Starting phenix.real_space_refine on Mon Jul 6 09:13:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kdq_62284/07_2026/9kdq_62284_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kdq_62284/07_2026/9kdq_62284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kdq_62284/07_2026/9kdq_62284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kdq_62284/07_2026/9kdq_62284.map" model { file = "/net/cci-nas-00/data/ceres_data/9kdq_62284/07_2026/9kdq_62284_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kdq_62284/07_2026/9kdq_62284_neut.cif" } resolution = 2.63 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 59 5.49 5 Mg 1 5.21 5 S 181 5.16 5 C 20839 2.51 5 N 5794 2.21 5 O 6442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33324 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11221 Classifications: {'peptide': 1426} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1359} Chain breaks: 3 Chain: "B" Number of atoms: 9479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9479 Classifications: {'peptide': 1190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1137} Chain breaks: 3 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} 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 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: 4 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: "O" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "O" 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 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" 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 O 6 " pdbres="THR O 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 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: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "Q" 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 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "Q" 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 Q 6 " pdbres="THR Q 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 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: "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 97.273 83.644 33.946 1.00109.63 S ATOM 844 SG CYS A 110 99.125 86.932 34.276 1.00125.14 S ATOM 1149 SG CYS A 148 96.358 86.682 31.669 1.00128.48 S ATOM 1287 SG CYS A 167 99.465 84.721 31.113 1.00121.72 S ATOM 515 SG CYS A 67 112.141 79.446 79.788 1.00 83.51 S ATOM 537 SG CYS A 70 110.841 82.692 81.276 1.00 73.94 S ATOM 590 SG CYS A 77 108.403 79.810 80.406 1.00 92.26 S ATOM 20206 SG CYS B1163 106.103 94.224 70.681 1.00 85.76 S ATOM 20224 SG CYS B1166 104.828 91.334 68.630 1.00 89.80 S ATOM 20349 SG CYS B1182 108.328 91.214 70.533 1.00 91.14 S ATOM 20368 SG CYS B1185 107.772 93.164 67.332 1.00 92.88 S ATOM 21347 SG CYS C 86 81.899 60.754 139.639 1.00101.27 S ATOM 21364 SG CYS C 88 84.280 59.141 137.104 1.00108.34 S ATOM 21397 SG CYS C 92 83.008 57.279 140.267 1.00 86.92 S ATOM 21420 SG CYS C 95 80.739 58.000 137.240 1.00 89.36 S ATOM 29087 SG CYS I 7 52.371 32.545 21.053 1.00103.07 S ATOM 29112 SG CYS I 10 56.129 32.810 21.850 1.00117.81 S ATOM 29278 SG CYS I 29 54.321 35.941 20.820 1.00111.10 S ATOM 29302 SG CYS I 32 54.789 33.164 18.295 1.00125.02 S ATOM 29629 SG CYS I 75 22.015 33.295 54.827 1.00 81.06 S ATOM 29651 SG CYS I 78 21.761 29.398 54.111 1.00 97.52 S ATOM 29867 SG CYS I 103 24.452 30.992 56.666 1.00 84.03 S ATOM 29887 SG CYS I 106 24.464 31.153 52.960 1.00 84.11 S ATOM 30032 SG CYS J 7 56.445 49.547 119.011 1.00 69.62 S ATOM 30055 SG CYS J 10 54.992 50.879 122.256 1.00 64.48 S ATOM 30335 SG CYS J 45 52.771 50.488 119.092 1.00 70.05 S ATOM 30341 SG CYS J 46 54.040 47.499 121.171 1.00 65.98 S ATOM 31521 SG CYS L 31 92.995 27.842 105.505 1.00 81.08 S ATOM 31541 SG CYS L 34 92.251 24.481 106.953 1.00 88.31 S ATOM 31645 SG CYS L 48 96.029 25.895 106.380 1.00 73.24 S ATOM 31668 SG CYS L 51 93.574 24.381 103.808 1.00 91.43 S Time building chain proxies: 6.24, per 1000 atoms: 0.19 Number of scatterers: 33324 At special positions: 0 Unit cell: (159.96, 153.45, 157.17, 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 181 16.00 P 59 15.00 Mg 1 11.99 O 6442 8.00 N 5794 7.00 C 20839 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=13, symmetry=0 Links applied TRANS " DVA M 2 " - " THR M 1 " " DVA O 2 " - " THR O 1 " " DVA Q 2 " - " THR Q 1 " Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 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 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 45 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 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 " pdb=" CB DVA Q 2 " pdb=" CB DVA Q 8 " Number of C-beta restraints generated: 7562 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 51 sheets defined 38.9% alpha, 19.9% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.011A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.357A 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 Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.680A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.578A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.526A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.602A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.845A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) 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 913 through 918 removed outlier: 4.341A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.620A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.566A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.579A 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 1164 through 1177 removed outlier: 4.069A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.929A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A1188 " --> pdb=" O PHE A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1188' Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1255 through 1269 removed outlier: 3.648A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 4.064A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.577A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.094A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.644A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.600A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 4.004A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (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 removed outlier: 3.668A pdb=" N ASP B 82 " --> pdb=" O THR B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.491A 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: 3.541A 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 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.812A pdb=" N TYR B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.653A 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: 4.370A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.892A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.519A pdb=" N LEU B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.525A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.571A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.563A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.775A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.111A pdb=" N THR B 882 " --> pdb=" O ARG B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.945A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.663A pdb=" N CYS C 86 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.855A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 removed outlier: 3.591A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 removed outlier: 3.540A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) 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 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 removed outlier: 3.771A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.705A 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 55 through 59 removed outlier: 3.718A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.633A 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 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.797A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.773A 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: 3.505A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.512A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 removed outlier: 3.569A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain '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 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 63 removed outlier: 4.028A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.864A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.642A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.898A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.649A 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: 3.561A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 6.094A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.024A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.694A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.177A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.552A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.685A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.792A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.729A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.035A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.035A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.356A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.974A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 242 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.386A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.784A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.784A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.968A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.594A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.529A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.941A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.451A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE9, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.211A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AF2, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.649A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.856A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 14 through 18 removed outlier: 3.534A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23 1430 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 9.06 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5547 1.28 - 1.42: 8343 1.42 - 1.55: 19732 1.55 - 1.69: 124 1.69 - 1.82: 290 Bond restraints: 34036 Sorted by residual: bond pdb=" N MVA M 5 " pdb=" CA MVA M 5 " ideal model delta sigma weight residual 1.458 1.232 0.226 1.90e-02 2.77e+03 1.41e+02 bond pdb=" N MVA M 5 " pdb=" CN MVA M 5 " ideal model delta sigma weight residual 1.449 1.239 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" N MVA M 11 " pdb=" CA MVA M 11 " ideal model delta sigma weight residual 1.458 1.275 0.183 1.90e-02 2.77e+03 9.29e+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 8.86e+01 bond pdb=" C12 PXZ Q 6 " pdb=" C4 PXZ Q 6 " ideal model delta sigma weight residual 1.354 1.541 -0.187 2.00e-02 2.50e+03 8.78e+01 ... (remaining 34031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 45590 2.70 - 5.40: 528 5.40 - 8.10: 96 8.10 - 10.81: 7 10.81 - 13.51: 3 Bond angle restraints: 46224 Sorted by residual: angle pdb=" N GLU B 526 " pdb=" CA GLU B 526 " pdb=" CB GLU B 526 " ideal model delta sigma weight residual 110.49 124.00 -13.51 1.69e+00 3.50e-01 6.39e+01 angle pdb=" N ILE B 502 " pdb=" CA ILE B 502 " pdb=" C ILE B 502 " ideal model delta sigma weight residual 109.20 99.46 9.74 1.55e+00 4.16e-01 3.95e+01 angle pdb=" CA GLY A 331 " pdb=" C GLY A 331 " pdb=" O GLY A 331 " ideal model delta sigma weight residual 122.22 118.39 3.83 6.50e-01 2.37e+00 3.48e+01 angle pdb=" CA SAR M 4 " pdb=" C SAR M 4 " pdb=" N MVA M 5 " ideal model delta sigma weight residual 116.20 127.77 -11.57 2.00e+00 2.50e-01 3.34e+01 angle pdb=" N ASP B 505 " pdb=" CA ASP B 505 " pdb=" C ASP B 505 " ideal model delta sigma weight residual 114.12 106.52 7.60 1.39e+00 5.18e-01 2.99e+01 ... (remaining 46219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 20173 34.66 - 69.32: 470 69.32 - 103.98: 33 103.98 - 138.65: 0 138.65 - 173.31: 8 Dihedral angle restraints: 20684 sinusoidal: 8999 harmonic: 11685 Sorted by residual: dihedral pdb=" N MVA M 5 " pdb=" C MVA M 5 " pdb=" CA MVA M 5 " pdb=" CB MVA M 5 " ideal model delta harmonic sigma weight residual 122.80 143.10 -20.30 0 2.50e+00 1.60e-01 6.60e+01 dihedral pdb=" C MVA M 5 " pdb=" N MVA M 5 " pdb=" CA MVA M 5 " pdb=" CB MVA M 5 " ideal model delta harmonic sigma weight residual -122.60 -142.79 20.19 0 2.50e+00 1.60e-01 6.52e+01 dihedral pdb=" CA ARG A 446 " pdb=" C ARG A 446 " pdb=" N GLN A 447 " pdb=" CA GLN A 447 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 20681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 5139 0.214 - 0.427: 10 0.427 - 0.641: 36 0.641 - 0.855: 3 0.855 - 1.068: 2 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CB DVA M 2 " pdb=" CA DVA M 2 " pdb=" CG1 DVA M 2 " pdb=" CG2 DVA M 2 " both_signs ideal model delta sigma weight residual False -2.63 -1.56 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA MVA M 5 " pdb=" N MVA M 5 " pdb=" C MVA M 5 " pdb=" CB MVA M 5 " both_signs ideal model delta sigma weight residual False 2.44 1.41 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA DVA M 2 " pdb=" N DVA M 2 " pdb=" C DVA M 2 " pdb=" CB DVA M 2 " both_signs ideal model delta sigma weight residual False -2.44 -1.76 -0.68 2.00e-01 2.50e+01 1.17e+01 ... (remaining 5187 not shown) Planarity restraints: 5788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C0 PXZ O 6 " -0.021 2.00e-02 2.50e+03 2.75e-02 3.78e+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 " -0.025 2.00e-02 2.50e+03 pdb=" C13 PXZ O 6 " -0.020 2.00e-02 2.50e+03 pdb=" C14 PXZ O 6 " -0.010 2.00e-02 2.50e+03 pdb=" C15 PXZ O 6 " -0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ O 6 " 0.012 2.00e-02 2.50e+03 pdb=" C2 PXZ O 6 " 0.017 2.00e-02 2.50e+03 pdb=" C3 PXZ O 6 " 0.018 2.00e-02 2.50e+03 pdb=" C4 PXZ O 6 " -0.015 2.00e-02 2.50e+03 pdb=" C6 PXZ O 6 " 0.008 2.00e-02 2.50e+03 pdb=" C7 PXZ O 6 " 0.029 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 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C0 PXZ Q 6 " -0.021 2.00e-02 2.50e+03 2.74e-02 3.75e+01 pdb=" C0' PXZ Q 6 " 0.007 2.00e-02 2.50e+03 pdb=" C1 PXZ Q 6 " 0.003 2.00e-02 2.50e+03 pdb=" C11 PXZ Q 6 " -0.028 2.00e-02 2.50e+03 pdb=" C12 PXZ Q 6 " -0.025 2.00e-02 2.50e+03 pdb=" C13 PXZ Q 6 " -0.021 2.00e-02 2.50e+03 pdb=" C14 PXZ Q 6 " -0.009 2.00e-02 2.50e+03 pdb=" C15 PXZ Q 6 " -0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ Q 6 " 0.011 2.00e-02 2.50e+03 pdb=" C2 PXZ Q 6 " 0.016 2.00e-02 2.50e+03 pdb=" C3 PXZ Q 6 " 0.018 2.00e-02 2.50e+03 pdb=" C4 PXZ Q 6 " -0.015 2.00e-02 2.50e+03 pdb=" C6 PXZ Q 6 " 0.009 2.00e-02 2.50e+03 pdb=" C7 PXZ Q 6 " 0.029 2.00e-02 2.50e+03 pdb=" C8 PXZ Q 6 " 0.043 2.00e-02 2.50e+03 pdb=" C9 PXZ Q 6 " 0.020 2.00e-02 2.50e+03 pdb=" N10 PXZ Q 6 " -0.054 2.00e-02 2.50e+03 pdb=" N2 PXZ Q 6 " 0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ Q 6 " 0.039 2.00e-02 2.50e+03 pdb=" O5 PXZ Q 6 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " -0.003 2.00e-02 2.50e+03 1.89e-02 1.79e+01 pdb=" C0' PXZ M 6 " 0.007 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " -0.016 2.00e-02 2.50e+03 pdb=" C11 PXZ M 6 " -0.012 2.00e-02 2.50e+03 pdb=" C12 PXZ M 6 " -0.019 2.00e-02 2.50e+03 pdb=" C13 PXZ M 6 " -0.001 2.00e-02 2.50e+03 pdb=" C14 PXZ M 6 " -0.013 2.00e-02 2.50e+03 pdb=" C15 PXZ M 6 " 0.020 2.00e-02 2.50e+03 pdb=" C16 PXZ M 6 " -0.030 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " -0.010 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " 0.020 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " 0.009 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " -0.003 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " 0.004 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 " -0.017 2.00e-02 2.50e+03 pdb=" N2 PXZ M 6 " -0.003 2.00e-02 2.50e+03 pdb=" O3 PXZ M 6 " 0.030 2.00e-02 2.50e+03 pdb=" O5 PXZ M 6 " -0.027 2.00e-02 2.50e+03 ... (remaining 5785 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 113 2.49 - 3.09: 22978 3.09 - 3.69: 50412 3.69 - 4.30: 76033 4.30 - 4.90: 125432 Nonbonded interactions: 274968 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 1.883 2.170 nonbonded pdb=" OD2 ASP A1166 " pdb=" NH1 ARG A1239 " model vdw 2.156 3.120 nonbonded pdb=" NH2 ARG A 469 " pdb=" O GLY B 991 " model vdw 2.172 3.120 nonbonded pdb=" O LEU D 167 " pdb=" OG1 THR D 170 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR B 487 " pdb=" O ALA B 777 " model vdw 2.212 3.040 ... (remaining 274963 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' selection = chain 'Q' } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.670 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.008 0.726 34084 Z= 0.565 Angle : 0.757 14.647 46278 Z= 0.415 Chirality : 0.071 1.068 5190 Planarity : 0.005 0.073 5785 Dihedral : 15.111 173.308 13113 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Rotamer: Outliers : 0.11 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.40 (0.13), residues: 3964 helix: 1.15 (0.14), residues: 1363 sheet: -0.26 (0.20), residues: 660 loop : -0.07 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1386 TYR 0.022 0.002 TYR B1092 PHE 0.022 0.002 PHE G 18 TRP 0.022 0.002 TRP C 170 HIS 0.007 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.35 (34036) covalent geometry : angle 0.74104 / 0.41 (46224) hydrogen bonds : bond 0.14672 / 9.62 ( 1442) hydrogen bonds : angle 6.07917 / 4.25 ( 4036) metal coordination : bond 0.00623 / 0.42 ( 32) metal coordination : angle 4.96955 / 2.97 ( 45) Misc. bond : bond 0.22759 / 11.56 ( 13) link_TRANS : bond 0.00777 / 0.41 ( 3) link_TRANS : angle 1.01963 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 832 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.8260 (mm) cc_final: 0.8025 (mm) REVERT: A 453 MET cc_start: 0.9037 (mpp) cc_final: 0.8813 (mpp) REVERT: A 795 GLU cc_start: 0.8673 (pm20) cc_final: 0.8394 (pm20) REVERT: A 818 MET cc_start: 0.8890 (mtp) cc_final: 0.8664 (mtm) REVERT: A 1109 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8394 (mmmt) REVERT: A 1112 LYS cc_start: 0.8636 (mmpt) cc_final: 0.8323 (mmtt) REVERT: A 1259 MET cc_start: 0.7862 (tpt) cc_final: 0.7568 (tpp) REVERT: A 1263 ILE cc_start: 0.7777 (mm) cc_final: 0.7510 (mp) REVERT: A 1285 MET cc_start: 0.8262 (mmm) cc_final: 0.7947 (mmm) REVERT: A 1287 TYR cc_start: 0.7234 (m-80) cc_final: 0.6717 (m-10) REVERT: B 101 MET cc_start: 0.8611 (mtp) cc_final: 0.8410 (mtt) REVERT: B 259 TYR cc_start: 0.8321 (m-80) cc_final: 0.8050 (m-80) REVERT: B 268 THR cc_start: 0.8876 (p) cc_final: 0.8613 (t) REVERT: B 315 LYS cc_start: 0.6680 (mmtt) cc_final: 0.6475 (mmtt) REVERT: B 325 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6875 (mm110) REVERT: B 326 ASP cc_start: 0.6845 (t70) cc_final: 0.5991 (t70) REVERT: B 350 GLN cc_start: 0.7989 (tp40) cc_final: 0.7278 (tp40) REVERT: B 357 GLN cc_start: 0.8047 (tt0) cc_final: 0.7788 (tm-30) REVERT: B 381 MET cc_start: 0.8616 (mtp) cc_final: 0.8331 (mtp) REVERT: B 444 MET cc_start: 0.6873 (mpp) cc_final: 0.6525 (pp-130) REVERT: B 513 GLN cc_start: 0.8456 (mt0) cc_final: 0.8083 (mm110) REVERT: B 606 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7915 (pttp) REVERT: B 662 MET cc_start: 0.8641 (mmp) cc_final: 0.8387 (mmm) REVERT: B 864 LYS cc_start: 0.7791 (ptpp) cc_final: 0.7469 (pttp) REVERT: B 1057 LYS cc_start: 0.8203 (mttt) cc_final: 0.7987 (mtpp) REVERT: B 1222 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7641 (mtm110) REVERT: C 75 MET cc_start: 0.8532 (tpp) cc_final: 0.8328 (mmm) REVERT: C 102 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7908 (mt0) REVERT: C 152 GLU cc_start: 0.7809 (tt0) cc_final: 0.7316 (tp30) REVERT: E 92 THR cc_start: 0.8015 (p) cc_final: 0.7715 (t) REVERT: E 172 GLU cc_start: 0.8071 (tp30) cc_final: 0.7630 (tt0) REVERT: E 192 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7764 (ttp80) REVERT: E 215 MET cc_start: 0.5805 (mmt) cc_final: 0.5293 (ptt) REVERT: F 112 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8079 (mm-30) REVERT: F 123 LYS cc_start: 0.8375 (tttm) cc_final: 0.8158 (tttm) REVERT: G 3 PHE cc_start: 0.6281 (m-80) cc_final: 0.5855 (m-80) REVERT: G 42 PHE cc_start: 0.8101 (m-80) cc_final: 0.7736 (m-80) REVERT: G 168 LEU cc_start: 0.8206 (mm) cc_final: 0.7298 (tp) REVERT: H 14 GLU cc_start: 0.8759 (tt0) cc_final: 0.8523 (tt0) REVERT: H 21 ASN cc_start: 0.8705 (m-40) cc_final: 0.8423 (m110) REVERT: H 53 ASP cc_start: 0.8302 (t0) cc_final: 0.7797 (m-30) REVERT: H 91 ASP cc_start: 0.8882 (m-30) cc_final: 0.8616 (m-30) REVERT: I 11 ASN cc_start: 0.8024 (t0) cc_final: 0.7496 (t0) REVERT: K 5 ASP cc_start: 0.8360 (m-30) cc_final: 0.8005 (m-30) REVERT: K 24 ASP cc_start: 0.8372 (t0) cc_final: 0.8014 (t0) outliers start: 4 outliers final: 3 residues processed: 833 average time/residue: 0.7098 time to fit residues: 694.0858 Evaluate side-chains 493 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 490 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain H residue 65 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 0.0070 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0370 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 169 ASN A 171 GLN A 256 GLN A 390 GLN A 394 ASN A 447 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN A 611 GLN A 975 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 469 GLN B 513 GLN B 862 GLN B 887 HIS B1093 GLN B1104 HIS B1179 GLN C 17 ASN C 214 ASN E 32 GLN E 179 GLN F 104 ASN G 71 ASN G 113 HIS H 11 GLN I 87 GLN J 64 ASN L 53 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105913 restraints weight = 42896.396| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.29 r_work: 0.3238 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 34084 Z= 0.137 Angle : 0.604 15.271 46278 Z= 0.311 Chirality : 0.045 0.268 5190 Planarity : 0.004 0.069 5785 Dihedral : 13.610 164.388 5085 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.38 % Allowed : 11.77 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.54 (0.13), residues: 3964 helix: 1.30 (0.14), residues: 1386 sheet: -0.15 (0.19), residues: 673 loop : -0.05 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 119 TYR 0.013 0.001 TYR B1092 PHE 0.020 0.002 PHE A 219 TRP 0.011 0.001 TRP B 31 HIS 0.013 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (34036) covalent geometry : angle 0.58321 / 0.31 (46224) hydrogen bonds : bond 0.04740 / 3.13 ( 1442) hydrogen bonds : angle 4.78256 / 3.39 ( 4036) metal coordination : bond 0.02336 / 0.99 ( 32) metal coordination : angle 5.08376 / 3.24 ( 45) Misc. bond : bond 0.00760 / 0.40 ( 13) link_TRANS : bond 0.00141 / 0.07 ( 3) link_TRANS : angle 0.63940 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 515 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8145 (pm20) cc_final: 0.7782 (pt0) REVERT: A 47 ARG cc_start: 0.6709 (ttp-110) cc_final: 0.5885 (ptt90) REVERT: A 415 LEU cc_start: 0.8037 (mm) cc_final: 0.7707 (mm) REVERT: A 453 MET cc_start: 0.8921 (mpp) cc_final: 0.8708 (mpp) REVERT: A 771 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8621 (mt-10) REVERT: A 795 GLU cc_start: 0.8774 (pm20) cc_final: 0.8435 (pm20) REVERT: A 822 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: A 838 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8209 (tp40) REVERT: A 1109 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8329 (mmmt) REVERT: A 1112 LYS cc_start: 0.8721 (mmpt) cc_final: 0.8328 (mmtt) REVERT: A 1207 LEU cc_start: 0.7575 (mm) cc_final: 0.7181 (mm) REVERT: A 1263 ILE cc_start: 0.7772 (mm) cc_final: 0.7466 (mp) REVERT: A 1285 MET cc_start: 0.8272 (mmm) cc_final: 0.7942 (mmm) REVERT: A 1452 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7604 (ttpp) REVERT: B 164 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8032 (mtmt) REVERT: B 259 TYR cc_start: 0.8487 (m-80) cc_final: 0.8156 (m-80) REVERT: B 268 THR cc_start: 0.8789 (p) cc_final: 0.8444 (t) REVERT: B 350 GLN cc_start: 0.7979 (tp40) cc_final: 0.7263 (tp40) REVERT: B 381 MET cc_start: 0.8528 (mtp) cc_final: 0.8281 (mtp) REVERT: B 444 MET cc_start: 0.6991 (mpp) cc_final: 0.6540 (pp-130) REVERT: B 504 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7180 (ttm170) REVERT: B 513 GLN cc_start: 0.8531 (mt0) cc_final: 0.8087 (mm110) REVERT: B 606 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7679 (pttp) REVERT: B 620 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7855 (ttm110) REVERT: B 706 GLN cc_start: 0.8844 (pm20) cc_final: 0.8635 (pm20) REVERT: B 730 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7740 (mtt180) REVERT: B 864 LYS cc_start: 0.7669 (ptpp) cc_final: 0.7334 (pttp) REVERT: B 962 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7406 (ttpp) REVERT: B 1057 LYS cc_start: 0.8191 (mttt) cc_final: 0.7784 (ttpp) REVERT: C 50 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: C 75 MET cc_start: 0.8596 (tpp) cc_final: 0.8379 (mmm) REVERT: C 102 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7932 (mt0) REVERT: C 214 ASN cc_start: 0.7707 (m-40) cc_final: 0.7015 (m110) REVERT: C 215 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7437 (pm20) REVERT: C 263 THR cc_start: 0.8592 (t) cc_final: 0.8183 (p) REVERT: D 54 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6702 (tp30) REVERT: D 123 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5604 (tt) REVERT: D 159 THR cc_start: 0.8855 (p) cc_final: 0.8186 (p) REVERT: D 208 GLU cc_start: 0.6528 (tp30) cc_final: 0.5964 (mm-30) REVERT: E 92 THR cc_start: 0.7931 (p) cc_final: 0.7714 (t) REVERT: E 172 GLU cc_start: 0.8485 (tp30) cc_final: 0.7917 (tt0) REVERT: E 179 GLN cc_start: 0.8487 (mt0) cc_final: 0.8286 (mt0) REVERT: E 192 ARG cc_start: 0.8250 (ptm-80) cc_final: 0.7801 (ttp80) REVERT: E 215 MET cc_start: 0.5922 (mmt) cc_final: 0.4998 (ptt) REVERT: F 71 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: F 110 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7717 (p0) REVERT: G 26 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7265 (mm) REVERT: G 42 PHE cc_start: 0.7503 (m-80) cc_final: 0.7227 (m-80) REVERT: G 168 LEU cc_start: 0.7139 (mm) cc_final: 0.6700 (tp) REVERT: H 14 GLU cc_start: 0.8852 (tt0) cc_final: 0.8606 (tt0) REVERT: H 21 ASN cc_start: 0.8819 (m-40) cc_final: 0.8562 (m110) REVERT: H 128 ASN cc_start: 0.8219 (p0) cc_final: 0.8018 (p0) REVERT: I 55 THR cc_start: 0.8672 (p) cc_final: 0.8376 (m) REVERT: I 92 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7471 (mtp85) REVERT: I 93 LYS cc_start: 0.8281 (pttp) cc_final: 0.7904 (mttm) REVERT: K 5 ASP cc_start: 0.8307 (m-30) cc_final: 0.7888 (m-30) REVERT: K 24 ASP cc_start: 0.8354 (t0) cc_final: 0.7847 (t0) REVERT: K 106 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6618 (mt-10) REVERT: L 28 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7802 (mmtm) outliers start: 84 outliers final: 25 residues processed: 562 average time/residue: 0.8092 time to fit residues: 535.2407 Evaluate side-chains 497 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 462 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 0.7980 chunk 354 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 389 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 394 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 415 GLN B 648 HIS B 887 HIS B1093 GLN E 32 GLN G 71 ASN H 11 GLN I 11 ASN J 64 ASN K 110 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102900 restraints weight = 42731.160| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34084 Z= 0.174 Angle : 0.608 16.301 46278 Z= 0.310 Chirality : 0.046 0.374 5190 Planarity : 0.005 0.068 5785 Dihedral : 13.395 154.609 5081 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.66 % Allowed : 13.38 % Favored : 83.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.13), residues: 3964 helix: 1.26 (0.14), residues: 1397 sheet: -0.11 (0.19), residues: 673 loop : -0.14 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 595 TYR 0.024 0.001 TYR B1092 PHE 0.028 0.002 PHE A 219 TRP 0.012 0.001 TRP B 31 HIS 0.012 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (34036) covalent geometry : angle 0.58626 / 0.31 (46224) hydrogen bonds : bond 0.04720 / 3.13 ( 1442) hydrogen bonds : angle 4.58944 / 3.27 ( 4036) metal coordination : bond 0.00927 / 0.48 ( 32) metal coordination : angle 5.17224 / 3.38 ( 45) Misc. bond : bond 0.00562 / 0.34 ( 13) link_TRANS : bond 0.00145 / 0.07 ( 3) link_TRANS : angle 0.19102 / 0.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 481 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8121 (pm20) cc_final: 0.7747 (pt0) REVERT: A 123 ARG cc_start: 0.7668 (mpp-170) cc_final: 0.7467 (mtt90) REVERT: A 415 LEU cc_start: 0.8122 (mm) cc_final: 0.7718 (mm) REVERT: A 601 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8407 (mtpp) REVERT: A 795 GLU cc_start: 0.8739 (pm20) cc_final: 0.8375 (pm20) REVERT: A 822 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: A 969 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 1109 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8304 (mmmt) REVERT: A 1112 LYS cc_start: 0.8680 (mmpt) cc_final: 0.8313 (mmtt) REVERT: A 1207 LEU cc_start: 0.7465 (mm) cc_final: 0.7027 (mm) REVERT: A 1263 ILE cc_start: 0.7714 (mm) cc_final: 0.7433 (mp) REVERT: A 1285 MET cc_start: 0.8300 (mmm) cc_final: 0.7983 (mmm) REVERT: A 1452 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7468 (ttpp) REVERT: B 22 SER cc_start: 0.8456 (m) cc_final: 0.8208 (p) REVERT: B 268 THR cc_start: 0.8753 (p) cc_final: 0.8388 (t) REVERT: B 325 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7285 (mm110) REVERT: B 350 GLN cc_start: 0.7988 (tp40) cc_final: 0.7329 (tp-100) REVERT: B 381 MET cc_start: 0.8591 (mtp) cc_final: 0.8332 (mtp) REVERT: B 444 MET cc_start: 0.7048 (mpp) cc_final: 0.6601 (pp-130) REVERT: B 504 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7033 (ttm170) REVERT: B 513 GLN cc_start: 0.8649 (mt0) cc_final: 0.8161 (mm110) REVERT: B 591 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8156 (mmt90) REVERT: B 606 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7784 (pttp) REVERT: B 620 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7843 (ttm110) REVERT: B 730 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7749 (mtt180) REVERT: B 864 LYS cc_start: 0.7648 (ptpp) cc_final: 0.7235 (pttp) REVERT: B 868 MET cc_start: 0.7260 (mmt) cc_final: 0.6806 (mmm) REVERT: B 962 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7475 (ttpp) REVERT: B 1057 LYS cc_start: 0.8310 (mttt) cc_final: 0.8056 (mtpp) REVERT: C 50 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: C 75 MET cc_start: 0.8591 (tpp) cc_final: 0.8322 (tpt) REVERT: C 102 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7972 (mt0) REVERT: C 214 ASN cc_start: 0.7859 (m-40) cc_final: 0.6987 (t0) REVERT: C 215 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7434 (pm20) REVERT: C 263 THR cc_start: 0.8621 (t) cc_final: 0.8223 (p) REVERT: D 123 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5756 (tt) REVERT: D 155 ARG cc_start: 0.7508 (tpt-90) cc_final: 0.7292 (tpt-90) REVERT: D 194 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.4248 (tp) REVERT: E 57 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7024 (tmm) REVERT: E 58 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8493 (ttm) REVERT: E 92 THR cc_start: 0.7930 (p) cc_final: 0.7694 (t) REVERT: E 172 GLU cc_start: 0.8686 (tp30) cc_final: 0.8126 (tt0) REVERT: E 179 GLN cc_start: 0.8537 (mt0) cc_final: 0.8331 (mt0) REVERT: E 192 ARG cc_start: 0.8221 (ptm-80) cc_final: 0.7774 (ttp80) REVERT: E 215 MET cc_start: 0.5781 (mmt) cc_final: 0.4948 (ptm) REVERT: F 71 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: F 114 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: F 149 GLU cc_start: 0.8644 (tt0) cc_final: 0.8441 (tt0) REVERT: G 26 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7362 (mm) REVERT: G 42 PHE cc_start: 0.7550 (m-80) cc_final: 0.7291 (m-80) REVERT: G 168 LEU cc_start: 0.7137 (mm) cc_final: 0.6712 (tp) REVERT: H 14 GLU cc_start: 0.8867 (tt0) cc_final: 0.8630 (tt0) REVERT: H 21 ASN cc_start: 0.8798 (m-40) cc_final: 0.8536 (m110) REVERT: I 55 THR cc_start: 0.8710 (p) cc_final: 0.8416 (m) REVERT: I 92 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7463 (mtp85) REVERT: I 93 LYS cc_start: 0.8396 (pttp) cc_final: 0.8047 (mttm) REVERT: K 5 ASP cc_start: 0.8305 (m-30) cc_final: 0.8082 (m-30) REVERT: K 24 ASP cc_start: 0.8382 (t0) cc_final: 0.7897 (t0) REVERT: K 106 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6651 (mt-10) REVERT: L 28 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7857 (mmtp) outliers start: 94 outliers final: 38 residues processed: 528 average time/residue: 0.7894 time to fit residues: 492.3464 Evaluate side-chains 503 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 452 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 112 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 380 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 415 GLN B 469 GLN B 887 HIS B1093 GLN B1176 ASN E 32 GLN G 71 ASN I 11 ASN I 90 GLN J 64 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104135 restraints weight = 42523.723| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.28 r_work: 0.3219 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34084 Z= 0.128 Angle : 0.553 15.430 46278 Z= 0.284 Chirality : 0.044 0.319 5190 Planarity : 0.004 0.067 5785 Dihedral : 13.285 153.894 5081 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.41 % Allowed : 15.14 % Favored : 82.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 3964 helix: 1.43 (0.14), residues: 1389 sheet: -0.05 (0.19), residues: 675 loop : -0.08 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 348 TYR 0.011 0.001 TYR A1349 PHE 0.024 0.002 PHE B 333 TRP 0.010 0.001 TRP B 31 HIS 0.017 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (34036) covalent geometry : angle 0.53077 / 0.28 (46224) hydrogen bonds : bond 0.04108 / 2.74 ( 1442) hydrogen bonds : angle 4.41413 / 3.14 ( 4036) metal coordination : bond 0.00886 / 0.44 ( 32) metal coordination : angle 4.99722 / 3.35 ( 45) Misc. bond : bond 0.00355 / 0.22 ( 13) link_TRANS : bond 0.00045 / 0.02 ( 3) link_TRANS : angle 0.39092 / 0.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 480 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: A 5 GLN cc_start: 0.8111 (pm20) cc_final: 0.7811 (pt0) REVERT: A 123 ARG cc_start: 0.7686 (mpp-170) cc_final: 0.7368 (mtt90) REVERT: A 398 GLU cc_start: 0.8110 (pt0) cc_final: 0.7501 (pt0) REVERT: A 415 LEU cc_start: 0.8114 (mm) cc_final: 0.7756 (mm) REVERT: A 601 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8393 (mtpp) REVERT: A 706 HIS cc_start: 0.8252 (t-90) cc_final: 0.7939 (t-90) REVERT: A 771 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8636 (mt-10) REVERT: A 795 GLU cc_start: 0.8778 (pm20) cc_final: 0.8421 (pm20) REVERT: A 822 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: A 1079 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6725 (mmm) REVERT: A 1109 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8324 (mmmt) REVERT: A 1112 LYS cc_start: 0.8684 (mmpt) cc_final: 0.8330 (mmtt) REVERT: A 1207 LEU cc_start: 0.7445 (mm) cc_final: 0.7014 (mm) REVERT: A 1259 MET cc_start: 0.8364 (ttp) cc_final: 0.8075 (ttp) REVERT: A 1263 ILE cc_start: 0.7769 (mm) cc_final: 0.7488 (mp) REVERT: A 1285 MET cc_start: 0.8261 (mmm) cc_final: 0.7931 (mmm) REVERT: A 1452 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7522 (ttpp) REVERT: B 22 SER cc_start: 0.8501 (m) cc_final: 0.8249 (p) REVERT: B 227 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8213 (mtmt) REVERT: B 268 THR cc_start: 0.8763 (p) cc_final: 0.8419 (t) REVERT: B 325 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7321 (mm110) REVERT: B 350 GLN cc_start: 0.8037 (tp40) cc_final: 0.7357 (tp-100) REVERT: B 381 MET cc_start: 0.8624 (mtp) cc_final: 0.8373 (mtp) REVERT: B 444 MET cc_start: 0.7051 (mpp) cc_final: 0.6601 (pp-130) REVERT: B 504 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7335 (ttm170) REVERT: B 513 GLN cc_start: 0.8670 (mt0) cc_final: 0.8232 (mm110) REVERT: B 591 ARG cc_start: 0.8424 (mmt90) cc_final: 0.8207 (mmt90) REVERT: B 606 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7731 (pttp) REVERT: B 620 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7785 (ttm110) REVERT: B 623 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 730 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7763 (mtt180) REVERT: B 864 LYS cc_start: 0.7605 (ptpp) cc_final: 0.7150 (pttp) REVERT: B 868 MET cc_start: 0.7250 (mmt) cc_final: 0.6830 (mmm) REVERT: B 962 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7555 (ttpp) REVERT: B 1057 LYS cc_start: 0.8297 (mttt) cc_final: 0.8046 (mtpp) REVERT: C 50 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: C 75 MET cc_start: 0.8549 (tpp) cc_final: 0.8337 (tpp) REVERT: C 102 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7958 (mt0) REVERT: D 26 THR cc_start: 0.7385 (OUTLIER) cc_final: 0.7182 (p) REVERT: D 54 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6819 (tp30) REVERT: D 123 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5739 (tt) REVERT: D 208 GLU cc_start: 0.6730 (tp30) cc_final: 0.6084 (mm-30) REVERT: E 57 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6993 (tmm) REVERT: E 92 THR cc_start: 0.7974 (p) cc_final: 0.7744 (t) REVERT: E 172 GLU cc_start: 0.8621 (tp30) cc_final: 0.8034 (tt0) REVERT: E 179 GLN cc_start: 0.8569 (mt0) cc_final: 0.8335 (mt0) REVERT: E 192 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7772 (ttp80) REVERT: E 215 MET cc_start: 0.5755 (mmt) cc_final: 0.4972 (ptm) REVERT: F 71 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: F 110 ASP cc_start: 0.8181 (p0) cc_final: 0.7912 (p0) REVERT: G 26 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7362 (mm) REVERT: G 42 PHE cc_start: 0.7601 (m-80) cc_final: 0.7313 (m-80) REVERT: G 168 LEU cc_start: 0.7254 (mm) cc_final: 0.6771 (tp) REVERT: H 14 GLU cc_start: 0.8873 (tt0) cc_final: 0.8642 (tt0) REVERT: H 21 ASN cc_start: 0.8799 (m-40) cc_final: 0.8546 (m110) REVERT: H 128 ASN cc_start: 0.8187 (p0) cc_final: 0.7937 (p0) REVERT: I 55 THR cc_start: 0.8721 (p) cc_final: 0.8436 (m) REVERT: I 92 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7483 (mtp85) REVERT: I 93 LYS cc_start: 0.8392 (pttp) cc_final: 0.8100 (mttm) REVERT: K 5 ASP cc_start: 0.8288 (m-30) cc_final: 0.7837 (m-30) REVERT: K 24 ASP cc_start: 0.8323 (t0) cc_final: 0.7825 (t0) REVERT: K 38 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8618 (mm-30) REVERT: L 68 GLU cc_start: 0.8247 (tt0) cc_final: 0.8013 (tt0) outliers start: 85 outliers final: 32 residues processed: 527 average time/residue: 0.7896 time to fit residues: 490.6389 Evaluate side-chains 492 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 449 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 271 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 292 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 390 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 469 GLN B 648 HIS B 862 GLN B 887 HIS B1093 GLN B1176 ASN E 32 GLN F 104 ASN I 11 ASN J 64 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102107 restraints weight = 42584.844| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.27 r_work: 0.3185 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34084 Z= 0.170 Angle : 0.582 16.333 46278 Z= 0.297 Chirality : 0.045 0.311 5190 Planarity : 0.004 0.066 5785 Dihedral : 13.245 154.072 5081 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.83 % Allowed : 15.42 % Favored : 81.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.56 (0.13), residues: 3964 helix: 1.37 (0.14), residues: 1395 sheet: -0.06 (0.19), residues: 674 loop : -0.12 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 348 TYR 0.016 0.001 TYR A 465 PHE 0.028 0.002 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.017 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (34036) covalent geometry : angle 0.56035 / 0.30 (46224) hydrogen bonds : bond 0.04420 / 2.94 ( 1442) hydrogen bonds : angle 4.41453 / 3.14 ( 4036) metal coordination : bond 0.00770 / 0.43 ( 32) metal coordination : angle 5.12123 / 3.36 ( 45) Misc. bond : bond 0.00203 / 0.13 ( 13) link_TRANS : bond 0.00085 / 0.04 ( 3) link_TRANS : angle 0.31630 / 0.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 463 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8097 (pm20) cc_final: 0.7741 (pt0) REVERT: A 47 ARG cc_start: 0.7176 (ttp-110) cc_final: 0.6884 (ttp-110) REVERT: A 398 GLU cc_start: 0.8317 (pt0) cc_final: 0.7968 (pt0) REVERT: A 415 LEU cc_start: 0.8160 (mm) cc_final: 0.7746 (mm) REVERT: A 427 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: A 601 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8378 (mtpp) REVERT: A 795 GLU cc_start: 0.8802 (pm20) cc_final: 0.8431 (pm20) REVERT: A 822 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: A 838 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8100 (tp40) REVERT: A 840 ARG cc_start: 0.7267 (mmt90) cc_final: 0.7001 (mmt-90) REVERT: A 895 LYS cc_start: 0.8952 (tttm) cc_final: 0.8271 (tppt) REVERT: A 969 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 1079 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6789 (mtt) REVERT: A 1109 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8291 (mmmt) REVERT: A 1112 LYS cc_start: 0.8706 (mmpt) cc_final: 0.8355 (mmtt) REVERT: A 1144 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8537 (ttmm) REVERT: A 1207 LEU cc_start: 0.7451 (mm) cc_final: 0.7029 (mm) REVERT: A 1214 GLU cc_start: 0.7985 (tp30) cc_final: 0.7758 (tp30) REVERT: A 1263 ILE cc_start: 0.7778 (mm) cc_final: 0.7446 (mp) REVERT: A 1285 MET cc_start: 0.8312 (mmm) cc_final: 0.8048 (mmm) REVERT: A 1452 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7564 (ttpp) REVERT: B 22 SER cc_start: 0.8567 (m) cc_final: 0.8341 (p) REVERT: B 325 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7285 (mm110) REVERT: B 350 GLN cc_start: 0.8096 (tp40) cc_final: 0.7245 (tp-100) REVERT: B 354 ASP cc_start: 0.8398 (m-30) cc_final: 0.7976 (m-30) REVERT: B 381 MET cc_start: 0.8609 (mtp) cc_final: 0.8356 (mtp) REVERT: B 444 MET cc_start: 0.7107 (mpp) cc_final: 0.6658 (pp-130) REVERT: B 445 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7619 (mtpm) REVERT: B 504 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7773 (ttm170) REVERT: B 591 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8250 (mmt90) REVERT: B 606 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7772 (pttp) REVERT: B 620 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7876 (ttm110) REVERT: B 623 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 864 LYS cc_start: 0.7622 (ptpp) cc_final: 0.7136 (pttp) REVERT: B 868 MET cc_start: 0.7282 (mmt) cc_final: 0.6854 (mmm) REVERT: B 962 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7536 (ttpp) REVERT: B 1057 LYS cc_start: 0.8300 (mttt) cc_final: 0.8016 (mtpp) REVERT: C 50 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: C 75 MET cc_start: 0.8564 (tpp) cc_final: 0.8296 (mmm) REVERT: C 102 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7926 (mt0) REVERT: C 215 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7323 (pm20) REVERT: D 26 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7178 (p) REVERT: D 123 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5687 (tt) REVERT: D 155 ARG cc_start: 0.7358 (tpt-90) cc_final: 0.7139 (tpt-90) REVERT: E 57 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6854 (tmm) REVERT: E 92 THR cc_start: 0.7983 (p) cc_final: 0.7778 (t) REVERT: E 172 GLU cc_start: 0.8689 (tp30) cc_final: 0.8094 (tt0) REVERT: E 179 GLN cc_start: 0.8562 (mt0) cc_final: 0.8339 (mt0) REVERT: E 192 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.7804 (ttp80) REVERT: E 215 MET cc_start: 0.5690 (mmt) cc_final: 0.4955 (ptm) REVERT: F 71 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: F 114 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: G 26 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7316 (mm) REVERT: G 42 PHE cc_start: 0.7597 (m-80) cc_final: 0.7332 (m-80) REVERT: G 168 LEU cc_start: 0.7398 (mm) cc_final: 0.6956 (tp) REVERT: H 14 GLU cc_start: 0.8861 (tt0) cc_final: 0.8628 (tt0) REVERT: H 21 ASN cc_start: 0.8781 (m-40) cc_final: 0.8532 (m110) REVERT: I 55 THR cc_start: 0.8823 (p) cc_final: 0.8519 (m) REVERT: I 92 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7522 (mtp85) REVERT: I 93 LYS cc_start: 0.8391 (pttp) cc_final: 0.8130 (mttm) REVERT: J 26 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7553 (tm-30) REVERT: K 5 ASP cc_start: 0.8217 (m-30) cc_final: 0.7795 (m-30) REVERT: K 22 ASP cc_start: 0.8283 (m-30) cc_final: 0.7977 (m-30) REVERT: K 24 ASP cc_start: 0.8147 (t0) cc_final: 0.7675 (t0) REVERT: K 38 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8722 (mm-30) REVERT: K 55 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8311 (mtpp) REVERT: L 28 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7874 (mmtp) outliers start: 100 outliers final: 41 residues processed: 523 average time/residue: 0.7672 time to fit residues: 472.4280 Evaluate side-chains 501 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 444 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 55 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 388 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 328 optimal weight: 5.9990 chunk 334 optimal weight: 4.9990 chunk 213 optimal weight: 0.0470 chunk 192 optimal weight: 1.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1265 ASN B 415 GLN B 469 GLN B 648 HIS B1093 GLN B1176 ASN E 32 GLN F 104 ASN J 64 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104466 restraints weight = 42568.663| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.27 r_work: 0.3220 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34084 Z= 0.109 Angle : 0.535 14.585 46278 Z= 0.274 Chirality : 0.043 0.301 5190 Planarity : 0.004 0.067 5785 Dihedral : 13.128 155.764 5081 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.41 % Allowed : 16.27 % Favored : 81.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.74 (0.13), residues: 3964 helix: 1.58 (0.14), residues: 1388 sheet: 0.00 (0.19), residues: 675 loop : -0.05 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 135 TYR 0.013 0.001 TYR B 666 PHE 0.027 0.001 PHE I 4 TRP 0.009 0.001 TRP B 31 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (34036) covalent geometry : angle 0.51570 / 0.27 (46224) hydrogen bonds : bond 0.03752 / 2.52 ( 1442) hydrogen bonds : angle 4.27119 / 3.04 ( 4036) metal coordination : bond 0.00652 / 0.36 ( 32) metal coordination : angle 4.65526 / 3.07 ( 45) Misc. bond : bond 0.00100 / 0.06 ( 13) link_TRANS : bond 0.00053 / 0.02 ( 3) link_TRANS : angle 0.39454 / 0.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 467 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8042 (pm20) cc_final: 0.7781 (pt0) REVERT: A 22 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: A 398 GLU cc_start: 0.8288 (pt0) cc_final: 0.7933 (pt0) REVERT: A 415 LEU cc_start: 0.8051 (mm) cc_final: 0.7662 (mm) REVERT: A 427 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: A 437 MET cc_start: 0.8569 (mtm) cc_final: 0.8153 (mtp) REVERT: A 771 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8645 (mt-10) REVERT: A 795 GLU cc_start: 0.8788 (pm20) cc_final: 0.8415 (pm20) REVERT: A 822 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: A 840 ARG cc_start: 0.7091 (mmt90) cc_final: 0.6826 (mmt90) REVERT: A 895 LYS cc_start: 0.8937 (tttm) cc_final: 0.8253 (tppt) REVERT: A 1079 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6666 (mtt) REVERT: A 1109 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8354 (mmmt) REVERT: A 1112 LYS cc_start: 0.8700 (mmpt) cc_final: 0.8312 (mmtt) REVERT: A 1207 LEU cc_start: 0.7355 (mm) cc_final: 0.7032 (mm) REVERT: A 1214 GLU cc_start: 0.7925 (tp30) cc_final: 0.7710 (tp30) REVERT: A 1259 MET cc_start: 0.8373 (ttp) cc_final: 0.8076 (ttp) REVERT: A 1263 ILE cc_start: 0.7788 (mm) cc_final: 0.7490 (mp) REVERT: A 1285 MET cc_start: 0.8298 (mmm) cc_final: 0.8027 (mmm) REVERT: A 1452 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (ttpp) REVERT: B 22 SER cc_start: 0.8546 (m) cc_final: 0.8293 (p) REVERT: B 227 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8113 (mtmt) REVERT: B 325 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7291 (mm110) REVERT: B 350 GLN cc_start: 0.8015 (tp40) cc_final: 0.7094 (tp-100) REVERT: B 354 ASP cc_start: 0.8402 (m-30) cc_final: 0.7915 (m-30) REVERT: B 381 MET cc_start: 0.8586 (mtp) cc_final: 0.8346 (mtp) REVERT: B 444 MET cc_start: 0.7019 (mpp) cc_final: 0.6594 (pp-130) REVERT: B 445 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7597 (mtpm) REVERT: B 504 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: B 513 GLN cc_start: 0.8666 (mt0) cc_final: 0.8235 (mm110) REVERT: B 591 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8262 (mmt90) REVERT: B 606 LYS cc_start: 0.7995 (ptpt) cc_final: 0.7775 (pttp) REVERT: B 620 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7861 (ttm110) REVERT: B 623 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 864 LYS cc_start: 0.7562 (ptpp) cc_final: 0.7223 (pttp) REVERT: B 868 MET cc_start: 0.7250 (mmt) cc_final: 0.6824 (mmm) REVERT: B 962 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7559 (ttpp) REVERT: B 1057 LYS cc_start: 0.8238 (mttt) cc_final: 0.7980 (mtpp) REVERT: C 50 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: C 75 MET cc_start: 0.8536 (tpp) cc_final: 0.8303 (tpt) REVERT: C 102 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7879 (mt0) REVERT: D 26 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7228 (p) REVERT: D 54 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6885 (tp30) REVERT: D 123 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5633 (tt) REVERT: E 172 GLU cc_start: 0.8620 (tp30) cc_final: 0.7988 (tt0) REVERT: E 179 GLN cc_start: 0.8573 (mt0) cc_final: 0.8349 (mt0) REVERT: E 192 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.7798 (ttp80) REVERT: E 215 MET cc_start: 0.5654 (mmt) cc_final: 0.4994 (ptm) REVERT: F 71 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: G 26 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7297 (mm) REVERT: G 42 PHE cc_start: 0.7609 (m-80) cc_final: 0.7326 (m-80) REVERT: G 168 LEU cc_start: 0.7473 (mm) cc_final: 0.7018 (tp) REVERT: H 14 GLU cc_start: 0.8881 (tt0) cc_final: 0.8463 (tt0) REVERT: H 21 ASN cc_start: 0.8706 (m-40) cc_final: 0.8421 (m110) REVERT: H 27 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: I 55 THR cc_start: 0.8858 (p) cc_final: 0.8585 (m) REVERT: I 59 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7786 (m) REVERT: I 92 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7527 (mtp85) REVERT: I 93 LYS cc_start: 0.8402 (pttp) cc_final: 0.8120 (mttp) REVERT: J 26 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7558 (tm-30) REVERT: K 5 ASP cc_start: 0.8192 (m-30) cc_final: 0.7716 (m-30) REVERT: K 20 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7917 (tttp) REVERT: K 22 ASP cc_start: 0.8249 (m-30) cc_final: 0.7990 (m-30) REVERT: K 24 ASP cc_start: 0.8112 (t0) cc_final: 0.7605 (t0) REVERT: K 38 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8683 (mm-30) REVERT: K 55 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8269 (mtpp) REVERT: L 40 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6884 (tt) outliers start: 85 outliers final: 29 residues processed: 524 average time/residue: 0.7815 time to fit residues: 482.7537 Evaluate side-chains 494 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 449 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 231 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 356 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1211 GLN B 469 GLN B 648 HIS B1093 GLN E 32 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100781 restraints weight = 42945.123| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.27 r_work: 0.3163 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34084 Z= 0.206 Angle : 0.610 16.773 46278 Z= 0.310 Chirality : 0.046 0.280 5190 Planarity : 0.005 0.066 5785 Dihedral : 13.142 156.102 5081 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.69 % Allowed : 16.33 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.56 (0.13), residues: 3964 helix: 1.37 (0.14), residues: 1394 sheet: -0.04 (0.19), residues: 675 loop : -0.13 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 595 TYR 0.019 0.002 TYR A 465 PHE 0.030 0.002 PHE A 219 TRP 0.010 0.002 TRP C 170 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (34036) covalent geometry : angle 0.58804 / 0.31 (46224) hydrogen bonds : bond 0.04635 / 3.08 ( 1442) hydrogen bonds : angle 4.41620 / 3.14 ( 4036) metal coordination : bond 0.00881 / 0.46 ( 32) metal coordination : angle 5.28327 / 3.53 ( 45) Misc. bond : bond 0.00228 / 0.14 ( 13) link_TRANS : bond 0.00100 / 0.05 ( 3) link_TRANS : angle 0.29342 / 0.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 451 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8103 (pm20) cc_final: 0.7789 (pt0) REVERT: A 22 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: A 398 GLU cc_start: 0.8335 (pt0) cc_final: 0.8002 (pt0) REVERT: A 415 LEU cc_start: 0.8127 (mm) cc_final: 0.7686 (mm) REVERT: A 427 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: A 437 MET cc_start: 0.8680 (mtm) cc_final: 0.8305 (mtp) REVERT: A 771 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8682 (mt-10) REVERT: A 795 GLU cc_start: 0.8768 (pm20) cc_final: 0.8391 (pm20) REVERT: A 822 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: A 838 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8060 (tp40) REVERT: A 840 ARG cc_start: 0.7317 (mmt90) cc_final: 0.7089 (mmt-90) REVERT: A 895 LYS cc_start: 0.8960 (tttm) cc_final: 0.8279 (tppt) REVERT: A 969 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 1079 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6776 (mtt) REVERT: A 1109 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8378 (mmmt) REVERT: A 1112 LYS cc_start: 0.8742 (mmpt) cc_final: 0.8365 (mmtt) REVERT: A 1207 LEU cc_start: 0.7382 (mm) cc_final: 0.7070 (mm) REVERT: A 1214 GLU cc_start: 0.7908 (tp30) cc_final: 0.7682 (tp30) REVERT: A 1259 MET cc_start: 0.8337 (ttp) cc_final: 0.7974 (ttp) REVERT: A 1263 ILE cc_start: 0.7809 (mm) cc_final: 0.7488 (mp) REVERT: A 1285 MET cc_start: 0.8361 (mmm) cc_final: 0.8066 (mmm) REVERT: A 1391 ARG cc_start: 0.8333 (tpp80) cc_final: 0.7648 (mmt90) REVERT: A 1452 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7742 (ttpp) REVERT: B 22 SER cc_start: 0.8615 (m) cc_final: 0.8350 (p) REVERT: B 227 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8166 (mtmt) REVERT: B 325 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7245 (mm110) REVERT: B 350 GLN cc_start: 0.8044 (tp40) cc_final: 0.7117 (tp-100) REVERT: B 381 MET cc_start: 0.8654 (mtp) cc_final: 0.8402 (mtp) REVERT: B 444 MET cc_start: 0.7099 (mpp) cc_final: 0.6672 (pp-130) REVERT: B 445 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7645 (mtpm) REVERT: B 504 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7380 (ttm170) REVERT: B 591 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8289 (mmt90) REVERT: B 606 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7818 (pttp) REVERT: B 620 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7858 (ttm110) REVERT: B 623 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 864 LYS cc_start: 0.7614 (ptpp) cc_final: 0.6809 (pttp) REVERT: B 868 MET cc_start: 0.7240 (mmt) cc_final: 0.6896 (mpt) REVERT: B 962 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7570 (ttpp) REVERT: B 1057 LYS cc_start: 0.8344 (mttt) cc_final: 0.8071 (mtpp) REVERT: B 1136 ASP cc_start: 0.7832 (m-30) cc_final: 0.7627 (m-30) REVERT: C 75 MET cc_start: 0.8562 (tpp) cc_final: 0.8316 (tpp) REVERT: C 102 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7898 (mt0) REVERT: D 26 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7167 (p) REVERT: D 123 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5566 (tt) REVERT: D 148 LEU cc_start: 0.6883 (mt) cc_final: 0.6415 (mt) REVERT: D 155 ARG cc_start: 0.7302 (tpt-90) cc_final: 0.7058 (tpt-90) REVERT: E 172 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: E 179 GLN cc_start: 0.8587 (mt0) cc_final: 0.8381 (mt0) REVERT: E 192 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.7867 (ttp80) REVERT: E 215 MET cc_start: 0.5722 (mmt) cc_final: 0.5193 (ptm) REVERT: F 71 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5874 (mp0) REVERT: G 26 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7342 (mm) REVERT: G 49 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6955 (mt) REVERT: G 168 LEU cc_start: 0.7572 (mm) cc_final: 0.7137 (tp) REVERT: H 14 GLU cc_start: 0.8864 (tt0) cc_final: 0.8539 (tt0) REVERT: H 21 ASN cc_start: 0.8739 (m-40) cc_final: 0.8500 (m110) REVERT: H 27 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: I 8 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7112 (ppt90) REVERT: I 13 MET cc_start: 0.5742 (ppp) cc_final: 0.5524 (ppp) REVERT: I 55 THR cc_start: 0.8926 (p) cc_final: 0.8587 (m) REVERT: I 59 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7896 (m) REVERT: I 92 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7557 (mtp85) REVERT: I 93 LYS cc_start: 0.8381 (pttp) cc_final: 0.8118 (mttm) REVERT: J 26 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7780 (tm-30) REVERT: K 5 ASP cc_start: 0.8213 (m-30) cc_final: 0.7729 (m-30) REVERT: K 20 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8004 (tttp) REVERT: K 22 ASP cc_start: 0.8283 (m-30) cc_final: 0.8004 (m-30) REVERT: K 38 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8723 (mm-30) REVERT: K 55 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8351 (mtpp) REVERT: L 40 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.6913 (tt) outliers start: 95 outliers final: 44 residues processed: 512 average time/residue: 0.7519 time to fit residues: 452.5757 Evaluate side-chains 502 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 438 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 107 optimal weight: 0.0370 chunk 253 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.0060 overall best weight: 0.9676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 469 GLN B 648 HIS B1093 GLN B1176 ASN E 32 GLN F 104 ASN G 96 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103244 restraints weight = 42584.062| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.25 r_work: 0.3200 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34084 Z= 0.121 Angle : 0.562 15.375 46278 Z= 0.285 Chirality : 0.043 0.275 5190 Planarity : 0.004 0.066 5785 Dihedral : 13.076 157.542 5081 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.01 % Allowed : 17.63 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.67 (0.13), residues: 3964 helix: 1.52 (0.14), residues: 1388 sheet: -0.00 (0.19), residues: 675 loop : -0.10 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1094 TYR 0.011 0.001 TYR B 486 PHE 0.025 0.001 PHE A 219 TRP 0.010 0.001 TRP C 201 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (34036) covalent geometry : angle 0.54089 / 0.28 (46224) hydrogen bonds : bond 0.03961 / 2.65 ( 1442) hydrogen bonds : angle 4.31060 / 3.07 ( 4036) metal coordination : bond 0.00728 / 0.39 ( 32) metal coordination : angle 4.89864 / 3.31 ( 45) Misc. bond : bond 0.00356 / 0.23 ( 13) link_TRANS : bond 0.00060 / 0.03 ( 3) link_TRANS : angle 0.36715 / 0.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 459 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8068 (pm20) cc_final: 0.7707 (pt0) REVERT: A 22 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8666 (m-80) REVERT: A 398 GLU cc_start: 0.8331 (pt0) cc_final: 0.7983 (pt0) REVERT: A 415 LEU cc_start: 0.8093 (mm) cc_final: 0.7688 (mm) REVERT: A 427 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7370 (mt0) REVERT: A 437 MET cc_start: 0.8564 (mtm) cc_final: 0.8166 (mtp) REVERT: A 771 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 795 GLU cc_start: 0.8812 (pm20) cc_final: 0.8435 (pm20) REVERT: A 822 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: A 895 LYS cc_start: 0.8958 (tttm) cc_final: 0.8280 (tppt) REVERT: A 969 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: A 1079 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6746 (mtt) REVERT: A 1109 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8392 (mmmt) REVERT: A 1112 LYS cc_start: 0.8728 (mmpt) cc_final: 0.8346 (mmtt) REVERT: A 1144 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8502 (ttmm) REVERT: A 1207 LEU cc_start: 0.7490 (mm) cc_final: 0.7058 (mm) REVERT: A 1214 GLU cc_start: 0.7877 (tp30) cc_final: 0.7666 (tp30) REVERT: A 1259 MET cc_start: 0.8376 (ttp) cc_final: 0.8032 (ttp) REVERT: A 1263 ILE cc_start: 0.7803 (mm) cc_final: 0.7476 (mp) REVERT: A 1285 MET cc_start: 0.8293 (mmm) cc_final: 0.8022 (mmm) REVERT: A 1391 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7627 (mmt90) REVERT: A 1452 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7728 (ttpp) REVERT: B 22 SER cc_start: 0.8585 (m) cc_final: 0.8340 (p) REVERT: B 227 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8113 (mtmt) REVERT: B 325 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7274 (mm110) REVERT: B 350 GLN cc_start: 0.7951 (tp40) cc_final: 0.7133 (tp-100) REVERT: B 381 MET cc_start: 0.8626 (mtp) cc_final: 0.8392 (mtp) REVERT: B 444 MET cc_start: 0.7058 (mpp) cc_final: 0.6629 (pp-130) REVERT: B 445 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7603 (mtpm) REVERT: B 504 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7544 (ttm170) REVERT: B 591 ARG cc_start: 0.8477 (mmt90) cc_final: 0.8277 (mmt90) REVERT: B 606 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7808 (pttp) REVERT: B 620 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7857 (ttm110) REVERT: B 623 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8398 (mt-10) REVERT: B 864 LYS cc_start: 0.7621 (ptpp) cc_final: 0.6816 (pttp) REVERT: B 868 MET cc_start: 0.7125 (mmt) cc_final: 0.6803 (mpt) REVERT: B 873 THR cc_start: 0.7919 (m) cc_final: 0.7454 (t) REVERT: B 962 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7524 (ttpp) REVERT: B 1057 LYS cc_start: 0.8288 (mttt) cc_final: 0.7998 (mtpp) REVERT: B 1136 ASP cc_start: 0.7778 (m-30) cc_final: 0.7577 (m-30) REVERT: C 75 MET cc_start: 0.8524 (tpp) cc_final: 0.8256 (mmm) REVERT: C 102 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7901 (mt0) REVERT: D 26 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7181 (p) REVERT: D 120 GLU cc_start: 0.5726 (mp0) cc_final: 0.5237 (mt-10) REVERT: D 123 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5548 (tt) REVERT: D 155 ARG cc_start: 0.7236 (tpt-90) cc_final: 0.6948 (tpt-90) REVERT: E 57 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6904 (tmm) REVERT: E 58 MET cc_start: 0.8390 (ttm) cc_final: 0.8179 (ttm) REVERT: E 172 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: E 192 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.7793 (ttp80) REVERT: E 215 MET cc_start: 0.5715 (mmt) cc_final: 0.5069 (ptm) REVERT: F 71 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6035 (mp0) REVERT: G 26 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7331 (mm) REVERT: G 49 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6933 (mt) REVERT: G 168 LEU cc_start: 0.7561 (mm) cc_final: 0.7124 (tp) REVERT: H 14 GLU cc_start: 0.8831 (tt0) cc_final: 0.8513 (tt0) REVERT: H 21 ASN cc_start: 0.8731 (m-40) cc_final: 0.8478 (m110) REVERT: H 27 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: I 55 THR cc_start: 0.8892 (p) cc_final: 0.8585 (m) REVERT: I 59 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7880 (m) REVERT: I 92 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7543 (mtp85) REVERT: I 93 LYS cc_start: 0.8362 (pttp) cc_final: 0.8139 (mttp) REVERT: J 26 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7846 (tm-30) REVERT: K 5 ASP cc_start: 0.8210 (m-30) cc_final: 0.7747 (m-30) REVERT: K 20 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (tttp) REVERT: K 22 ASP cc_start: 0.8257 (m-30) cc_final: 0.7997 (m-30) REVERT: K 24 ASP cc_start: 0.8068 (t0) cc_final: 0.7810 (t0) REVERT: K 38 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8715 (mm-30) REVERT: K 55 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8283 (mtpp) REVERT: L 40 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.6976 (tt) outliers start: 71 outliers final: 31 residues processed: 508 average time/residue: 0.7566 time to fit residues: 452.3509 Evaluate side-chains 493 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 443 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 159 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 313 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 515 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B1093 GLN E 32 GLN E 179 GLN F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103046 restraints weight = 42470.780| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.26 r_work: 0.3198 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34084 Z= 0.130 Angle : 0.563 14.910 46278 Z= 0.287 Chirality : 0.043 0.251 5190 Planarity : 0.004 0.067 5785 Dihedral : 13.041 157.766 5081 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.90 % Allowed : 17.77 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.70 (0.13), residues: 3964 helix: 1.55 (0.14), residues: 1387 sheet: 0.02 (0.19), residues: 675 loop : -0.09 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 595 TYR 0.012 0.001 TYR A 465 PHE 0.026 0.001 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.034 0.001 HIS B 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (34036) covalent geometry : angle 0.54286 / 0.29 (46224) hydrogen bonds : bond 0.03945 / 2.64 ( 1442) hydrogen bonds : angle 4.27214 / 3.04 ( 4036) metal coordination : bond 0.00717 / 0.39 ( 32) metal coordination : angle 4.80314 / 3.26 ( 45) Misc. bond : bond 0.00185 / 0.12 ( 13) link_TRANS : bond 0.00053 / 0.02 ( 3) link_TRANS : angle 0.33565 / 0.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 453 time to evaluate : 1.174 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 5 GLN cc_start: 0.8048 (pm20) cc_final: 0.7749 (pt0) REVERT: A 22 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: A 47 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6539 (ptt90) REVERT: A 398 GLU cc_start: 0.8315 (pt0) cc_final: 0.7964 (pt0) REVERT: A 415 LEU cc_start: 0.8084 (mm) cc_final: 0.7673 (mm) REVERT: A 427 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7392 (mt0) REVERT: A 437 MET cc_start: 0.8565 (mtm) cc_final: 0.8167 (mtp) REVERT: A 771 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8682 (mt-10) REVERT: A 795 GLU cc_start: 0.8816 (pm20) cc_final: 0.8439 (pm20) REVERT: A 822 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7783 (tp30) REVERT: A 895 LYS cc_start: 0.8947 (tttm) cc_final: 0.8277 (tppt) REVERT: A 969 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: A 1079 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6665 (mtt) REVERT: A 1109 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8373 (mmmt) REVERT: A 1112 LYS cc_start: 0.8737 (mmpt) cc_final: 0.8338 (mmtt) REVERT: A 1144 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8523 (ttmm) REVERT: A 1207 LEU cc_start: 0.7430 (mm) cc_final: 0.7013 (mm) REVERT: A 1214 GLU cc_start: 0.7888 (tp30) cc_final: 0.7674 (tp30) REVERT: A 1259 MET cc_start: 0.8377 (ttp) cc_final: 0.8034 (ttp) REVERT: A 1263 ILE cc_start: 0.7794 (mm) cc_final: 0.7467 (mp) REVERT: A 1285 MET cc_start: 0.8307 (mmm) cc_final: 0.8022 (mmm) REVERT: A 1391 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7637 (mmt90) REVERT: A 1452 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7727 (ttpp) REVERT: B 22 SER cc_start: 0.8587 (m) cc_final: 0.8340 (p) REVERT: B 227 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8118 (mtmt) REVERT: B 325 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7166 (mm110) REVERT: B 336 ARG cc_start: 0.6122 (mmp-170) cc_final: 0.5900 (mmp-170) REVERT: B 350 GLN cc_start: 0.7911 (tp40) cc_final: 0.7077 (tp-100) REVERT: B 381 MET cc_start: 0.8628 (mtp) cc_final: 0.8390 (mtp) REVERT: B 444 MET cc_start: 0.7056 (mpp) cc_final: 0.6629 (pp-130) REVERT: B 445 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7605 (mtpm) REVERT: B 504 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7530 (ttm170) REVERT: B 591 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8276 (mmt90) REVERT: B 606 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7814 (pttp) REVERT: B 620 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7838 (ttm110) REVERT: B 864 LYS cc_start: 0.7626 (ptpp) cc_final: 0.6820 (pttp) REVERT: B 868 MET cc_start: 0.7136 (mmt) cc_final: 0.6814 (mpt) REVERT: B 873 THR cc_start: 0.7905 (m) cc_final: 0.7430 (t) REVERT: B 962 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7499 (ttpp) REVERT: B 1057 LYS cc_start: 0.8288 (mttt) cc_final: 0.7999 (mtpp) REVERT: B 1136 ASP cc_start: 0.7790 (m-30) cc_final: 0.7588 (m-30) REVERT: C 75 MET cc_start: 0.8541 (tpp) cc_final: 0.8250 (mmm) REVERT: C 102 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7891 (mt0) REVERT: D 26 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7110 (p) REVERT: D 120 GLU cc_start: 0.5804 (mp0) cc_final: 0.5291 (mt-10) REVERT: D 123 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5536 (tt) REVERT: D 155 ARG cc_start: 0.7304 (tpt-90) cc_final: 0.7011 (tpt-90) REVERT: E 172 GLU cc_start: 0.8652 (tp30) cc_final: 0.8086 (tt0) REVERT: E 192 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.7819 (ttp80) REVERT: E 215 MET cc_start: 0.5843 (mmt) cc_final: 0.5095 (ptm) REVERT: F 71 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6083 (mp0) REVERT: F 114 GLU cc_start: 0.8143 (tt0) cc_final: 0.7887 (tt0) REVERT: G 26 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7330 (mm) REVERT: G 49 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6926 (mt) REVERT: G 168 LEU cc_start: 0.7514 (mm) cc_final: 0.7087 (tp) REVERT: H 14 GLU cc_start: 0.8830 (tt0) cc_final: 0.8449 (tt0) REVERT: H 21 ASN cc_start: 0.8726 (m-40) cc_final: 0.8490 (m110) REVERT: H 27 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: I 8 ARG cc_start: 0.7423 (ppt90) cc_final: 0.7215 (ppt90) REVERT: I 55 THR cc_start: 0.8892 (p) cc_final: 0.8581 (m) REVERT: I 59 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (m) REVERT: I 92 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7532 (mtp85) REVERT: I 93 LYS cc_start: 0.8386 (pttp) cc_final: 0.8163 (mttp) REVERT: J 26 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7874 (tm-30) REVERT: K 5 ASP cc_start: 0.8197 (m-30) cc_final: 0.7717 (m-30) REVERT: K 20 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7961 (tttp) REVERT: K 22 ASP cc_start: 0.8260 (m-30) cc_final: 0.8004 (m-30) REVERT: K 24 ASP cc_start: 0.8075 (t0) cc_final: 0.7820 (t0) REVERT: K 38 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8702 (mm-30) REVERT: K 55 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8294 (mtpp) REVERT: L 40 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.6963 (tt) outliers start: 67 outliers final: 32 residues processed: 501 average time/residue: 0.7388 time to fit residues: 436.1249 Evaluate side-chains 489 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 440 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 380 optimal weight: 0.0670 chunk 365 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN A1387 HIS B 469 GLN B1093 GLN E 32 GLN E 179 GLN F 104 ASN I 11 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095500 restraints weight = 41757.486| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.31 r_work: 0.3059 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 34084 Z= 0.238 Angle : 0.660 18.175 46278 Z= 0.333 Chirality : 0.048 0.230 5190 Planarity : 0.005 0.067 5785 Dihedral : 13.174 159.208 5081 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.92 % Allowed : 17.80 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 3964 helix: 1.23 (0.14), residues: 1389 sheet: -0.08 (0.19), residues: 688 loop : -0.22 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 595 TYR 0.024 0.002 TYR A 465 PHE 0.030 0.002 PHE A 219 TRP 0.012 0.002 TRP C 170 HIS 0.009 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (34036) covalent geometry : angle 0.63587 / 0.33 (46224) hydrogen bonds : bond 0.05028 / 3.33 ( 1442) hydrogen bonds : angle 4.51608 / 3.21 ( 4036) metal coordination : bond 0.00926 / 0.51 ( 32) metal coordination : angle 5.68073 / 3.75 ( 45) Misc. bond : bond 0.00155 / 0.09 ( 13) link_TRANS : bond 0.00091 / 0.04 ( 3) link_TRANS : angle 0.30954 / 0.16 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 433 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8161 (pm20) cc_final: 0.7788 (pt0) REVERT: A 22 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: A 398 GLU cc_start: 0.8383 (pt0) cc_final: 0.8066 (pt0) REVERT: A 415 LEU cc_start: 0.8332 (mm) cc_final: 0.7862 (mm) REVERT: A 771 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8729 (mt-10) REVERT: A 795 GLU cc_start: 0.8790 (pm20) cc_final: 0.8414 (pm20) REVERT: A 822 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: A 840 ARG cc_start: 0.7467 (mmt90) cc_final: 0.7266 (mmt-90) REVERT: A 969 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: A 1079 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6611 (mtt) REVERT: A 1109 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8424 (mmmt) REVERT: A 1112 LYS cc_start: 0.8822 (mmpt) cc_final: 0.8411 (mmtt) REVERT: A 1207 LEU cc_start: 0.7448 (mm) cc_final: 0.7041 (mm) REVERT: A 1214 GLU cc_start: 0.7899 (tp30) cc_final: 0.7672 (tp30) REVERT: A 1263 ILE cc_start: 0.7866 (mm) cc_final: 0.7551 (mp) REVERT: A 1285 MET cc_start: 0.8260 (mmm) cc_final: 0.7981 (mmm) REVERT: A 1391 ARG cc_start: 0.8333 (tpp80) cc_final: 0.7674 (mmt90) REVERT: A 1452 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7706 (ttpp) REVERT: B 227 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8196 (mtmt) REVERT: B 325 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7251 (mm110) REVERT: B 336 ARG cc_start: 0.6305 (mmp-170) cc_final: 0.6101 (mmp-170) REVERT: B 350 GLN cc_start: 0.7943 (tp40) cc_final: 0.7208 (tp-100) REVERT: B 381 MET cc_start: 0.8685 (mtp) cc_final: 0.8426 (mtp) REVERT: B 444 MET cc_start: 0.7132 (mpp) cc_final: 0.6766 (pp-130) REVERT: B 445 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7653 (mtpm) REVERT: B 504 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: B 591 ARG cc_start: 0.8551 (mmt90) cc_final: 0.8341 (mmt90) REVERT: B 606 LYS cc_start: 0.8292 (ptpt) cc_final: 0.7903 (pttp) REVERT: B 620 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7750 (ttm110) REVERT: B 864 LYS cc_start: 0.7674 (ptpp) cc_final: 0.7011 (pttp) REVERT: B 868 MET cc_start: 0.7411 (mmt) cc_final: 0.7056 (mpt) REVERT: B 962 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7572 (ttpp) REVERT: B 1057 LYS cc_start: 0.8465 (mttt) cc_final: 0.7953 (ttpp) REVERT: C 75 MET cc_start: 0.8611 (tpp) cc_final: 0.8395 (tpp) REVERT: C 102 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7963 (mt0) REVERT: D 26 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7185 (p) REVERT: D 123 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5536 (tt) REVERT: D 155 ARG cc_start: 0.7258 (tpt-90) cc_final: 0.6961 (tpt-90) REVERT: E 57 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: E 58 MET cc_start: 0.8479 (ttm) cc_final: 0.8237 (ttm) REVERT: E 172 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: E 192 ARG cc_start: 0.8327 (ptm-80) cc_final: 0.7860 (ttp80) REVERT: E 215 MET cc_start: 0.5740 (mmt) cc_final: 0.5299 (ptm) REVERT: F 71 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5666 (mp0) REVERT: F 114 GLU cc_start: 0.8142 (tt0) cc_final: 0.7800 (tp30) REVERT: G 26 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7418 (mm) REVERT: G 49 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6979 (mt) REVERT: G 163 ILE cc_start: 0.4499 (pt) cc_final: 0.4051 (pp) REVERT: G 168 LEU cc_start: 0.7555 (mm) cc_final: 0.7168 (tp) REVERT: H 14 GLU cc_start: 0.8788 (tt0) cc_final: 0.8467 (tt0) REVERT: H 21 ASN cc_start: 0.8849 (m-40) cc_final: 0.8631 (m110) REVERT: H 27 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: H 62 SER cc_start: 0.9072 (t) cc_final: 0.8776 (t) REVERT: H 87 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: I 8 ARG cc_start: 0.7507 (ppt90) cc_final: 0.7293 (ppt90) REVERT: I 92 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7070 (mtp85) REVERT: I 93 LYS cc_start: 0.8353 (pttp) cc_final: 0.8149 (mttp) REVERT: J 26 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7876 (tm-30) REVERT: K 5 ASP cc_start: 0.8127 (m-30) cc_final: 0.7662 (m-30) REVERT: K 20 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (tttp) REVERT: K 55 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8370 (mtpp) REVERT: L 40 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.6978 (tt) outliers start: 68 outliers final: 36 residues processed: 482 average time/residue: 0.7508 time to fit residues: 426.6494 Evaluate side-chains 479 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 425 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 250 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 348 optimal weight: 8.9990 chunk 262 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B 887 HIS B1093 GLN E 32 GLN E 99 HIS E 179 GLN F 104 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.149960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098312 restraints weight = 41351.294| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.29 r_work: 0.3103 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34084 Z= 0.132 Angle : 0.583 16.123 46278 Z= 0.296 Chirality : 0.043 0.285 5190 Planarity : 0.004 0.066 5785 Dihedral : 13.086 160.773 5081 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 18.05 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.16 % 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: 0.57 (0.13), residues: 3964 helix: 1.43 (0.14), residues: 1393 sheet: -0.03 (0.19), residues: 678 loop : -0.17 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 595 TYR 0.013 0.001 TYR H 102 PHE 0.026 0.001 PHE A 219 TRP 0.011 0.001 TRP C 201 HIS 0.012 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (34036) covalent geometry : angle 0.56099 / 0.29 (46224) hydrogen bonds : bond 0.04110 / 2.75 ( 1442) hydrogen bonds : angle 4.34181 / 3.09 ( 4036) metal coordination : bond 0.00748 / 0.40 ( 32) metal coordination : angle 5.06475 / 3.38 ( 45) Misc. bond : bond 0.00223 / 0.13 ( 13) link_TRANS : bond 0.00073 / 0.03 ( 3) link_TRANS : angle 0.41437 / 0.21 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15308.86 seconds wall clock time: 260 minutes 28.41 seconds (15628.41 seconds total)