Starting phenix.real_space_refine on Tue Sep 15 18:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvt_12612/09_2026/7nvt_12612.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.975 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 10 6.06 5 P 99 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 27540 2.51 5 N 7757 2.21 5 O 8458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44114 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1034 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1013 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" 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 464 SG CYS A 71 97.735 108.567 64.770 1.00 35.17 S ATOM 486 SG CYS A 74 97.759 106.056 61.908 1.00 33.79 S ATOM 533 SG CYS A 81 96.646 105.100 65.461 1.00 27.87 S ATOM 768 SG CYS A 111 138.954 83.261 70.361 1.00 42.25 S ATOM 796 SG CYS A 114 139.563 84.016 66.857 1.00 43.36 S ATOM 1109 SG CYS A 154 140.811 80.740 68.280 1.00 42.96 S ATOM 1132 SG CYS A 184 142.419 84.013 69.321 1.00 42.73 S ATOM 19919 SG CYS B1119 107.589 97.383 53.237 1.00 30.52 S ATOM 19941 SG CYS B1122 109.072 96.430 56.690 1.00 31.55 S ATOM 20056 SG CYS B1137 107.811 99.943 56.028 1.00 35.46 S ATOM 20077 SG CYS B1140 110.969 98.442 54.341 1.00 37.60 S ATOM 21044 SG CYS C 88 32.550 100.756 74.559 1.00 20.33 S ATOM 21057 SG CYS C 90 35.378 102.699 76.596 1.00 28.06 S ATOM 21092 SG CYS C 94 31.896 102.420 77.674 1.00 16.21 S ATOM 21114 SG CYS C 97 34.158 99.442 77.694 1.00 12.35 S ATOM 28400 SG CYS I 17 125.974 40.822 128.723 1.00 33.68 S ATOM 28424 SG CYS I 20 125.982 44.383 127.571 1.00 34.15 S ATOM 28585 SG CYS I 39 126.969 41.735 125.217 1.00 33.18 S ATOM 28610 SG CYS I 42 129.128 42.682 128.468 1.00 34.51 S ATOM 28962 SG CYS I 86 85.412 23.461 125.773 1.00 26.06 S ATOM 28986 SG CYS I 89 83.518 23.749 129.003 1.00 30.82 S ATOM 29190 SG CYS I 114 83.639 26.645 126.742 1.00 21.42 S ATOM 29225 SG CYS I 119 86.709 25.551 128.637 1.00 30.55 S ATOM 29336 SG CYS J 7 40.801 72.332 92.087 1.00 21.13 S ATOM 29360 SG CYS J 10 37.759 71.972 89.973 1.00 7.97 S ATOM 29624 SG CYS J 44 39.615 68.896 91.062 1.00 3.67 S ATOM 29630 SG CYS J 45 37.449 70.892 93.215 1.00 1.28 S ATOM 30750 SG CYS L 19 61.085 104.341 113.269 1.00 19.01 S ATOM 30769 SG CYS L 22 58.226 105.862 114.979 1.00 24.56 S ATOM 30886 SG CYS L 36 61.005 108.059 113.964 1.00 21.23 S ATOM 30912 SG CYS L 39 61.345 104.907 117.151 1.00 26.93 S ATOM 31094 SG CYS M 15 77.052 113.524 60.306 1.00 31.90 S ATOM 31241 SG CYS M 34 74.439 113.338 62.992 1.00 29.78 S ATOM 31263 SG CYS M 37 73.895 111.370 58.975 1.00 29.58 S ATOM 42163 SG CYS W 129 105.355 127.129 60.860 1.00 43.56 S ATOM 42183 SG CYS W 132 104.411 125.099 61.843 1.00 42.00 S ATOM 42355 SG CYS W 154 101.545 127.187 58.992 1.00 45.96 S Time building chain proxies: 7.93, per 1000 atoms: 0.18 Number of scatterers: 44114 At special positions: 0 Unit cell: (174.3, 172.2, 189, 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 10 29.99 S 249 16.00 P 99 15.00 Mg 1 11.99 O 8458 8.00 N 7757 7.00 C 27540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 132 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " Number of angles added : 48 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9910 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 0 sheets defined 36.6% alpha, 0.0% beta 44 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.642A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.577A pdb=" N CYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.570A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.698A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.514A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 486 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.621A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.592A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.678A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 772 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.571A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.697A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 removed outlier: 3.504A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1077 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.032A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1187 through 1197 removed outlier: 4.087A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1239 removed outlier: 3.691A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 4.809A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1406 Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 3.943A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 3.501A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.621A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 37 removed outlier: 4.428A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.617A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.674A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.517A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.504A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.529A pdb=" N SER B 441 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 443 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 445 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 446 " --> pdb=" O GLY B 443 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 447 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.749A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 495' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.611A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.863A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.634A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 3.623A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.710A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.965A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.567A pdb=" N PHE E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.986A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.703A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.901A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.643A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.598A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 48 through 51 No H-bonds generated for 'chain 'M' and resid 48 through 51' Processing helix chain 'M' and resid 109 through 128 removed outlier: 3.504A pdb=" N ARG M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 215 through 221 Processing helix chain 'M' and resid 226 through 242 Processing helix chain 'M' and resid 250 through 264 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 299 Proline residue: M 294 - end of helix Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 243 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 6 through 9 No H-bonds generated for 'chain 'Q' and resid 6 through 9' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 166 removed outlier: 3.905A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 4.220A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 14 Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.063A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 122 through 138 removed outlier: 4.146A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Proline residue: R 138 - end of helix Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 192 removed outlier: 4.048A pdb=" N GLU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.568A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 4.400A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.562A pdb=" N LYS U 43 " --> pdb=" O MET U 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU U 45 " --> pdb=" O LEU U 42 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS U 49 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 329 No H-bonds generated for 'chain 'U' and resid 326 through 329' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.519A pdb=" N LYS W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.722A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE W 114 " --> pdb=" O MET W 110 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR W 116 " --> pdb=" O ARG W 112 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP W 120 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 removed outlier: 3.658A pdb=" N ASN W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 195 Proline residue: W 169 - end of helix removed outlier: 3.602A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG W 174 " --> pdb=" O LYS W 170 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR W 175 " --> pdb=" O LYS W 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU W 182 " --> pdb=" O ALA W 178 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN W 183 " --> pdb=" O ARG W 179 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE W 184 " --> pdb=" O PHE W 180 " (cutoff:3.500A) Proline residue: W 186 - end of helix removed outlier: 3.771A pdb=" N ALA W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG W 192 " --> pdb=" O TYR W 188 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR W 194 " --> pdb=" O LEU W 190 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 91 removed outlier: 3.548A pdb=" N LYS X 80 " --> pdb=" O GLY X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 removed outlier: 3.823A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 121 Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 Processing helix chain 'X' and resid 178 through 188 removed outlier: 5.956A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 4.079A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14394 1.34 - 1.46: 9880 1.46 - 1.58: 20266 1.58 - 1.71: 197 1.71 - 1.83: 392 Bond restraints: 45129 Sorted by residual: bond pdb=" C1' DT N 36 " pdb=" N1 DT N 36 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DT N 38 " pdb=" C2' DT N 38 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.76e+00 bond pdb=" C1' DC T -20 " pdb=" N1 DC T -20 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.58e+00 bond pdb=" C3' DT N 39 " pdb=" C2' DT N 39 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.52e+00 bond pdb=" C3' DC T -14 " pdb=" C2' DC T -14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.46e+00 ... (remaining 45124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 60218 1.44 - 2.89: 845 2.89 - 4.33: 280 4.33 - 5.78: 8 5.78 - 7.22: 1 Bond angle restraints: 61352 Sorted by residual: angle pdb=" N3 DT N 1 " pdb=" C4 DT N 1 " pdb=" O4 DT N 1 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT N 24 " pdb=" C4 DT N 24 " pdb=" O4 DT N 24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT N 36 " pdb=" C4 DT N 36 " pdb=" O4 DT N 36 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT N 27 " pdb=" C4 DT N 27 " pdb=" O4 DT N 27 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 ... (remaining 61347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 26289 31.16 - 62.31: 1036 62.31 - 93.47: 74 93.47 - 124.63: 0 124.63 - 155.79: 2 Dihedral angle restraints: 27401 sinusoidal: 12103 harmonic: 15298 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ILE C 39 " pdb=" C ILE C 39 " pdb=" N ALA C 40 " pdb=" CA ALA C 40 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 27398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4825 0.034 - 0.068: 1274 0.068 - 0.102: 377 0.102 - 0.136: 298 0.136 - 0.170: 70 Chirality restraints: 6844 Sorted by residual: chirality pdb=" C3' DG N 18 " pdb=" C4' DG N 18 " pdb=" O3' DG N 18 " pdb=" C2' DG N 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA PRO A 478 " pdb=" N PRO A 478 " pdb=" C PRO A 478 " pdb=" CB PRO A 478 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" C3' DG T -33 " pdb=" C4' DG T -33 " pdb=" O3' DG T -33 " pdb=" C2' DG T -33 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 6841 not shown) Planarity restraints: 7605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS M 18 " -0.020 2.00e-02 2.50e+03 2.23e-02 7.44e+00 pdb=" CG HIS M 18 " 0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS M 18 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS M 18 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS M 18 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS M 18 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 297 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO O 298 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO O 298 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 298 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 477 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 478 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 478 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 478 " -0.022 5.00e-02 4.00e+02 ... (remaining 7602 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 438 2.56 - 3.15: 36808 3.15 - 3.73: 72468 3.73 - 4.32: 104371 4.32 - 4.90: 167762 Nonbonded interactions: 381847 Sorted by model distance: nonbonded pdb=" O ALA R 190 " pdb=" OH TYR R 197 " model vdw 1.979 3.040 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.008 3.040 nonbonded pdb=" OH TYR B 814 " pdb=" OE1 GLU B 900 " model vdw 2.015 3.040 nonbonded pdb=" O PRO A 911 " pdb=" NH2 ARG A 963 " model vdw 2.059 3.120 nonbonded pdb=" O ALA E 114 " pdb=" OG SER E 117 " model vdw 2.079 3.040 ... (remaining 381842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 44.750 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 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:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.388 45168 Z= 0.237 Angle : 0.511 18.471 61400 Z= 0.320 Chirality : 0.043 0.170 6844 Planarity : 0.003 0.067 7605 Dihedral : 15.596 155.785 17491 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5187 helix: 1.98 (0.12), residues: 1895 sheet: 0.76 (0.18), residues: 840 loop : 0.24 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG E 52 TYR 0.020 0.001 TYR K 81 PHE 0.022 0.001 PHE B 918 TRP 0.013 0.001 TRP B 453 HIS 0.025 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.21 (45129) covalent geometry : angle 0.48942 / 0.32 (61352) hydrogen bonds : bond 0.21174 / 14.34 ( 1163) hydrogen bonds : angle 5.56383 / 3.95 ( 3309) metal coordination : bond 0.11628 / 7.05 ( 39) metal coordination : angle 5.24385 / 3.27 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1000 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.8984 (mtp) cc_final: 0.8758 (mtp) REVERT: A 861 GLN cc_start: 0.8357 (tt0) cc_final: 0.8096 (mt0) REVERT: A 960 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7079 (ttm-80) REVERT: A 1484 MET cc_start: 0.5014 (pmm) cc_final: 0.4812 (pmm) REVERT: B 840 MET cc_start: 0.3979 (mtp) cc_final: 0.3299 (pmm) REVERT: B 1125 MET cc_start: 0.8047 (mtm) cc_final: 0.7806 (mtm) REVERT: E 125 TYR cc_start: 0.5899 (m-80) cc_final: 0.5662 (m-80) REVERT: H 33 GLU cc_start: 0.6817 (pm20) cc_final: 0.6420 (pm20) REVERT: I 54 TYR cc_start: 0.7150 (t80) cc_final: 0.6858 (t80) REVERT: K 22 ASN cc_start: 0.8095 (m-40) cc_final: 0.7830 (m-40) REVERT: K 23 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7874 (tptt) REVERT: Q 31 PHE cc_start: 0.7196 (m-80) cc_final: 0.6738 (m-80) REVERT: U 51 MET cc_start: 0.2209 (mmp) cc_final: 0.1575 (mpm) REVERT: W 110 MET cc_start: 0.1485 (mmt) cc_final: 0.1063 (mmt) outliers start: 0 outliers final: 2 residues processed: 1000 average time/residue: 0.8535 time to fit residues: 1034.6822 Evaluate side-chains 644 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 642 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain E residue 57 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 313 HIS A 372 ASN A 410 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A1077 ASN A1190 GLN A1220 HIS ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B 649 ASN B 941 GLN B1049 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 217 GLN C 260 GLN G 28 GLN I 22 ASN K 89 ASN L 26 ASN M 221 ASN M 263 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 ASN Q 129 GLN R 223 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.211175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156388 restraints weight = 55221.542| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.30 r_work: 0.3516 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 45168 Z= 0.330 Angle : 0.721 18.901 61400 Z= 0.368 Chirality : 0.049 0.356 6844 Planarity : 0.006 0.061 7605 Dihedral : 13.111 154.762 6815 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 2.97 % Allowed : 11.77 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.65 (0.12), residues: 5187 helix: 1.09 (0.11), residues: 1952 sheet: 0.53 (0.18), residues: 842 loop : -0.04 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 47 TYR 0.035 0.003 TYR R 124 PHE 0.041 0.002 PHE C 63 TRP 0.029 0.003 TRP B 453 HIS 0.008 0.002 HIS X 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.33 (45129) covalent geometry : angle 0.70563 / 0.37 (61352) hydrogen bonds : bond 0.05765 / 3.88 ( 1163) hydrogen bonds : angle 4.16244 / 2.96 ( 3309) metal coordination : bond 0.01984 / 1.38 ( 39) metal coordination : angle 5.40337 / 3.15 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 679 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7348 (m90) REVERT: A 700 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7262 (tm130) REVERT: A 841 MET cc_start: 0.9167 (mtp) cc_final: 0.8880 (mtp) REVERT: A 861 GLN cc_start: 0.8733 (tt0) cc_final: 0.8492 (mt0) REVERT: A 1452 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7302 (mptt) REVERT: B 300 MET cc_start: 0.8861 (mmm) cc_final: 0.8607 (mmt) REVERT: B 324 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: B 345 LYS cc_start: 0.8496 (mptt) cc_final: 0.8285 (mptp) REVERT: B 543 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 840 MET cc_start: 0.4674 (mtp) cc_final: 0.3528 (pmm) REVERT: B 976 MET cc_start: 0.9271 (mtm) cc_final: 0.8989 (mtp) REVERT: B 1072 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8316 (mmm-85) REVERT: B 1091 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8683 (ttp-110) REVERT: B 1125 MET cc_start: 0.8487 (mtm) cc_final: 0.8181 (mtm) REVERT: G 16 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8435 (ptp-170) REVERT: H 74 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: I 82 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: K 22 ASN cc_start: 0.8832 (m-40) cc_final: 0.8596 (m-40) REVERT: K 23 LYS cc_start: 0.8574 (ttmt) cc_final: 0.7975 (tptt) REVERT: L 50 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7992 (mppt) REVERT: M 126 ASP cc_start: 0.7144 (t0) cc_final: 0.6916 (t0) REVERT: R 128 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.4880 (mtpm) REVERT: U 51 MET cc_start: 0.2518 (mmp) cc_final: 0.1903 (mpm) REVERT: W 110 MET cc_start: 0.1187 (mmt) cc_final: 0.0639 (mmt) outliers start: 138 outliers final: 45 residues processed: 748 average time/residue: 0.8281 time to fit residues: 757.9769 Evaluate side-chains 656 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 602 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 192 TYR Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 247 optimal weight: 0.6980 chunk 496 optimal weight: 30.0000 chunk 170 optimal weight: 0.0980 chunk 413 optimal weight: 10.0000 chunk 499 optimal weight: 30.0000 chunk 433 optimal weight: 10.0000 chunk 476 optimal weight: 30.0000 chunk 246 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 409 optimal weight: 30.0000 chunk 190 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 GLN A 410 ASN A 723 ASN A1194 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN E 138 ASN G 24 ASN G 28 GLN M 229 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.212763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.158767 restraints weight = 54892.425| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.17 r_work: 0.3543 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45168 Z= 0.181 Angle : 0.612 18.118 61400 Z= 0.312 Chirality : 0.044 0.333 6844 Planarity : 0.004 0.052 7605 Dihedral : 13.192 159.282 6810 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.93 % Allowed : 14.01 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.11), residues: 5187 helix: 1.07 (0.11), residues: 1959 sheet: 0.42 (0.18), residues: 838 loop : -0.07 (0.13), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 244 TYR 0.023 0.002 TYR E 90 PHE 0.023 0.002 PHE G 119 TRP 0.043 0.002 TRP A 247 HIS 0.007 0.001 HIS A1445 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (45129) covalent geometry : angle 0.59609 / 0.31 (61352) hydrogen bonds : bond 0.04781 / 3.22 ( 1163) hydrogen bonds : angle 3.88752 / 2.74 ( 3309) metal coordination : bond 0.01403 / 0.96 ( 39) metal coordination : angle 4.95577 / 2.91 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 646 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7367 (m90) REVERT: A 841 MET cc_start: 0.9171 (mtp) cc_final: 0.8871 (mtp) REVERT: A 861 GLN cc_start: 0.8645 (tt0) cc_final: 0.8322 (mt0) REVERT: A 1310 HIS cc_start: 0.7564 (p90) cc_final: 0.7277 (p-80) REVERT: A 1351 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8008 (t0) REVERT: B 155 MET cc_start: 0.9293 (ttm) cc_final: 0.9064 (ttm) REVERT: B 299 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: B 300 MET cc_start: 0.8845 (mmm) cc_final: 0.8583 (mmt) REVERT: B 345 LYS cc_start: 0.8504 (mptt) cc_final: 0.8277 (mptp) REVERT: B 385 ARG cc_start: 0.8467 (mtt90) cc_final: 0.8245 (ttp-170) REVERT: B 543 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8176 (mt-10) REVERT: B 554 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 840 MET cc_start: 0.4486 (mtp) cc_final: 0.3425 (pmm) REVERT: B 976 MET cc_start: 0.9219 (mtm) cc_final: 0.8950 (mtp) REVERT: B 1091 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8602 (ttp-110) REVERT: B 1161 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7348 (tm-30) REVERT: E 27 LEU cc_start: 0.8280 (tm) cc_final: 0.8060 (mm) REVERT: G 16 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8403 (ptp-170) REVERT: K 22 ASN cc_start: 0.8814 (m-40) cc_final: 0.8587 (m-40) REVERT: K 23 LYS cc_start: 0.8592 (ttmt) cc_final: 0.7993 (tptt) REVERT: L 50 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7991 (mppt) REVERT: U 51 MET cc_start: 0.2762 (mmp) cc_final: 0.1996 (mpm) REVERT: W 110 MET cc_start: 0.1204 (mmt) cc_final: 0.0907 (mmt) outliers start: 136 outliers final: 45 residues processed: 720 average time/residue: 0.7822 time to fit residues: 695.5889 Evaluate side-chains 666 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 615 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 192 TYR Chi-restraints excluded: chain O residue 254 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 335 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 457 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 465 optimal weight: 50.0000 chunk 254 optimal weight: 4.9990 chunk 358 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 371 optimal weight: 0.8980 chunk 456 optimal weight: 6.9990 chunk 502 optimal weight: 0.8980 chunk 350 optimal weight: 4.9990 chunk 455 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN A 723 ASN A1194 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN G 24 ASN G 28 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.212319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161285 restraints weight = 55121.094| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.23 r_work: 0.3586 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45168 Z= 0.154 Angle : 0.586 16.688 61400 Z= 0.299 Chirality : 0.043 0.331 6844 Planarity : 0.004 0.051 7605 Dihedral : 13.250 159.068 6810 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.65 % Allowed : 15.60 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.11), residues: 5187 helix: 1.07 (0.11), residues: 1957 sheet: 0.35 (0.17), residues: 844 loop : -0.09 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 33 TYR 0.041 0.002 TYR V 65 PHE 0.021 0.001 PHE G 119 TRP 0.024 0.002 TRP A 247 HIS 0.005 0.001 HIS X 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (45129) covalent geometry : angle 0.57293 / 0.30 (61352) hydrogen bonds : bond 0.04277 / 2.90 ( 1163) hydrogen bonds : angle 3.75327 / 2.65 ( 3309) metal coordination : bond 0.01236 / 0.83 ( 39) metal coordination : angle 4.49043 / 2.61 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 646 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.7409 (mmt) cc_final: 0.7119 (mpm) REVERT: A 439 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7329 (m90) REVERT: A 762 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 841 MET cc_start: 0.9168 (mtp) cc_final: 0.8853 (mtp) REVERT: A 861 GLN cc_start: 0.8583 (tt0) cc_final: 0.8209 (mt0) REVERT: A 1130 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7163 (mm) REVERT: A 1310 HIS cc_start: 0.7496 (p90) cc_final: 0.7247 (p-80) REVERT: B 155 MET cc_start: 0.9275 (ttm) cc_final: 0.9037 (ttm) REVERT: B 299 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: B 300 MET cc_start: 0.8755 (mmm) cc_final: 0.8513 (mmt) REVERT: B 345 LYS cc_start: 0.8499 (mptt) cc_final: 0.8274 (mptp) REVERT: B 358 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6748 (pp20) REVERT: B 543 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8147 (mt-10) REVERT: B 840 MET cc_start: 0.4252 (mtp) cc_final: 0.3191 (pmm) REVERT: B 1091 ARG cc_start: 0.8837 (ttp-110) cc_final: 0.8564 (ttp-110) REVERT: C 100 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: E 101 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6716 (ttp-170) REVERT: G 16 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8322 (ptp-170) REVERT: H 72 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7432 (p0) REVERT: I 82 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: K 22 ASN cc_start: 0.8832 (m-40) cc_final: 0.8602 (m-40) REVERT: K 23 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8089 (tptt) REVERT: K 68 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: M 115 MET cc_start: 0.8070 (ttp) cc_final: 0.7266 (mmt) REVERT: U 51 MET cc_start: 0.2660 (mmp) cc_final: 0.1962 (mpm) REVERT: W 110 MET cc_start: 0.1500 (mmt) cc_final: 0.1178 (mmt) REVERT: X 85 MET cc_start: 0.1892 (ppp) cc_final: 0.1463 (pp-130) outliers start: 123 outliers final: 42 residues processed: 709 average time/residue: 0.7927 time to fit residues: 692.7401 Evaluate side-chains 654 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 602 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 518 optimal weight: 30.0000 chunk 191 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 455 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 419 optimal weight: 6.9990 chunk 424 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 387 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN A 723 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1120 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 138 ASN E 189 GLN G 24 ASN G 28 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.211387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153402 restraints weight = 55382.420| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.46 r_work: 0.3111 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45168 Z= 0.170 Angle : 0.597 16.349 61400 Z= 0.303 Chirality : 0.043 0.328 6844 Planarity : 0.004 0.117 7605 Dihedral : 13.307 158.934 6810 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 2.78 % Allowed : 16.21 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.11), residues: 5187 helix: 1.06 (0.12), residues: 1951 sheet: 0.33 (0.17), residues: 849 loop : -0.15 (0.13), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 33 TYR 0.027 0.002 TYR A1196 PHE 0.019 0.001 PHE M 195 TRP 0.050 0.002 TRP A 247 HIS 0.006 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (45129) covalent geometry : angle 0.58392 / 0.30 (61352) hydrogen bonds : bond 0.04177 / 2.84 ( 1163) hydrogen bonds : angle 3.70587 / 2.62 ( 3309) metal coordination : bond 0.01152 / 0.77 ( 39) metal coordination : angle 4.44317 / 2.55 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 630 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.7921 (mmt) cc_final: 0.7572 (mpm) REVERT: A 439 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7624 (m90) REVERT: A 841 MET cc_start: 0.9206 (mtp) cc_final: 0.8869 (mtp) REVERT: A 1130 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7201 (mm) REVERT: A 1310 HIS cc_start: 0.8099 (p90) cc_final: 0.7778 (p-80) REVERT: A 1344 MET cc_start: 0.8028 (tpt) cc_final: 0.7783 (mmp) REVERT: A 1428 MET cc_start: 0.6965 (tpt) cc_final: 0.6212 (mmm) REVERT: B 155 MET cc_start: 0.9353 (ttm) cc_final: 0.9114 (ttm) REVERT: B 300 MET cc_start: 0.8817 (mmm) cc_final: 0.8584 (mmt) REVERT: B 358 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: B 473 LEU cc_start: 0.9304 (tt) cc_final: 0.9098 (tp) REVERT: B 474 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8888 (m) REVERT: B 543 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8264 (mt-10) REVERT: B 840 MET cc_start: 0.4824 (mtp) cc_final: 0.3411 (pmm) REVERT: B 1091 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8434 (ttp-110) REVERT: B 1120 ASN cc_start: 0.8982 (m110) cc_final: 0.8626 (m110) REVERT: B 1161 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7878 (mt-10) REVERT: C 100 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: C 205 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8517 (mmtm) REVERT: E 71 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8470 (mm-40) REVERT: E 210 GLN cc_start: 0.7551 (tm-30) cc_final: 0.6959 (pp30) REVERT: G 16 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8411 (ptp-170) REVERT: G 77 PHE cc_start: 0.4166 (p90) cc_final: 0.3965 (p90) REVERT: G 153 ASP cc_start: 0.6005 (m-30) cc_final: 0.5543 (m-30) REVERT: I 27 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7419 (ttmt) REVERT: I 55 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8998 (m) REVERT: I 82 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: K 22 ASN cc_start: 0.8673 (m-40) cc_final: 0.8412 (m-40) REVERT: K 23 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8051 (tptt) REVERT: K 68 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: L 50 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8247 (mppt) REVERT: M 115 MET cc_start: 0.8067 (ttp) cc_final: 0.6692 (mmt) REVERT: R 85 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5994 (pt) REVERT: R 233 TRP cc_start: 0.6291 (m100) cc_final: 0.5491 (m100) REVERT: U 51 MET cc_start: 0.3387 (mmp) cc_final: 0.2491 (mpm) REVERT: W 48 MET cc_start: 0.4922 (mmt) cc_final: 0.4584 (mmm) REVERT: W 110 MET cc_start: 0.1663 (mmt) cc_final: 0.1317 (mmt) outliers start: 129 outliers final: 45 residues processed: 700 average time/residue: 0.7790 time to fit residues: 674.2289 Evaluate side-chains 654 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 595 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 335 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 97 optimal weight: 0.1980 chunk 442 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 296 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN A 410 ASN A 723 ASN A1093 GLN A1194 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN B 683 GLN B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 132 GLN E 148 HIS G 28 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.211859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153825 restraints weight = 55502.546| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.36 r_work: 0.3300 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45168 Z= 0.145 Angle : 0.589 15.729 61400 Z= 0.297 Chirality : 0.043 0.326 6844 Planarity : 0.004 0.119 7605 Dihedral : 13.334 158.564 6810 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.69 % Allowed : 17.33 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.11), residues: 5187 helix: 1.07 (0.12), residues: 1952 sheet: 0.36 (0.17), residues: 841 loop : -0.17 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 244 TYR 0.025 0.002 TYR R 212 PHE 0.021 0.001 PHE M 195 TRP 0.075 0.002 TRP A 247 HIS 0.007 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (45129) covalent geometry : angle 0.57736 / 0.30 (61352) hydrogen bonds : bond 0.03962 / 2.70 ( 1163) hydrogen bonds : angle 3.63694 / 2.57 ( 3309) metal coordination : bond 0.01072 / 0.72 ( 39) metal coordination : angle 4.22428 / 2.43 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 624 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.7723 (mmt) cc_final: 0.7472 (mpm) REVERT: A 439 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (m90) REVERT: A 841 MET cc_start: 0.9178 (mtp) cc_final: 0.8837 (mtp) REVERT: A 1130 ILE cc_start: 0.7514 (tp) cc_final: 0.7114 (mm) REVERT: A 1310 HIS cc_start: 0.7905 (p90) cc_final: 0.7672 (p-80) REVERT: A 1327 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8297 (mm-30) REVERT: A 1344 MET cc_start: 0.7920 (tpt) cc_final: 0.7688 (mmp) REVERT: A 1428 MET cc_start: 0.6390 (tpt) cc_final: 0.5946 (mmm) REVERT: B 53 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8261 (mtm) REVERT: B 86 LEU cc_start: 0.8536 (mt) cc_final: 0.8330 (mt) REVERT: B 155 MET cc_start: 0.9306 (ttm) cc_final: 0.9059 (ttm) REVERT: B 222 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7765 (mtt-85) REVERT: B 358 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6740 (pp20) REVERT: B 474 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8800 (m) REVERT: B 543 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 637 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8763 (mtmt) REVERT: B 840 MET cc_start: 0.4302 (mtp) cc_final: 0.3037 (pmm) REVERT: B 1091 ARG cc_start: 0.8768 (ttp-110) cc_final: 0.8524 (ttp-110) REVERT: B 1120 ASN cc_start: 0.8796 (m110) cc_final: 0.8555 (m-40) REVERT: C 100 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 205 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8495 (mmtm) REVERT: G 16 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8360 (ptp-170) REVERT: G 29 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8473 (ttmm) REVERT: G 104 MET cc_start: 0.6569 (mtp) cc_final: 0.5376 (mpt) REVERT: I 27 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7507 (ttmt) REVERT: I 82 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: J 31 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: K 22 ASN cc_start: 0.8710 (m-40) cc_final: 0.8443 (m-40) REVERT: K 23 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8053 (tptt) REVERT: K 68 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: L 50 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8191 (mppt) REVERT: M 107 MET cc_start: 0.6808 (ttm) cc_final: 0.5829 (mmt) REVERT: M 115 MET cc_start: 0.8094 (ttp) cc_final: 0.6902 (mmt) REVERT: Q 12 THR cc_start: 0.5878 (OUTLIER) cc_final: 0.5547 (p) REVERT: R 85 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5739 (pt) REVERT: U 51 MET cc_start: 0.3090 (mmp) cc_final: 0.2227 (mpm) REVERT: W 48 MET cc_start: 0.3935 (mmt) cc_final: 0.3679 (mmm) REVERT: W 110 MET cc_start: 0.1424 (mmt) cc_final: 0.1082 (mmt) REVERT: X 85 MET cc_start: 0.2830 (ppp) cc_final: 0.2432 (pp-130) outliers start: 125 outliers final: 54 residues processed: 697 average time/residue: 0.7560 time to fit residues: 649.7579 Evaluate side-chains 671 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 601 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 219 MET Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 317 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 378 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 519 optimal weight: 9.9990 chunk 293 optimal weight: 0.6980 chunk 396 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 723 ASN A1093 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 ASN B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.210831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150051 restraints weight = 55080.327| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.41 r_work: 0.3147 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 45168 Z= 0.256 Angle : 0.654 20.999 61400 Z= 0.328 Chirality : 0.045 0.325 6844 Planarity : 0.005 0.082 7605 Dihedral : 13.444 158.455 6810 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.95 % Allowed : 17.74 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.11), residues: 5187 helix: 0.94 (0.12), residues: 1955 sheet: 0.29 (0.18), residues: 846 loop : -0.26 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 241 TYR 0.026 0.002 TYR A1196 PHE 0.023 0.002 PHE M 195 TRP 0.069 0.003 TRP A 247 HIS 0.021 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (45129) covalent geometry : angle 0.64063 / 0.33 (61352) hydrogen bonds : bond 0.04324 / 2.94 ( 1163) hydrogen bonds : angle 3.69859 / 2.61 ( 3309) metal coordination : bond 0.01275 / 0.84 ( 39) metal coordination : angle 4.80854 / 2.75 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 622 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.7947 (mmt) cc_final: 0.7607 (mpm) REVERT: A 397 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: A 439 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7565 (m90) REVERT: A 841 MET cc_start: 0.9202 (mtp) cc_final: 0.8870 (mtp) REVERT: A 1130 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7158 (mm) REVERT: A 1310 HIS cc_start: 0.8016 (p90) cc_final: 0.7651 (p-80) REVERT: B 53 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8294 (mtm) REVERT: B 222 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: B 358 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6854 (pp20) REVERT: B 543 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 629 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 637 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8856 (mtmt) REVERT: B 671 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: B 840 MET cc_start: 0.4691 (mtp) cc_final: 0.3298 (pmm) REVERT: B 1120 ASN cc_start: 0.8913 (m110) cc_final: 0.8520 (m-40) REVERT: C 82 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 205 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8574 (mmtm) REVERT: C 210 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: D 62 MET cc_start: 0.5786 (ppp) cc_final: 0.5123 (mpp) REVERT: E 110 MET cc_start: 0.6492 (tpt) cc_final: 0.6111 (tpt) REVERT: E 210 GLN cc_start: 0.7642 (tm-30) cc_final: 0.6981 (pp30) REVERT: G 16 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8378 (ptp-170) REVERT: G 29 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8445 (ttmm) REVERT: G 153 ASP cc_start: 0.5858 (m-30) cc_final: 0.5347 (m-30) REVERT: I 27 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7579 (ttmt) REVERT: I 82 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: I 92 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7167 (tttp) REVERT: J 31 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: K 22 ASN cc_start: 0.8686 (m-40) cc_final: 0.8413 (m-40) REVERT: K 23 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8073 (tptt) REVERT: K 68 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: L 35 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8130 (ttt180) REVERT: L 50 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8324 (mppt) REVERT: M 107 MET cc_start: 0.6759 (ttm) cc_final: 0.5772 (mmt) REVERT: M 115 MET cc_start: 0.8104 (ttp) cc_final: 0.6768 (mmt) REVERT: R 85 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5991 (pt) REVERT: U 51 MET cc_start: 0.2931 (mmp) cc_final: 0.2222 (mpm) REVERT: W 48 MET cc_start: 0.4173 (mmt) cc_final: 0.3891 (mmm) REVERT: W 110 MET cc_start: 0.1555 (mmt) cc_final: 0.1192 (mmt) REVERT: X 85 MET cc_start: 0.3047 (ppp) cc_final: 0.2700 (pp-130) outliers start: 137 outliers final: 64 residues processed: 708 average time/residue: 0.7503 time to fit residues: 657.6356 Evaluate side-chains 685 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 601 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 335 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 276 optimal weight: 0.9980 chunk 324 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 496 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 518 optimal weight: 40.0000 chunk 346 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 358 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.210894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150771 restraints weight = 55374.385| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.45 r_work: 0.3128 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 45168 Z= 0.227 Angle : 0.653 17.613 61400 Z= 0.326 Chirality : 0.045 0.425 6844 Planarity : 0.004 0.077 7605 Dihedral : 13.466 158.245 6810 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.82 % Allowed : 18.36 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % 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: 0.32 (0.11), residues: 5187 helix: 0.91 (0.12), residues: 1950 sheet: 0.19 (0.18), residues: 834 loop : -0.26 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 335 TYR 0.027 0.002 TYR R 212 PHE 0.028 0.002 PHE G 77 TRP 0.069 0.002 TRP A 247 HIS 0.008 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (45129) covalent geometry : angle 0.63901 / 0.33 (61352) hydrogen bonds : bond 0.04214 / 2.86 ( 1163) hydrogen bonds : angle 3.70560 / 2.61 ( 3309) metal coordination : bond 0.01210 / 0.81 ( 39) metal coordination : angle 4.78212 / 2.74 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 616 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: A 439 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.7583 (m90) REVERT: A 841 MET cc_start: 0.9200 (mtp) cc_final: 0.8864 (mtp) REVERT: A 930 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8472 (mp) REVERT: A 1071 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: A 1130 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7154 (mm) REVERT: A 1310 HIS cc_start: 0.7929 (p90) cc_final: 0.7495 (p-80) REVERT: B 53 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8329 (mtm) REVERT: B 222 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7917 (mtt-85) REVERT: B 358 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6864 (pp20) REVERT: B 543 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 629 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: B 637 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (mtmt) REVERT: B 671 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: B 840 MET cc_start: 0.4719 (mtp) cc_final: 0.3308 (pmm) REVERT: B 1120 ASN cc_start: 0.8901 (m110) cc_final: 0.8475 (m-40) REVERT: C 82 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8979 (mp) REVERT: C 205 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8544 (mmtm) REVERT: C 210 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: D 62 MET cc_start: 0.6149 (ppp) cc_final: 0.5621 (mpp) REVERT: E 110 MET cc_start: 0.6533 (tpt) cc_final: 0.6228 (tpt) REVERT: E 210 GLN cc_start: 0.7589 (tm-30) cc_final: 0.6858 (pp30) REVERT: G 16 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8393 (ptp-170) REVERT: G 29 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8532 (ttmm) REVERT: G 44 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5568 (m-10) REVERT: I 19 GLU cc_start: 0.8317 (mp0) cc_final: 0.8043 (mp0) REVERT: I 40 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7478 (mtt-85) REVERT: J 31 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: J 47 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.9184 (ttp-170) REVERT: K 22 ASN cc_start: 0.8670 (m-40) cc_final: 0.8410 (m-40) REVERT: K 23 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8083 (tptt) REVERT: K 68 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: L 35 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8128 (ttt180) REVERT: L 50 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8288 (mppt) REVERT: M 107 MET cc_start: 0.6709 (ttm) cc_final: 0.5762 (mmt) REVERT: M 115 MET cc_start: 0.8135 (ttp) cc_final: 0.6771 (mmt) REVERT: R 85 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6089 (pt) REVERT: R 125 MET cc_start: 0.4463 (mmp) cc_final: 0.3559 (mtt) REVERT: U 51 MET cc_start: 0.2999 (mmp) cc_final: 0.2290 (mpm) REVERT: W 48 MET cc_start: 0.4504 (mmt) cc_final: 0.4212 (mmm) REVERT: W 110 MET cc_start: 0.1611 (mmt) cc_final: 0.1274 (mmt) REVERT: X 85 MET cc_start: 0.3195 (ppp) cc_final: 0.2890 (pp-130) outliers start: 131 outliers final: 66 residues processed: 692 average time/residue: 0.7790 time to fit residues: 665.9904 Evaluate side-chains 690 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 602 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 132 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 329 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.211537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.151883 restraints weight = 55020.745| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.47 r_work: 0.3013 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 45168 Z= 0.189 Angle : 0.650 17.360 61400 Z= 0.326 Chirality : 0.044 0.324 6844 Planarity : 0.004 0.074 7605 Dihedral : 13.456 158.059 6810 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.41 % Allowed : 19.16 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: 0.32 (0.11), residues: 5187 helix: 0.93 (0.12), residues: 1940 sheet: 0.18 (0.18), residues: 823 loop : -0.26 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 241 TYR 0.031 0.002 TYR R 212 PHE 0.022 0.002 PHE E 73 TRP 0.068 0.002 TRP A 247 HIS 0.036 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (45129) covalent geometry : angle 0.63738 / 0.32 (61352) hydrogen bonds : bond 0.04073 / 2.76 ( 1163) hydrogen bonds : angle 3.74388 / 2.65 ( 3309) metal coordination : bond 0.01117 / 0.76 ( 39) metal coordination : angle 4.60784 / 2.65 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 609 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 PRO cc_start: 0.9117 (Cg_endo) cc_final: 0.8690 (Cg_exo) REVERT: A 31 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8934 (mm) REVERT: A 397 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6166 (m-80) REVERT: A 439 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7569 (m90) REVERT: A 841 MET cc_start: 0.9245 (mtp) cc_final: 0.8901 (mtp) REVERT: A 930 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 1071 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: A 1130 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7118 (mm) REVERT: A 1310 HIS cc_start: 0.7851 (p90) cc_final: 0.7310 (p-80) REVERT: A 1412 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6644 (mmp) REVERT: B 53 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: B 83 ARG cc_start: 0.7527 (ttm110) cc_final: 0.7216 (ttm110) REVERT: B 155 MET cc_start: 0.9372 (ttm) cc_final: 0.9141 (ttm) REVERT: B 222 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7886 (mtt-85) REVERT: B 335 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.6867 (mpp80) REVERT: B 358 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6842 (pp20) REVERT: B 543 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 629 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 637 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8635 (mtmt) REVERT: B 840 MET cc_start: 0.4843 (mtp) cc_final: 0.3155 (pmm) REVERT: B 1120 ASN cc_start: 0.8828 (m110) cc_final: 0.8297 (m-40) REVERT: C 82 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8895 (mp) REVERT: C 205 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8625 (mmtm) REVERT: E 67 ASP cc_start: 0.8341 (t0) cc_final: 0.8009 (t0) REVERT: E 210 GLN cc_start: 0.7513 (tm-30) cc_final: 0.6881 (pp30) REVERT: G 16 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8274 (ptp-170) REVERT: G 29 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8271 (ttmm) REVERT: I 19 GLU cc_start: 0.8484 (mp0) cc_final: 0.8213 (mp0) REVERT: I 40 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7493 (mtt-85) REVERT: I 92 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7107 (ttmm) REVERT: J 31 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: J 47 ARG cc_start: 0.9430 (OUTLIER) cc_final: 0.9192 (ttp-170) REVERT: K 22 ASN cc_start: 0.8773 (m-40) cc_final: 0.8460 (m-40) REVERT: K 23 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7926 (tptt) REVERT: K 68 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: L 35 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7988 (ttt180) REVERT: L 50 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8276 (mppt) REVERT: M 107 MET cc_start: 0.6594 (ttm) cc_final: 0.5565 (mmt) REVERT: M 111 ASP cc_start: 0.7919 (m-30) cc_final: 0.7504 (m-30) REVERT: M 115 MET cc_start: 0.7749 (ttp) cc_final: 0.6344 (mmt) REVERT: R 85 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6313 (pt) REVERT: U 51 MET cc_start: 0.3547 (mmp) cc_final: 0.2737 (mpm) REVERT: W 48 MET cc_start: 0.5291 (mmt) cc_final: 0.4972 (mmm) REVERT: W 110 MET cc_start: 0.2045 (mmt) cc_final: 0.1715 (mmt) outliers start: 112 outliers final: 62 residues processed: 674 average time/residue: 0.7765 time to fit residues: 647.3794 Evaluate side-chains 672 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 589 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 144 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 491 optimal weight: 50.0000 chunk 487 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 480 optimal weight: 30.0000 chunk 442 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 2 optimal weight: 0.0270 chunk 304 optimal weight: 4.9990 chunk 362 optimal weight: 0.8980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A1190 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.211164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152735 restraints weight = 55341.772| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.38 r_work: 0.3044 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 45168 Z= 0.174 Angle : 0.653 16.431 61400 Z= 0.326 Chirality : 0.044 0.322 6844 Planarity : 0.004 0.070 7605 Dihedral : 13.445 157.871 6810 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.13 % Allowed : 19.76 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: 0.31 (0.11), residues: 5187 helix: 0.94 (0.12), residues: 1936 sheet: 0.17 (0.18), residues: 823 loop : -0.29 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 608 TYR 0.036 0.002 TYR E 125 PHE 0.034 0.002 PHE G 77 TRP 0.067 0.002 TRP A 247 HIS 0.007 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (45129) covalent geometry : angle 0.64119 / 0.33 (61352) hydrogen bonds : bond 0.04037 / 2.74 ( 1163) hydrogen bonds : angle 3.75925 / 2.65 ( 3309) metal coordination : bond 0.01088 / 0.75 ( 39) metal coordination : angle 4.52531 / 2.60 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 612 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 PRO cc_start: 0.9097 (Cg_endo) cc_final: 0.8799 (Cg_exo) REVERT: A 70 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: A 247 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7522 (p90) REVERT: A 347 GLU cc_start: 0.6570 (pm20) cc_final: 0.6286 (mp0) REVERT: A 397 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: A 439 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7548 (m90) REVERT: A 841 MET cc_start: 0.9237 (mtp) cc_final: 0.8891 (mtp) REVERT: A 930 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8354 (mp) REVERT: A 1071 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: A 1130 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7099 (mm) REVERT: A 1337 GLU cc_start: 0.7566 (pm20) cc_final: 0.7276 (pm20) REVERT: A 1412 MET cc_start: 0.6804 (tpp) cc_final: 0.6593 (mmp) REVERT: B 53 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: B 83 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7380 (ttm110) REVERT: B 155 MET cc_start: 0.9366 (ttm) cc_final: 0.9124 (ttm) REVERT: B 222 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7848 (mtt-85) REVERT: B 358 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6816 (pp20) REVERT: B 543 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 637 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8642 (mtmt) REVERT: B 840 MET cc_start: 0.4884 (mtp) cc_final: 0.3247 (pmm) REVERT: C 82 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8875 (mp) REVERT: C 205 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8613 (mmtm) REVERT: C 210 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: D 62 MET cc_start: 0.6824 (ppp) cc_final: 0.6081 (mpp) REVERT: E 94 MET cc_start: 0.8589 (ttp) cc_final: 0.8384 (ttp) REVERT: E 210 GLN cc_start: 0.7503 (tm-30) cc_final: 0.6900 (pp30) REVERT: G 16 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8273 (ptp-170) REVERT: G 29 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8309 (ttmm) REVERT: I 15 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7478 (mmt90) REVERT: I 19 GLU cc_start: 0.8522 (mp0) cc_final: 0.8257 (mp0) REVERT: I 40 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7506 (mtt-85) REVERT: I 92 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7150 (ttmm) REVERT: J 31 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: J 47 ARG cc_start: 0.9421 (OUTLIER) cc_final: 0.9186 (ttp-170) REVERT: K 22 ASN cc_start: 0.8783 (m-40) cc_final: 0.8482 (m-40) REVERT: K 23 LYS cc_start: 0.8685 (ttmt) cc_final: 0.7928 (tptt) REVERT: L 35 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: L 50 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8312 (mppt) REVERT: L 51 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7860 (mtt180) REVERT: M 107 MET cc_start: 0.6596 (ttm) cc_final: 0.5567 (mmt) REVERT: M 111 ASP cc_start: 0.7928 (m-30) cc_final: 0.7531 (m-30) REVERT: M 115 MET cc_start: 0.7728 (ttp) cc_final: 0.6357 (mmt) REVERT: O 284 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7826 (mp0) REVERT: Q 26 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: R 85 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6267 (pt) REVERT: R 125 MET cc_start: 0.4464 (mmp) cc_final: 0.3576 (mtt) REVERT: U 51 MET cc_start: 0.3535 (mmp) cc_final: 0.2720 (mpm) REVERT: W 48 MET cc_start: 0.5216 (mmt) cc_final: 0.4897 (mmm) REVERT: W 110 MET cc_start: 0.2033 (mmt) cc_final: 0.1709 (mmt) outliers start: 99 outliers final: 62 residues processed: 669 average time/residue: 0.7096 time to fit residues: 586.4346 Evaluate side-chains 676 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 593 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 519 optimal weight: 0.6980 chunk 503 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 418 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 510 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.210333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149042 restraints weight = 55357.472| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.51 r_work: 0.2984 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 45168 Z= 0.291 Angle : 0.714 18.648 61400 Z= 0.355 Chirality : 0.047 0.321 6844 Planarity : 0.005 0.075 7605 Dihedral : 13.512 157.822 6810 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 19.87 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % 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: 0.14 (0.11), residues: 5187 helix: 0.77 (0.12), residues: 1946 sheet: 0.08 (0.18), residues: 830 loop : -0.35 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 241 TYR 0.032 0.002 TYR R 212 PHE 0.022 0.002 PHE B 918 TRP 0.066 0.003 TRP A 247 HIS 0.024 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.29 (45129) covalent geometry : angle 0.69995 / 0.35 (61352) hydrogen bonds : bond 0.04433 / 3.01 ( 1163) hydrogen bonds : angle 3.85493 / 2.72 ( 3309) metal coordination : bond 0.01313 / 0.89 ( 39) metal coordination : angle 5.01852 / 2.87 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17007.70 seconds wall clock time: 290 minutes 20.91 seconds (17420.91 seconds total)