ptm-80) REVERT: A 63 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8533 (ptp-170) REVERT: A 234 MET cc_start: 0.9346 (mtt) cc_final: 0.9137 (mtm) REVERT: A 260 ASP cc_start: 0.7871 (t70) cc_final: 0.7315 (t0) REVERT: A 453 MET cc_start: 0.8860 (mpp) cc_final: 0.8263 (mpp) REVERT: A 618 GLU cc_start: 0.7725 (pt0) cc_final: 0.7417 (pm20) REVERT: A 710 LEU cc_start: 0.8513 (mt) cc_final: 0.8270 (tp) REVERT: A 712 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8137 (mm-30) REVERT: A 720 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7257 (ttm-80) REVERT: A 801 GLU cc_start: 0.8183 (pm20) cc_final: 0.7766 (pm20) REVERT: A 833 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 874 ASP cc_start: 0.8449 (t0) cc_final: 0.8219 (t0) REVERT: A 900 ASP cc_start: 0.6438 (t0) cc_final: 0.5316 (p0) REVERT: A 1111 MET cc_start: 0.8375 (ptp) cc_final: 0.8058 (ptt) REVERT: A 1116 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 1121 GLU cc_start: 0.8470 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 1151 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: A 1262 LYS cc_start: 0.8731 (tppt) cc_final: 0.8368 (tppt) REVERT: A 1278 ASN cc_start: 0.8217 (m110) cc_final: 0.7846 (m110) REVERT: A 1280 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6799 (tm-30) REVERT: A 1281 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6853 (ttp-110) REVERT: A 1448 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 1454 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6020 (pp-130) REVERT: B 89 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: B 241 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8101 (mmm-85) REVERT: B 258 LEU cc_start: 0.8447 (tt) cc_final: 0.8106 (tt) REVERT: B 309 GLN cc_start: 0.8175 (mm110) cc_final: 0.7836 (mm-40) REVERT: B 359 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: B 368 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: B 392 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7162 (mtm-85) REVERT: B 434 ARG cc_start: 0.7421 (ttp80) cc_final: 0.6808 (ttp80) REVERT: B 529 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: B 564 GLU cc_start: 0.7947 (tt0) cc_final: 0.7341 (mp0) REVERT: B 592 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7657 (t0) REVERT: B 595 ARG cc_start: 0.6841 (ttm170) cc_final: 0.6353 (ttp-170) REVERT: B 620 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7326 (tpp-160) REVERT: B 686 ASN cc_start: 0.7830 (m-40) cc_final: 0.7000 (t0) REVERT: B 694 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8089 (p0) REVERT: B 706 GLN cc_start: 0.8390 (pm20) cc_final: 0.7757 (mt0) REVERT: B 739 THR cc_start: 0.9090 (p) cc_final: 0.8827 (p) REVERT: B 773 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8397 (mtm) REVERT: B 872 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6512 (mm-30) REVERT: B 873 THR cc_start: 0.8015 (m) cc_final: 0.7756 (t) REVERT: B 895 ASP cc_start: 0.7873 (m-30) cc_final: 0.7125 (t0) REVERT: B 908 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7205 (tm-30) REVERT: B 935 ARG cc_start: 0.7536 (ttm110) cc_final: 0.7299 (ttm-80) REVERT: B 961 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7546 (mp) REVERT: B 987 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8661 (ptpt) REVERT: B 1133 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (ptm) REVERT: B 1222 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8043 (ttp-110) REVERT: C 16 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7631 (t0) REVERT: C 29 MET cc_start: 0.9099 (ttm) cc_final: 0.8742 (ttp) REVERT: C 81 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7121 (mt-10) REVERT: C 111 THR cc_start: 0.8500 (m) cc_final: 0.8183 (p) REVERT: C 195 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8058 (mp-120) REVERT: C 230 MET cc_start: 0.8695 (mtp) cc_final: 0.8359 (mtp) REVERT: D 67 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7662 (ttm-80) REVERT: D 131 GLU cc_start: 0.6444 (mm-30) cc_final: 0.5881 (tp30) REVERT: D 213 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: E 25 ASP cc_start: 0.7834 (m-30) cc_final: 0.7454 (m-30) REVERT: E 67 GLU cc_start: 0.8086 (tp30) cc_final: 0.7835 (tp30) REVERT: E 93 MET cc_start: 0.8849 (tpp) cc_final: 0.7857 (tmt) REVERT: E 137 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7417 (mt-10) REVERT: E 215 MET cc_start: 0.6139 (mmt) cc_final: 0.5167 (ptt) REVERT: G 22 MET cc_start: 0.7818 (ttp) cc_final: 0.7242 (ttm) REVERT: G 32 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7685 (pp20) REVERT: G 50 ASP cc_start: 0.7549 (t0) cc_final: 0.7271 (t0) REVERT: G 115 MET cc_start: 0.6823 (mpp) cc_final: 0.6414 (mpp) REVERT: G 140 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6589 (tmmt) REVERT: G 167 TYR cc_start: 0.6899 (t80) cc_final: 0.6592 (t80) REVERT: G 168 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6374 (tp) REVERT: H 8 ASP cc_start: 0.8239 (t0) cc_final: 0.7536 (t70) REVERT: H 62 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8230 (p) REVERT: H 109 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8503 (ttmt) REVERT: H 126 GLU cc_start: 0.8429 (tt0) cc_final: 0.8150 (tt0) REVERT: I 13 MET cc_start: 0.5597 (mmm) cc_final: 0.5188 (mmm) REVERT: I 23 ASN cc_start: 0.5964 (p0) cc_final: 0.5751 (p0) REVERT: I 30 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7169 (mtt-85) REVERT: I 36 GLU cc_start: 0.7975 (pp20) cc_final: 0.7683 (pp20) REVERT: I 45 ARG cc_start: 0.6937 (tpp80) cc_final: 0.5976 (ttm-80) REVERT: I 59 VAL cc_start: 0.8155 (p) cc_final: 0.7909 (m) REVERT: I 64 SER cc_start: 0.8542 (m) cc_final: 0.8227 (t) REVERT: J 19 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: J 27 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8203 (mm-30) REVERT: K 5 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: K 9 LEU cc_start: 0.8131 (mt) cc_final: 0.7786 (mt) REVERT: K 29 ASN cc_start: 0.8060 (t0) cc_final: 0.7735 (t0) REVERT: K 64 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7828 (mt-10) REVERT: L 38 LEU cc_start: 0.7929 (mt) cc_final: 0.7455 (pp) REVERT: L 42 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7073 (mmt90) REVERT: L 44 ASP cc_start: 0.8206 (t0) cc_final: 0.7788 (t0) outliers start: 120 outliers final: 66 residues processed: 544 average time/residue: 0.7431 time to fit residues: 480.2137 Evaluate side-chains 541 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 447 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 62 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 222 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 354 optimal weight: 0.0470 chunk 72 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS A1004 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 932 HIS B 951 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 114 ASN G 10 ASN G 57 GLN H 139 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113220 restraints weight = 47971.148| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.49 r_work: 0.3346 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33815 Z= 0.136 Angle : 0.607 13.216 45905 Z= 0.308 Chirality : 0.044 0.211 5155 Planarity : 0.004 0.072 5746 Dihedral : 12.935 173.231 5030 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 3.13 % Allowed : 20.79 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.53 (0.14), residues: 3945 helix: 1.16 (0.14), residues: 1385 sheet: -0.30 (0.20), residues: 657 loop : 0.12 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 130 TYR 0.018 0.001 TYR E 187 PHE 0.037 0.002 PHE A1402 TRP 0.039 0.001 TRP A1191 HIS 0.003 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (33773) covalent geometry : angle 0.59525 / 0.31 (45854) hydrogen bonds : bond 0.03778 / 2.56 ( 1449) hydrogen bonds : angle 4.58202 / 3.29 ( 4075) metal coordination : bond 0.00502 / 0.33 ( 32) metal coordination : angle 3.91716 / 2.68 ( 45) Misc. bond : bond 0.00062 / 0.03 ( 8) link_TRANS : bond 0.00045 / 0.02 ( 2) link_TRANS : angle 0.20596 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 482 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7421 (mtm110) cc_final: 0.7182 (ptm-80) REVERT: A 234 MET cc_start: 0.9319 (mtt) cc_final: 0.9081 (mtm) REVERT: A 260 ASP cc_start: 0.7852 (t70) cc_final: 0.7281 (t0) REVERT: A 304 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8594 (mtt) REVERT: A 398 GLU cc_start: 0.7844 (pt0) cc_final: 0.7387 (pp20) REVERT: A 453 MET cc_start: 0.8826 (mpp) cc_final: 0.8264 (mpp) REVERT: A 618 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: A 710 LEU cc_start: 0.8481 (mt) cc_final: 0.8256 (tp) REVERT: A 712 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8134 (mm-30) REVERT: A 720 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7217 (ttm-80) REVERT: A 801 GLU cc_start: 0.8166 (pm20) cc_final: 0.7759 (pm20) REVERT: A 833 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 840 ARG cc_start: 0.8407 (mtp180) cc_final: 0.7673 (mtp180) REVERT: A 874 ASP cc_start: 0.8396 (t0) cc_final: 0.8150 (t0) REVERT: A 900 ASP cc_start: 0.6354 (t0) cc_final: 0.5273 (p0) REVERT: A 969 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 1004 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8199 (p0) REVERT: A 1112 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8612 (mmmm) REVERT: A 1121 GLU cc_start: 0.8429 (tt0) cc_final: 0.7914 (tm-30) REVERT: A 1151 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: A 1192 LEU cc_start: 0.5152 (pt) cc_final: 0.4369 (tp) REVERT: A 1209 MET cc_start: 0.5672 (mmm) cc_final: 0.5321 (mtm) REVERT: A 1262 LYS cc_start: 0.8715 (tppt) cc_final: 0.8343 (tppt) REVERT: A 1278 ASN cc_start: 0.8217 (m110) cc_final: 0.7846 (m110) REVERT: A 1280 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6933 (tm-30) REVERT: A 1281 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6875 (ttp-110) REVERT: A 1448 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 89 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: B 135 ARG cc_start: 0.7842 (mtt90) cc_final: 0.7202 (mtp-110) REVERT: B 258 LEU cc_start: 0.8395 (tt) cc_final: 0.8088 (tt) REVERT: B 348 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6697 (mtt180) REVERT: B 368 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: B 434 ARG cc_start: 0.7394 (ttp80) cc_final: 0.6778 (ttp80) REVERT: B 529 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: B 564 GLU cc_start: 0.7936 (tt0) cc_final: 0.7316 (mp0) REVERT: B 592 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7647 (t0) REVERT: B 595 ARG cc_start: 0.6789 (ttm170) cc_final: 0.6257 (ttp-170) REVERT: B 620 ARG cc_start: 0.7573 (tpp80) cc_final: 0.7318 (tpp-160) REVERT: B 686 ASN cc_start: 0.7862 (m-40) cc_final: 0.6965 (t0) REVERT: B 694 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8087 (p0) REVERT: B 706 GLN cc_start: 0.8372 (pm20) cc_final: 0.7752 (mt0) REVERT: B 739 THR cc_start: 0.9094 (p) cc_final: 0.8805 (p) REVERT: B 773 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8455 (mtt) REVERT: B 872 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6451 (mm-30) REVERT: B 873 THR cc_start: 0.8007 (m) cc_final: 0.7741 (t) REVERT: B 879 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6674 (mmm160) REVERT: B 895 ASP cc_start: 0.7913 (m-30) cc_final: 0.7196 (t0) REVERT: B 908 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7171 (tm-30) REVERT: B 935 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7262 (ttm-80) REVERT: B 987 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8579 (ptpt) REVERT: B 1004 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: B 1133 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8125 (ptm) REVERT: B 1222 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8035 (ttp-110) REVERT: C 16 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7623 (t0) REVERT: C 29 MET cc_start: 0.9094 (ttm) cc_final: 0.8736 (ttp) REVERT: C 81 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7105 (mt-10) REVERT: C 111 THR cc_start: 0.8545 (m) cc_final: 0.8235 (p) REVERT: C 230 MET cc_start: 0.8721 (mtp) cc_final: 0.8394 (mtp) REVERT: D 67 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7712 (ttm-80) REVERT: D 131 GLU cc_start: 0.6367 (mm-30) cc_final: 0.5928 (tp30) REVERT: D 213 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: E 25 ASP cc_start: 0.7837 (m-30) cc_final: 0.7439 (m-30) REVERT: E 67 GLU cc_start: 0.8078 (tp30) cc_final: 0.7824 (tp30) REVERT: E 94 LYS cc_start: 0.8875 (tppp) cc_final: 0.8585 (ttpp) REVERT: E 137 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7442 (mt-10) REVERT: E 215 MET cc_start: 0.6053 (mmt) cc_final: 0.5111 (ptt) REVERT: G 1 MET cc_start: 0.6541 (mpp) cc_final: 0.6205 (mpp) REVERT: G 22 MET cc_start: 0.7826 (ttp) cc_final: 0.7255 (ttm) REVERT: G 32 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7675 (pp20) REVERT: G 50 ASP cc_start: 0.7546 (t0) cc_final: 0.7253 (t0) REVERT: G 115 MET cc_start: 0.6838 (mpp) cc_final: 0.6443 (mpp) REVERT: G 140 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6535 (tmmt) REVERT: G 167 TYR cc_start: 0.6777 (t80) cc_final: 0.6398 (t80) REVERT: G 168 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6406 (tp) REVERT: H 8 ASP cc_start: 0.8191 (t0) cc_final: 0.7494 (t70) REVERT: H 62 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8285 (p) REVERT: H 109 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8516 (ttmt) REVERT: H 126 GLU cc_start: 0.8392 (tt0) cc_final: 0.8145 (tt0) REVERT: I 13 MET cc_start: 0.5535 (mmm) cc_final: 0.5039 (mmm) REVERT: I 23 ASN cc_start: 0.5980 (p0) cc_final: 0.5772 (p0) REVERT: I 30 ARG cc_start: 0.7505 (mtp180) cc_final: 0.7263 (mtt-85) REVERT: I 36 GLU cc_start: 0.8054 (pp20) cc_final: 0.7824 (pp20) REVERT: I 45 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6026 (ttm-80) REVERT: I 59 VAL cc_start: 0.8144 (p) cc_final: 0.7904 (m) REVERT: I 64 SER cc_start: 0.8540 (m) cc_final: 0.8201 (t) REVERT: J 19 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: J 27 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8212 (mm-30) REVERT: K 9 LEU cc_start: 0.8097 (mt) cc_final: 0.7748 (mt) REVERT: K 29 ASN cc_start: 0.8031 (t0) cc_final: 0.7696 (t0) REVERT: L 38 LEU cc_start: 0.7908 (mt) cc_final: 0.7460 (pp) REVERT: L 42 ARG cc_start: 0.8488 (mtp85) cc_final: 0.7136 (mmt90) REVERT: L 44 ASP cc_start: 0.8196 (t0) cc_final: 0.7788 (t0) outliers start: 110 outliers final: 56 residues processed: 557 average time/residue: 0.7434 time to fit residues: 493.5945 Evaluate side-chains 540 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 460 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 62 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 325 optimal weight: 6.9990 chunk 382 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 372 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 ASN A 975 HIS A1070 GLN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN G 10 ASN H 139 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.154326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113366 restraints weight = 47869.401| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.47 r_work: 0.3345 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33815 Z= 0.147 Angle : 0.615 11.038 45905 Z= 0.311 Chirality : 0.044 0.196 5155 Planarity : 0.004 0.079 5746 Dihedral : 12.904 172.962 5030 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 2.67 % Allowed : 21.53 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.52 (0.14), residues: 3945 helix: 1.17 (0.14), residues: 1385 sheet: -0.29 (0.20), residues: 639 loop : 0.09 (0.15), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 155 TYR 0.018 0.001 TYR E 187 PHE 0.039 0.002 PHE A1402 TRP 0.047 0.001 TRP A1191 HIS 0.003 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (33773) covalent geometry : angle 0.60300 / 0.31 (45854) hydrogen bonds : bond 0.03776 / 2.55 ( 1449) hydrogen bonds : angle 4.57254 / 3.28 ( 4075) metal coordination : bond 0.00496 / 0.32 ( 32) metal coordination : angle 3.85865 / 2.64 ( 45) Misc. bond : bond 0.00063 / 0.03 ( 8) link_TRANS : bond 0.00051 / 0.03 ( 2) link_TRANS : angle 0.19226 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 479 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7402 (mtm110) cc_final: 0.7176 (ptm-80) REVERT: A 234 MET cc_start: 0.9308 (mtt) cc_final: 0.9075 (mtm) REVERT: A 260 ASP cc_start: 0.7866 (t70) cc_final: 0.7302 (t0) REVERT: A 286 HIS cc_start: 0.6607 (t70) cc_final: 0.5519 (t-90) REVERT: A 398 GLU cc_start: 0.7833 (pt0) cc_final: 0.7381 (pp20) REVERT: A 453 MET cc_start: 0.8839 (mpp) cc_final: 0.8232 (mpp) REVERT: A 618 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: A 710 LEU cc_start: 0.8490 (mt) cc_final: 0.8249 (tp) REVERT: A 712 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8139 (mm-30) REVERT: A 720 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7223 (ttm-80) REVERT: A 801 GLU cc_start: 0.8159 (pm20) cc_final: 0.7744 (pm20) REVERT: A 833 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 874 ASP cc_start: 0.8405 (t0) cc_final: 0.8168 (t0) REVERT: A 900 ASP cc_start: 0.6310 (t0) cc_final: 0.5288 (p0) REVERT: A 969 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 1004 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8117 (p0) REVERT: A 1112 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8584 (mmmm) REVERT: A 1120 LEU cc_start: 0.8126 (mm) cc_final: 0.7864 (mm) REVERT: A 1121 GLU cc_start: 0.8412 (tt0) cc_final: 0.7904 (tm-30) REVERT: A 1151 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6352 (mp0) REVERT: A 1192 LEU cc_start: 0.5204 (pt) cc_final: 0.4506 (tp) REVERT: A 1198 ASP cc_start: 0.7575 (t0) cc_final: 0.7189 (p0) REVERT: A 1209 MET cc_start: 0.5662 (mmm) cc_final: 0.5329 (mtm) REVERT: A 1262 LYS cc_start: 0.8696 (tppt) cc_final: 0.8316 (tppt) REVERT: A 1278 ASN cc_start: 0.8239 (m110) cc_final: 0.7873 (m110) REVERT: A 1280 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 1281 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6834 (ttp-110) REVERT: A 1448 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 89 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: B 135 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7179 (mtp-110) REVERT: B 241 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8141 (mmm-85) REVERT: B 258 LEU cc_start: 0.8406 (tt) cc_final: 0.8093 (tt) REVERT: B 368 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: B 434 ARG cc_start: 0.7472 (ttp80) cc_final: 0.6926 (ttp80) REVERT: B 504 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7524 (ttm170) REVERT: B 529 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 564 GLU cc_start: 0.7914 (tt0) cc_final: 0.7354 (mp0) REVERT: B 592 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7638 (t0) REVERT: B 595 ARG cc_start: 0.6792 (ttm170) cc_final: 0.6266 (ttp-170) REVERT: B 620 ARG cc_start: 0.7603 (tpp80) cc_final: 0.7386 (tpp-160) REVERT: B 686 ASN cc_start: 0.7884 (m-40) cc_final: 0.6959 (t0) REVERT: B 694 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (p0) REVERT: B 706 GLN cc_start: 0.8373 (pm20) cc_final: 0.7794 (mt0) REVERT: B 739 THR cc_start: 0.9102 (p) cc_final: 0.8820 (p) REVERT: B 773 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8465 (mtt) REVERT: B 872 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6481 (mm-30) REVERT: B 873 THR cc_start: 0.8017 (m) cc_final: 0.7755 (t) REVERT: B 879 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7222 (mmm-85) REVERT: B 895 ASP cc_start: 0.7980 (m-30) cc_final: 0.7152 (t0) REVERT: B 908 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7169 (tm-30) REVERT: B 935 ARG cc_start: 0.7496 (ttm110) cc_final: 0.7270 (ttm-80) REVERT: B 961 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7507 (mp) REVERT: B 987 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8604 (ptpt) REVERT: B 1004 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: B 1133 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8111 (ptm) REVERT: B 1222 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8045 (ttp-110) REVERT: C 16 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7623 (t0) REVERT: C 29 MET cc_start: 0.9088 (ttm) cc_final: 0.8730 (ttp) REVERT: C 81 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7104 (mt-10) REVERT: C 111 THR cc_start: 0.8546 (m) cc_final: 0.8236 (p) REVERT: C 230 MET cc_start: 0.8732 (mtp) cc_final: 0.8402 (mtp) REVERT: D 67 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7712 (ttm-80) REVERT: D 131 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5984 (tp30) REVERT: D 155 ARG cc_start: 0.7689 (mmm160) cc_final: 0.7226 (tpp-160) REVERT: D 213 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: E 25 ASP cc_start: 0.7840 (m-30) cc_final: 0.7436 (m-30) REVERT: E 67 GLU cc_start: 0.8078 (tp30) cc_final: 0.7823 (tp30) REVERT: E 94 LYS cc_start: 0.8899 (tppp) cc_final: 0.8660 (ttpp) REVERT: E 137 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7437 (mt-10) REVERT: E 215 MET cc_start: 0.6063 (mmt) cc_final: 0.5109 (ptt) REVERT: G 1 MET cc_start: 0.6638 (mpp) cc_final: 0.6397 (mpp) REVERT: G 22 MET cc_start: 0.7850 (ttp) cc_final: 0.7338 (ttm) REVERT: G 32 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7710 (pp20) REVERT: G 50 ASP cc_start: 0.7583 (t0) cc_final: 0.7292 (t0) REVERT: G 106 MET cc_start: 0.1755 (ptm) cc_final: 0.1438 (ptp) REVERT: G 115 MET cc_start: 0.6805 (mpp) cc_final: 0.6418 (mpp) REVERT: G 140 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6468 (tmmt) REVERT: G 167 TYR cc_start: 0.6780 (t80) cc_final: 0.6344 (t80) REVERT: G 168 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6218 (tp) REVERT: H 8 ASP cc_start: 0.8215 (t0) cc_final: 0.7520 (t70) REVERT: H 62 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8285 (p) REVERT: H 109 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8526 (ttmt) REVERT: H 126 GLU cc_start: 0.8387 (tt0) cc_final: 0.8131 (tt0) REVERT: I 13 MET cc_start: 0.5610 (mmm) cc_final: 0.5111 (mmm) REVERT: I 30 ARG cc_start: 0.7512 (mtp180) cc_final: 0.7285 (mtt-85) REVERT: I 36 GLU cc_start: 0.7971 (pp20) cc_final: 0.7675 (pp20) REVERT: I 45 ARG cc_start: 0.7035 (tpp80) cc_final: 0.6055 (ttm-80) REVERT: I 59 VAL cc_start: 0.8147 (p) cc_final: 0.7908 (m) REVERT: I 64 SER cc_start: 0.8553 (m) cc_final: 0.8220 (t) REVERT: J 27 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8218 (mm-30) REVERT: K 9 LEU cc_start: 0.8091 (mt) cc_final: 0.7746 (mt) REVERT: K 29 ASN cc_start: 0.8027 (t0) cc_final: 0.7691 (t0) REVERT: L 38 LEU cc_start: 0.7900 (mt) cc_final: 0.7464 (pp) REVERT: L 42 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7139 (mmt90) REVERT: L 44 ASP cc_start: 0.8188 (t0) cc_final: 0.7762 (t0) outliers start: 94 outliers final: 59 residues processed: 542 average time/residue: 0.7433 time to fit residues: 479.3410 Evaluate side-chains 542 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 459 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 62 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 272 optimal weight: 6.9990 chunk 286 optimal weight: 0.0040 chunk 95 optimal weight: 0.5980 chunk 209 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 280 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 HIS A1004 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 932 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN G 10 ASN H 139 ASN I 23 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114545 restraints weight = 48141.925| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.33 r_work: 0.3376 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33815 Z= 0.120 Angle : 0.619 16.394 45905 Z= 0.313 Chirality : 0.044 0.446 5155 Planarity : 0.004 0.079 5746 Dihedral : 12.855 173.281 5030 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.39 % Allowed : 22.04 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 0.59 (0.14), residues: 3945 helix: 1.22 (0.14), residues: 1385 sheet: -0.20 (0.20), residues: 637 loop : 0.12 (0.15), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 348 TYR 0.024 0.001 TYR E 187 PHE 0.033 0.001 PHE A1402 TRP 0.050 0.002 TRP A1191 HIS 0.003 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (33773) covalent geometry : angle 0.60998 / 0.31 (45854) hydrogen bonds : bond 0.03636 / 2.45 ( 1449) hydrogen bonds : angle 4.52241 / 3.24 ( 4075) metal coordination : bond 0.00455 / 0.30 ( 32) metal coordination : angle 3.48119 / 2.39 ( 45) Misc. bond : bond 0.00075 / 0.04 ( 8) link_TRANS : bond 0.00015 / 0.01 ( 2) link_TRANS : angle 0.19987 / 0.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 496 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.7734 (t70) cc_final: 0.7177 (t0) REVERT: A 398 GLU cc_start: 0.7724 (pt0) cc_final: 0.7322 (pp20) REVERT: A 453 MET cc_start: 0.8761 (mpp) cc_final: 0.8207 (mpp) REVERT: A 618 GLU cc_start: 0.7618 (pt0) cc_final: 0.7278 (pm20) REVERT: A 710 LEU cc_start: 0.8468 (mt) cc_final: 0.8236 (tp) REVERT: A 712 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8092 (mm-30) REVERT: A 720 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7141 (ttm-80) REVERT: A 801 GLU cc_start: 0.8204 (pm20) cc_final: 0.7780 (pm20) REVERT: A 833 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 874 ASP cc_start: 0.8328 (t0) cc_final: 0.8087 (t0) REVERT: A 900 ASP cc_start: 0.6123 (t0) cc_final: 0.5237 (p0) REVERT: A 1004 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8248 (p0) REVERT: A 1112 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8502 (mmmm) REVERT: A 1120 LEU cc_start: 0.8085 (mm) cc_final: 0.7830 (mm) REVERT: A 1121 GLU cc_start: 0.8359 (tt0) cc_final: 0.7888 (tm-30) REVERT: A 1151 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6692 (mp0) REVERT: A 1198 ASP cc_start: 0.7539 (t0) cc_final: 0.7305 (p0) REVERT: A 1209 MET cc_start: 0.5559 (mmm) cc_final: 0.5250 (mtm) REVERT: A 1258 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7683 (t-170) REVERT: A 1263 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 1278 ASN cc_start: 0.8206 (m110) cc_final: 0.7831 (m110) REVERT: A 1280 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6852 (tm-30) REVERT: A 1281 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6746 (ttp-110) REVERT: A 1448 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 89 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: B 135 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7186 (mtp-110) REVERT: B 241 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8084 (mmm-85) REVERT: B 258 LEU cc_start: 0.8251 (tt) cc_final: 0.7806 (tt) REVERT: B 259 TYR cc_start: 0.8260 (m-80) cc_final: 0.8003 (m-80) REVERT: B 336 ARG cc_start: 0.7402 (mpt180) cc_final: 0.6963 (mpt180) REVERT: B 345 LYS cc_start: 0.7325 (mmpt) cc_final: 0.6844 (mmtt) REVERT: B 348 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.6549 (mtm-85) REVERT: B 368 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: B 434 ARG cc_start: 0.7426 (ttp80) cc_final: 0.6872 (ttp80) REVERT: B 445 LYS cc_start: 0.8085 (mttm) cc_final: 0.7686 (mppt) REVERT: B 564 GLU cc_start: 0.7855 (tt0) cc_final: 0.7243 (mp0) REVERT: B 592 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7615 (t0) REVERT: B 595 ARG cc_start: 0.6750 (ttm170) cc_final: 0.6173 (ttp-170) REVERT: B 620 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7200 (tpp-160) REVERT: B 686 ASN cc_start: 0.7765 (m-40) cc_final: 0.6811 (t0) REVERT: B 694 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8076 (p0) REVERT: B 706 GLN cc_start: 0.8289 (pm20) cc_final: 0.7735 (mt0) REVERT: B 739 THR cc_start: 0.9038 (p) cc_final: 0.8745 (p) REVERT: B 773 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8387 (mtt) REVERT: B 872 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6458 (mm-30) REVERT: B 873 THR cc_start: 0.7979 (m) cc_final: 0.7719 (t) REVERT: B 879 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7310 (mmm-85) REVERT: B 895 ASP cc_start: 0.8001 (m-30) cc_final: 0.7131 (t0) REVERT: B 908 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7163 (tm-30) REVERT: B 987 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8448 (ptpt) REVERT: B 1004 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: B 1133 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7987 (ptm) REVERT: B 1222 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8069 (ttp-110) REVERT: C 16 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7580 (t0) REVERT: C 81 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7017 (mt-10) REVERT: C 111 THR cc_start: 0.8532 (m) cc_final: 0.8241 (p) REVERT: C 230 MET cc_start: 0.8662 (mtp) cc_final: 0.8367 (mtp) REVERT: D 16 LYS cc_start: 0.8320 (tmmt) cc_final: 0.8112 (tmmt) REVERT: D 67 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.7750 (ttm-80) REVERT: D 142 LYS cc_start: 0.8501 (pttm) cc_final: 0.7982 (mmtt) REVERT: D 213 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: E 25 ASP cc_start: 0.7702 (m-30) cc_final: 0.7230 (m-30) REVERT: E 57 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6843 (tmm) REVERT: E 67 GLU cc_start: 0.7999 (tp30) cc_final: 0.7742 (tp30) REVERT: E 94 LYS cc_start: 0.9021 (tppp) cc_final: 0.8654 (ttpp) REVERT: E 137 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7371 (mt-10) REVERT: E 215 MET cc_start: 0.6028 (mmt) cc_final: 0.4978 (ptt) REVERT: G 22 MET cc_start: 0.7885 (ttp) cc_final: 0.7333 (ttm) REVERT: G 32 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7885 (pp20) REVERT: G 50 ASP cc_start: 0.7496 (t0) cc_final: 0.7254 (t0) REVERT: G 69 GLU cc_start: 0.7921 (tt0) cc_final: 0.7194 (pt0) REVERT: G 106 MET cc_start: 0.1914 (ptm) cc_final: 0.1683 (ptp) REVERT: G 115 MET cc_start: 0.6673 (mpp) cc_final: 0.6307 (mpp) REVERT: G 140 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6449 (tmmt) REVERT: G 167 TYR cc_start: 0.6797 (t80) cc_final: 0.6355 (t80) REVERT: G 168 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6455 (tp) REVERT: H 8 ASP cc_start: 0.8179 (t0) cc_final: 0.7456 (t70) REVERT: H 62 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8322 (p) REVERT: H 103 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8081 (ptmm) REVERT: H 109 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (ttmt) REVERT: H 126 GLU cc_start: 0.8242 (tt0) cc_final: 0.8021 (tt0) REVERT: I 13 MET cc_start: 0.5583 (mmm) cc_final: 0.5109 (mmm) REVERT: I 30 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7269 (mtt-85) REVERT: I 36 GLU cc_start: 0.7931 (pp20) cc_final: 0.7621 (pp20) REVERT: I 59 VAL cc_start: 0.8108 (p) cc_final: 0.7874 (m) REVERT: I 64 SER cc_start: 0.8587 (m) cc_final: 0.8279 (t) REVERT: J 27 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8230 (mm-30) REVERT: J 31 ASP cc_start: 0.7584 (p0) cc_final: 0.6912 (p0) REVERT: K 9 LEU cc_start: 0.8050 (mt) cc_final: 0.7713 (mt) REVERT: K 24 ASP cc_start: 0.8018 (t0) cc_final: 0.7446 (t0) REVERT: K 29 ASN cc_start: 0.7947 (t0) cc_final: 0.7468 (t0) REVERT: L 38 LEU cc_start: 0.7830 (mt) cc_final: 0.7440 (pp) REVERT: L 44 ASP cc_start: 0.8140 (t0) cc_final: 0.7707 (t0) outliers start: 84 outliers final: 48 residues processed: 550 average time/residue: 0.7368 time to fit residues: 483.7989 Evaluate side-chains 534 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 463 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 62 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 34 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 271 optimal weight: 0.5980 chunk 39 optimal weight: 0.0020 chunk 330 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 367 optimal weight: 0.0980 chunk 364 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 115 ASN G 10 ASN G 57 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114605 restraints weight = 47954.889| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.32 r_work: 0.3376 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 33815 Z= 0.219 Angle : 0.804 59.186 45905 Z= 0.431 Chirality : 0.051 1.645 5155 Planarity : 0.005 0.186 5746 Dihedral : 12.858 173.281 5030 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.28 % Allowed : 22.61 % Favored : 75.11 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.11 % 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: 3945 helix: 1.24 (0.14), residues: 1380 sheet: -0.20 (0.20), residues: 637 loop : 0.11 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 155 TYR 0.022 0.001 TYR E 187 PHE 0.031 0.001 PHE A1402 TRP 0.042 0.002 TRP A1191 HIS 0.003 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.22 (33773) covalent geometry : angle 0.79682 / 0.43 (45854) hydrogen bonds : bond 0.03645 / 2.46 ( 1449) hydrogen bonds : angle 4.52683 / 3.24 ( 4075) metal coordination : bond 0.00453 / 0.30 ( 32) metal coordination : angle 3.47533 / 2.39 ( 45) Misc. bond : bond 0.00074 / 0.04 ( 8) link_TRANS : bond 0.00019 / 0.01 ( 2) link_TRANS : angle 0.20074 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14976.66 seconds wall clock time: 255 minutes 16.70 seconds (15316.70 seconds total)