Starting phenix.real_space_refine on Sat Mar 23 05:13:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wat_37404/03_2024/8wat_37404_updated.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22139 2.51 5 N 6268 2.21 5 O 6945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35676 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'CSX:plan-1': 1, 'HYP:plan-1': 1, 'ILX:plan-1': 1, 'TRX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" 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: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "X" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 876 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1114 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 219 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8, None: 1} Not linked: pdbres="ATP Z 1 " pdbres=" U Z 2 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "o" Number of atoms: 11510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 11510 Classifications: {'peptide': 1452} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1381} Chain breaks: 1 Chain: "p" Number of atoms: 9149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9149 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 53, 'TRANS': 1092} Chain breaks: 1 Chain: "q" 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: "r" 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: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "u" 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: "v" 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: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "y" 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: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" 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: "p" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, 'W0F': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" 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 4664 SG CYS o 71 113.770 112.453 115.403 1.00141.57 S ATOM 4686 SG CYS o 74 111.653 115.406 115.301 1.00137.29 S ATOM 4733 SG CYS o 81 110.176 111.864 114.857 1.00138.71 S ATOM 4968 SG CYS o 111 101.463 111.333 68.341 1.00164.45 S ATOM 4996 SG CYS o 114 103.688 114.522 68.150 1.00163.67 S ATOM 5342 SG CYS o 184 103.722 111.943 65.287 1.00171.81 S ATOM 24429 SG CYS p1119 105.520 125.056 104.181 1.00141.59 S ATOM 24451 SG CYS p1122 105.561 121.929 102.012 1.00142.57 S ATOM 24566 SG CYS p1137 108.352 122.568 104.001 1.00148.67 S ATOM 24587 SG CYS p1140 107.802 124.372 100.721 1.00152.98 S ATOM 25553 SG CYS q 88 85.746 90.812 173.268 1.00138.12 S ATOM 25566 SG CYS q 90 89.264 89.784 172.418 1.00147.15 S ATOM 25601 SG CYS q 94 87.316 87.489 174.536 1.00132.97 S ATOM 25623 SG CYS q 97 85.863 87.752 171.242 1.00132.45 S ATOM 32929 SG CYS w 17 75.537 52.464 55.879 1.00161.53 S ATOM 32953 SG CYS w 20 78.914 53.554 57.411 1.00163.91 S ATOM 33114 SG CYS w 39 76.788 56.242 56.470 1.00169.29 S ATOM 33139 SG CYS w 42 78.032 53.973 53.698 1.00167.79 S ATOM 33491 SG CYS w 86 44.281 43.137 86.175 1.00150.39 S ATOM 33515 SG CYS w 89 44.883 39.678 87.875 1.00155.57 S ATOM 33719 SG CYS w 114 46.606 42.898 89.156 1.00146.35 S ATOM 33754 SG CYS w 119 47.396 41.354 85.718 1.00152.45 S ATOM 33864 SG CYS x 7 65.587 72.326 151.627 1.00 98.61 S ATOM 33888 SG CYS x 10 63.942 73.216 154.803 1.00 95.35 S ATOM 34152 SG CYS x 44 61.706 72.538 151.602 1.00107.46 S ATOM 34158 SG CYS x 45 63.132 70.116 154.090 1.00108.23 S ATOM 35304 SG CYS z 19 107.105 61.289 142.381 1.00146.64 S ATOM 35323 SG CYS z 22 107.944 58.768 144.962 1.00145.85 S ATOM 35440 SG CYS z 36 110.742 61.282 143.982 1.00153.01 S ATOM 35466 SG CYS z 39 109.406 58.974 141.328 1.00150.68 S Time building chain proxies: 18.51, per 1000 atoms: 0.52 Number of scatterers: 35676 At special positions: 0 Unit cell: (165.416, 185.426, 192.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 203 16.00 P 112 15.00 Mg 1 11.99 O 6945 8.00 N 6268 7.00 C 22139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.48 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 74 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 184 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb=" ZN p1202 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1140 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1119 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 88 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " Number of angles added : 39 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 43 sheets defined 32.7% alpha, 15.0% beta 42 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 16.26 Creating SS restraints... Processing helix chain 'S' and resid 6 through 8 No H-bonds generated for 'chain 'S' and resid 6 through 8' Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 157 through 166 removed outlier: 3.638A pdb=" N ARG S 166 " --> pdb=" O GLU S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 179 Processing helix chain 'T' and resid 10 through 14 Processing helix chain 'T' and resid 25 through 34 removed outlier: 4.166A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 63 No H-bonds generated for 'chain 'T' and resid 60 through 63' Processing helix chain 'o' and resid 28 through 34 Processing helix chain 'o' and resid 99 through 109 Processing helix chain 'o' and resid 124 through 132 Processing helix chain 'o' and resid 137 through 150 removed outlier: 4.161A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.843A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 236 Processing helix chain 'o' and resid 245 through 248 No H-bonds generated for 'chain 'o' and resid 245 through 248' Processing helix chain 'o' and resid 275 through 296 Processing helix chain 'o' and resid 302 through 318 Processing helix chain 'o' and resid 339 through 342 No H-bonds generated for 'chain 'o' and resid 339 through 342' Processing helix chain 'o' and resid 349 through 352 No H-bonds generated for 'chain 'o' and resid 349 through 352' Processing helix chain 'o' and resid 382 through 387 Processing helix chain 'o' and resid 399 through 408 Processing helix chain 'o' and resid 436 through 438 No H-bonds generated for 'chain 'o' and resid 436 through 438' Processing helix chain 'o' and resid 466 through 468 No H-bonds generated for 'chain 'o' and resid 466 through 468' Processing helix chain 'o' and resid 486 through 492 removed outlier: 4.190A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 540 through 548 Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.782A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.931A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.147A pdb=" N SER o 615 " --> pdb=" O ASP o 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 611 through 615' Processing helix chain 'o' and resid 642 through 645 No H-bonds generated for 'chain 'o' and resid 642 through 645' Processing helix chain 'o' and resid 652 through 660 Processing helix chain 'o' and resid 662 through 683 Processing helix chain 'o' and resid 689 through 692 No H-bonds generated for 'chain 'o' and resid 689 through 692' Processing helix chain 'o' and resid 696 through 721 Processing helix chain 'o' and resid 733 through 759 Processing helix chain 'o' and resid 765 through 772 Processing helix chain 'o' and resid 778 through 785 Processing helix chain 'o' and resid 817 through 820 No H-bonds generated for 'chain 'o' and resid 817 through 820' Processing helix chain 'o' and resid 833 through 868 removed outlier: 4.357A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1018 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.021A pdb=" N GLN o1101 " --> pdb=" O GLU o1097 " (cutoff:3.500A) Processing helix chain 'o' and resid 1121 through 1129 Processing helix chain 'o' and resid 1151 through 1161 Processing helix chain 'o' and resid 1166 through 1169 No H-bonds generated for 'chain 'o' and resid 1166 through 1169' Processing helix chain 'o' and resid 1188 through 1198 removed outlier: 3.752A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL o1193 " --> pdb=" O GLN o1190 " (cutoff:3.500A) Processing helix chain 'o' and resid 1218 through 1224 Processing helix chain 'o' and resid 1228 through 1239 Processing helix chain 'o' and resid 1263 through 1267 Processing helix chain 'o' and resid 1282 through 1295 Processing helix chain 'o' and resid 1343 through 1347 Processing helix chain 'o' and resid 1362 through 1369 Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1395 through 1406 Processing helix chain 'o' and resid 1416 through 1419 No H-bonds generated for 'chain 'o' and resid 1416 through 1419' Processing helix chain 'o' and resid 1426 through 1431 Processing helix chain 'o' and resid 1435 through 1445 removed outlier: 3.663A pdb=" N MET o1440 " --> pdb=" O ASP o1437 " (cutoff:3.500A) Processing helix chain 'o' and resid 1454 through 1459 Processing helix chain 'o' and resid 1477 through 1481 Processing helix chain 'p' and resid 22 through 36 removed outlier: 3.940A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 61 Processing helix chain 'p' and resid 110 through 115 Processing helix chain 'p' and resid 168 through 173 Processing helix chain 'p' and resid 247 through 252 Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 281 through 288 Processing helix chain 'p' and resid 295 through 307 Proline residue: p 303 - end of helix Processing helix chain 'p' and resid 314 through 323 Processing helix chain 'p' and resid 332 through 345 Processing helix chain 'p' and resid 358 through 377 Processing helix chain 'p' and resid 388 through 390 No H-bonds generated for 'chain 'p' and resid 388 through 390' Processing helix chain 'p' and resid 396 through 425 Processing helix chain 'p' and resid 431 through 434 No H-bonds generated for 'chain 'p' and resid 431 through 434' Processing helix chain 'p' and resid 437 through 450 Processing helix chain 'p' and resid 475 through 482 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 539 through 548 Processing helix chain 'p' and resid 580 through 593 Processing helix chain 'p' and resid 637 through 644 Processing helix chain 'p' and resid 653 through 659 Processing helix chain 'p' and resid 667 through 672 removed outlier: 3.758A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 682 No H-bonds generated for 'chain 'p' and resid 679 through 682' Processing helix chain 'p' and resid 700 through 703 Processing helix chain 'p' and resid 706 through 710 removed outlier: 3.862A pdb=" N ILE p 710 " --> pdb=" O VAL p 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 706 through 710' Processing helix chain 'p' and resid 714 through 716 No H-bonds generated for 'chain 'p' and resid 714 through 716' Processing helix chain 'p' and resid 719 through 731 removed outlier: 3.540A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 740 No H-bonds generated for 'chain 'p' and resid 738 through 740' Processing helix chain 'p' and resid 762 through 767 Processing helix chain 'p' and resid 798 through 803 Processing helix chain 'p' and resid 969 through 975 Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 978 through 993 Processing helix chain 'p' and resid 1008 through 1018 removed outlier: 3.547A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR p1018 " --> pdb=" O LEU p1014 " (cutoff:3.500A) Processing helix chain 'p' and resid 1055 through 1058 No H-bonds generated for 'chain 'p' and resid 1055 through 1058' Processing helix chain 'p' and resid 1078 through 1080 No H-bonds generated for 'chain 'p' and resid 1078 through 1080' Processing helix chain 'p' and resid 1088 through 1097 Processing helix chain 'p' and resid 1100 through 1111 removed outlier: 4.104A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER p1111 " --> pdb=" O LEU p1107 " (cutoff:3.500A) Processing helix chain 'p' and resid 1153 through 1164 Processing helix chain 'q' and resid 28 through 40 Processing helix chain 'q' and resid 61 through 70 Processing helix chain 'q' and resid 78 through 81 No H-bonds generated for 'chain 'q' and resid 78 through 81' Processing helix chain 'q' and resid 117 through 119 No H-bonds generated for 'chain 'q' and resid 117 through 119' Processing helix chain 'q' and resid 174 through 176 No H-bonds generated for 'chain 'q' and resid 174 through 176' Processing helix chain 'q' and resid 200 through 202 No H-bonds generated for 'chain 'q' and resid 200 through 202' Processing helix chain 'q' and resid 241 through 270 removed outlier: 3.631A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 27 No H-bonds generated for 'chain 'r' and resid 24 through 27' Processing helix chain 'r' and resid 34 through 50 Processing helix chain 'r' and resid 59 through 70 Processing helix chain 'r' and resid 77 through 89 Processing helix chain 'r' and resid 94 through 103 Processing helix chain 'r' and resid 108 through 114 Processing helix chain 'r' and resid 116 through 118 No H-bonds generated for 'chain 'r' and resid 116 through 118' Processing helix chain 'r' and resid 124 through 137 Processing helix chain 's' and resid 3 through 23 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 132 through 136 Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 64 through 66 No H-bonds generated for 'chain 'w' and resid 64 through 66' Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 15 through 27 removed outlier: 3.954A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA x 20 " --> pdb=" O LYS x 17 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 38 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.542A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.627A pdb=" N ASN x 61 " --> pdb=" O GLU x 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 9 Processing helix chain 'y' and resid 40 through 52 removed outlier: 3.753A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'S' and resid 27 through 31 removed outlier: 6.814A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN S 145 " --> pdb=" O ILE S 113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 125 through 128 removed outlier: 3.581A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.282A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU T 115 " --> pdb=" O LYS T 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 93 through 98 removed outlier: 4.829A pdb=" N LEU T 93 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'o' and resid 86 through 89 Processing sheet with id= F, first strand: chain 'o' and resid 190 through 194 removed outlier: 4.644A pdb=" N LEU o 198 " --> pdb=" O LEU o 216 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'o' and resid 264 through 266 Processing sheet with id= H, first strand: chain 'o' and resid 362 through 366 removed outlier: 3.574A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'o' and resid 367 through 369 removed outlier: 6.052A pdb=" N PHE o 482 " --> pdb=" O THR o 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'o' and resid 389 through 393 removed outlier: 3.934A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'o' and resid 602 through 604 removed outlier: 3.598A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU o 635 " --> pdb=" O GLU o 631 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'o' and resid 902 through 905 Processing sheet with id= M, first strand: chain 'o' and resid 1138 through 1142 removed outlier: 3.693A pdb=" N LYS o1306 " --> pdb=" O ASP o1339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'o' and resid 1244 through 1247 removed outlier: 4.350A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA o1174 " --> pdb=" O ARG o1213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id= P, first strand: chain 'p' and resid 97 through 99 Processing sheet with id= Q, first strand: chain 'p' and resid 140 through 144 removed outlier: 3.934A pdb=" N GLN p 90 " --> pdb=" O ASP p 127 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR p 129 " --> pdb=" O PHE p 88 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N PHE p 88 " --> pdb=" O THR p 129 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR p 131 " --> pdb=" O LEU p 86 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU p 86 " --> pdb=" O THR p 131 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE p 133 " --> pdb=" O TYR p 84 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR p 84 " --> pdb=" O ILE p 133 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'p' and resid 185 through 187 Processing sheet with id= S, first strand: chain 'p' and resid 197 through 200 Processing sheet with id= T, first strand: chain 'p' and resid 205 through 208 removed outlier: 6.842A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'p' and resid 484 through 486 Processing sheet with id= V, first strand: chain 'p' and resid 530 through 532 Processing sheet with id= W, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.561A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL p 904 " --> pdb=" O ARG p 924 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'p' and resid 945 through 949 removed outlier: 6.913A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'p' and resid 827 through 829 Processing sheet with id= Z, first strand: chain 'p' and resid 1113 through 1119 Processing sheet with id= AA, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id= AB, first strand: chain 'p' and resid 121 through 126 removed outlier: 3.680A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE p 148 " --> pdb=" O VAL p 126 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 182 through 185 removed outlier: 6.896A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.044A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE q 45 " --> pdb=" O GLY q 168 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 113 through 116 removed outlier: 3.587A pdb=" N VAL q 151 " --> pdb=" O VAL q 115 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 's' and resid 60 through 62 removed outlier: 3.531A pdb=" N VAL s 60 " --> pdb=" O VAL s 74 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 's' and resid 147 through 150 removed outlier: 3.623A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AI, first strand: chain 'u' and resid 2 through 13 removed outlier: 3.540A pdb=" N ALA u 47 " --> pdb=" O ILE u 75 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE u 77 " --> pdb=" O VAL u 45 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL u 45 " --> pdb=" O PHE u 77 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'u' and resid 142 through 146 removed outlier: 7.007A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE u 147 " --> pdb=" O SER u 162 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'u' and resid 127 through 129 Processing sheet with id= AL, first strand: chain 'u' and resid 50 through 54 removed outlier: 6.844A pdb=" N LYS u 71 " --> pdb=" O ASP u 52 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'v' and resid 25 through 31 removed outlier: 5.388A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'w' and resid 24 through 28 Processing sheet with id= AO, first strand: chain 'w' and resid 79 through 81 removed outlier: 3.510A pdb=" N TRP w 123 " --> pdb=" O TYR w 112 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'y' and resid 19 through 23 Processing sheet with id= AQ, first strand: chain 'z' and resid 16 through 18 1135 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 17.00 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5843 1.31 - 1.44: 9765 1.44 - 1.57: 20423 1.57 - 1.70: 218 1.70 - 1.82: 323 Bond restraints: 36572 Sorted by residual: bond pdb=" C2' G2L Z 10 " pdb=" C1' G2L Z 10 " ideal model delta sigma weight residual 1.271 1.523 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C4' G2L Z 10 " pdb=" C3' G2L Z 10 " ideal model delta sigma weight residual 1.270 1.519 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" N PRO p 558 " pdb=" CD PRO p 558 " ideal model delta sigma weight residual 1.473 1.599 -0.126 1.40e-02 5.10e+03 8.14e+01 bond pdb=" N PRO o1098 " pdb=" CD PRO o1098 " ideal model delta sigma weight residual 1.473 1.597 -0.124 1.40e-02 5.10e+03 7.82e+01 bond pdb=" O3' C Z 9 " pdb=" P G2L Z 10 " ideal model delta sigma weight residual 1.607 1.484 0.123 1.50e-02 4.44e+03 6.68e+01 ... (remaining 36567 not shown) Histogram of bond angle deviations from ideal: 75.37 - 88.73: 2 88.73 - 102.10: 259 102.10 - 115.46: 24035 115.46 - 128.82: 25290 128.82 - 142.18: 286 Bond angle restraints: 49872 Sorted by residual: angle pdb=" O3' C Z 9 " pdb=" P G2L Z 10 " pdb=" O5' G2L Z 10 " ideal model delta sigma weight residual 104.00 79.62 24.38 1.50e+00 4.44e-01 2.64e+02 angle pdb=" N09 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" O05 W0F p1201 " ideal model delta sigma weight residual 110.18 75.37 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C07 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " ideal model delta sigma weight residual 110.46 136.28 -25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" O5' G2L Z 10 " pdb=" C5' G2L Z 10 " pdb=" C4' G2L Z 10 " ideal model delta sigma weight residual 109.55 128.76 -19.21 3.00e+00 1.11e-01 4.10e+01 angle pdb=" P26 W0F p1201 " pdb=" O29 W0F p1201 " pdb=" P30 W0F p1201 " ideal model delta sigma weight residual 123.60 142.18 -18.58 3.00e+00 1.11e-01 3.84e+01 ... (remaining 49867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 21299 35.84 - 71.68: 786 71.68 - 107.51: 22 107.51 - 143.35: 1 143.35 - 179.19: 1 Dihedral angle restraints: 22109 sinusoidal: 9949 harmonic: 12160 Sorted by residual: dihedral pdb=" CA TRP o 479 " pdb=" C TRP o 479 " pdb=" N SER o 480 " pdb=" CA SER o 480 " ideal model delta harmonic sigma weight residual 180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" C PHE s 44 " pdb=" N PHE s 44 " pdb=" CA PHE s 44 " pdb=" CB PHE s 44 " ideal model delta harmonic sigma weight residual -122.60 -134.12 11.52 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" CA GLU p 686 " pdb=" C GLU p 686 " pdb=" N VAL p 687 " pdb=" CA VAL p 687 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 22106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5142 0.092 - 0.184: 392 0.184 - 0.276: 8 0.276 - 0.368: 8 0.368 - 0.460: 2 Chirality restraints: 5552 Sorted by residual: chirality pdb=" C4' G2L Z 10 " pdb=" C5' G2L Z 10 " pdb=" O4' G2L Z 10 " pdb=" C3' G2L Z 10 " both_signs ideal model delta sigma weight residual False -2.47 -2.93 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C06 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" O05 W0F p1201 " both_signs ideal model delta sigma weight residual False 2.41 2.04 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA HYP N 8 " pdb=" N HYP N 8 " pdb=" C HYP N 8 " pdb=" CB HYP N 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 5549 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F p1201 " -0.108 2.00e-02 2.50e+03 4.14e-02 5.15e+01 pdb=" C10 W0F p1201 " 0.041 2.00e-02 2.50e+03 pdb=" C12 W0F p1201 " 0.007 2.00e-02 2.50e+03 pdb=" C13 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" C15 W0F p1201 " 0.007 2.00e-02 2.50e+03 pdb=" C17 W0F p1201 " -0.020 2.00e-02 2.50e+03 pdb=" N09 W0F p1201 " 0.051 2.00e-02 2.50e+03 pdb=" N11 W0F p1201 " 0.012 2.00e-02 2.50e+03 pdb=" N14 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" N16 W0F p1201 " -0.017 2.00e-02 2.50e+03 pdb=" N19 W0F p1201 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F p1201 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C ILE p 51 " 0.085 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.032 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR p 531 " 0.022 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C TYR p 531 " -0.072 2.00e-02 2.50e+03 pdb=" O TYR p 531 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE p 532 " 0.024 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 15 2.24 - 2.91: 14123 2.91 - 3.57: 51966 3.57 - 4.24: 89641 4.24 - 4.90: 148817 Nonbonded interactions: 304562 Sorted by model distance: nonbonded pdb=" NZ LYS r 75 " pdb=" OE1 GLN r 141 " model vdw 1.579 2.520 nonbonded pdb=" CE LYS r 75 " pdb=" OE1 GLN r 141 " model vdw 1.686 3.440 nonbonded pdb=" CD LYS r 75 " pdb=" OE1 GLN r 141 " model vdw 1.725 3.440 nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.863 2.170 nonbonded pdb=" C10 W0F p1201 " pdb=" O05 W0F p1201 " model vdw 1.871 2.608 ... (remaining 304557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.880 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: 0.030 Extract box with map and model: 8.860 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 110.130 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 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:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.252 36572 Z= 0.360 Angle : 0.786 34.806 49872 Z= 0.421 Chirality : 0.048 0.460 5552 Planarity : 0.005 0.097 6096 Dihedral : 15.582 179.189 14245 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.70 % Favored : 96.06 % Rotamer: Outliers : 1.08 % Allowed : 7.10 % Favored : 91.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 4137 helix: 1.39 (0.14), residues: 1406 sheet: 0.28 (0.19), residues: 703 loop : -0.21 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP o1192 HIS 0.007 0.001 HIS o 809 PHE 0.025 0.002 PHE q 93 TYR 0.030 0.002 TYR o 669 ARG 0.014 0.001 ARG p 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1002 time to evaluate : 4.090 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: o 19 LYS cc_start: 0.7282 (mttp) cc_final: 0.6961 (mtpp) REVERT: o 67 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8081 (ttp80) REVERT: o 92 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7929 (mttm) REVERT: o 151 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7399 (mmtp) REVERT: o 192 ARG cc_start: 0.7361 (ttm170) cc_final: 0.7092 (ptm-80) REVERT: o 194 SER cc_start: 0.8567 (t) cc_final: 0.7869 (p) REVERT: o 197 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7555 (mt-10) REVERT: o 226 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7976 (ttpp) REVERT: o 234 PHE cc_start: 0.8306 (t80) cc_final: 0.7992 (t80) REVERT: o 238 MET cc_start: 0.7960 (mtm) cc_final: 0.7658 (mtt) REVERT: o 347 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7340 (mm-30) REVERT: o 417 LYS cc_start: 0.7191 (ttpt) cc_final: 0.6754 (ttmm) REVERT: o 451 CYS cc_start: 0.6876 (m) cc_final: 0.6037 (p) REVERT: o 495 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6236 (p0) REVERT: o 508 SER cc_start: 0.6970 (t) cc_final: 0.6472 (p) REVERT: o 524 MET cc_start: 0.8419 (mmp) cc_final: 0.8120 (mmm) REVERT: o 700 GLN cc_start: 0.7357 (tt0) cc_final: 0.6494 (tp-100) REVERT: o 818 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7366 (mp0) REVERT: o 861 GLN cc_start: 0.7294 (tp40) cc_final: 0.6894 (mt0) REVERT: o 868 MET cc_start: 0.7777 (ptt) cc_final: 0.7452 (ptm) REVERT: o 962 ASP cc_start: 0.6735 (m-30) cc_final: 0.6383 (m-30) REVERT: o 1054 MET cc_start: 0.7265 (mmt) cc_final: 0.7046 (mmt) REVERT: o 1063 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7698 (mm-30) REVERT: o 1133 LYS cc_start: 0.8497 (mttt) cc_final: 0.8290 (mtmm) REVERT: o 1233 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8969 (tp30) REVERT: o 1256 VAL cc_start: 0.8697 (t) cc_final: 0.8268 (t) REVERT: o 1259 ILE cc_start: 0.8413 (mt) cc_final: 0.8103 (mm) REVERT: o 1295 ASP cc_start: 0.8901 (m-30) cc_final: 0.8476 (m-30) REVERT: o 1302 GLU cc_start: 0.8099 (pt0) cc_final: 0.7803 (mp0) REVERT: o 1303 GLN cc_start: 0.8189 (mt0) cc_final: 0.7945 (mt0) REVERT: o 1337 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6524 (mm-30) REVERT: o 1339 ASP cc_start: 0.7265 (t0) cc_final: 0.6801 (m-30) REVERT: o 1388 PHE cc_start: 0.8206 (t80) cc_final: 0.7883 (t80) REVERT: o 1391 SER cc_start: 0.7298 (t) cc_final: 0.6983 (p) REVERT: o 1412 MET cc_start: 0.7027 (ttp) cc_final: 0.6395 (ttp) REVERT: o 1422 GLN cc_start: 0.7965 (mt0) cc_final: 0.6688 (mm-40) REVERT: o 1423 ASP cc_start: 0.7806 (m-30) cc_final: 0.7116 (OUTLIER) REVERT: o 1428 MET cc_start: 0.7732 (ttm) cc_final: 0.7392 (ttm) REVERT: o 1434 GLU cc_start: 0.6127 (mt-10) cc_final: 0.5856 (mt-10) REVERT: o 1472 ASP cc_start: 0.6386 (t0) cc_final: 0.5761 (m-30) REVERT: p 17 ILE cc_start: 0.8182 (mt) cc_final: 0.7948 (mm) REVERT: p 87 LYS cc_start: 0.7705 (tttt) cc_final: 0.7436 (tptt) REVERT: p 89 GLU cc_start: 0.7945 (tt0) cc_final: 0.7364 (tt0) REVERT: p 191 GLU cc_start: 0.7228 (mp0) cc_final: 0.6006 (pt0) REVERT: p 198 GLU cc_start: 0.8217 (tt0) cc_final: 0.7892 (tt0) REVERT: p 225 LEU cc_start: 0.7508 (tp) cc_final: 0.7279 (tm) REVERT: p 257 VAL cc_start: 0.8347 (m) cc_final: 0.8108 (p) REVERT: p 265 GLN cc_start: 0.8855 (pt0) cc_final: 0.8417 (pm20) REVERT: p 281 ASP cc_start: 0.7035 (m-30) cc_final: 0.6779 (m-30) REVERT: p 297 MET cc_start: 0.8401 (mtm) cc_final: 0.8084 (mtm) REVERT: p 298 MET cc_start: 0.8801 (mmm) cc_final: 0.8508 (mmm) REVERT: p 309 PHE cc_start: 0.9141 (t80) cc_final: 0.8880 (t80) REVERT: p 313 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7446 (tt0) REVERT: p 324 ARG cc_start: 0.7994 (mtt90) cc_final: 0.6616 (mpt90) REVERT: p 337 LYS cc_start: 0.7579 (tttm) cc_final: 0.7344 (tppp) REVERT: p 348 LEU cc_start: 0.7842 (mp) cc_final: 0.7629 (mp) REVERT: p 386 ASP cc_start: 0.8412 (m-30) cc_final: 0.7973 (m-30) REVERT: p 420 GLN cc_start: 0.8575 (tt0) cc_final: 0.8292 (tp40) REVERT: p 471 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7143 (t0) REVERT: p 578 LYS cc_start: 0.9200 (mttm) cc_final: 0.8917 (mmtm) REVERT: p 606 ASP cc_start: 0.7001 (t0) cc_final: 0.6643 (t0) REVERT: p 674 MET cc_start: 0.8024 (mmm) cc_final: 0.7578 (mmm) REVERT: p 728 MET cc_start: 0.7502 (mtm) cc_final: 0.7136 (mtt) REVERT: p 739 ASN cc_start: 0.7311 (p0) cc_final: 0.6883 (p0) REVERT: p 747 LEU cc_start: 0.7861 (mt) cc_final: 0.7563 (mp) REVERT: p 796 MET cc_start: 0.8699 (mtm) cc_final: 0.8394 (mtm) REVERT: p 798 ARG cc_start: 0.6859 (ttt90) cc_final: 0.6548 (ttm-80) REVERT: p 834 ARG cc_start: 0.6948 (mmm-85) cc_final: 0.6723 (mpt180) REVERT: p 905 ASP cc_start: 0.7664 (t0) cc_final: 0.7418 (t0) REVERT: p 930 GLN cc_start: 0.7416 (mt0) cc_final: 0.6988 (mt0) REVERT: p 1007 ASN cc_start: 0.7745 (m-40) cc_final: 0.7489 (m-40) REVERT: p 1054 MET cc_start: 0.8638 (mtm) cc_final: 0.8095 (mtt) REVERT: p 1076 GLU cc_start: 0.7631 (tt0) cc_final: 0.7415 (tt0) REVERT: p 1143 LYS cc_start: 0.6356 (tttp) cc_final: 0.5907 (tmtt) REVERT: p 1151 MET cc_start: 0.7866 (ptm) cc_final: 0.7653 (ptm) REVERT: p 1163 MET cc_start: 0.7462 (mtp) cc_final: 0.7088 (mtm) REVERT: q 27 ASP cc_start: 0.7602 (m-30) cc_final: 0.7215 (t0) REVERT: q 111 GLN cc_start: 0.7841 (tt0) cc_final: 0.7278 (mp10) REVERT: q 199 LYS cc_start: 0.8246 (mttt) cc_final: 0.7998 (mtmm) REVERT: q 202 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7316 (mt-10) REVERT: q 217 GLN cc_start: 0.8319 (mt0) cc_final: 0.8109 (mt0) REVERT: q 265 HIS cc_start: 0.7644 (m-70) cc_final: 0.7299 (t-170) REVERT: r 38 HIS cc_start: 0.7875 (t70) cc_final: 0.7333 (t70) REVERT: r 61 PHE cc_start: 0.7826 (t80) cc_final: 0.7262 (t80) REVERT: s 3 ASP cc_start: 0.6990 (m-30) cc_final: 0.6773 (t0) REVERT: s 26 TYR cc_start: 0.7336 (m-80) cc_final: 0.6885 (m-80) REVERT: s 91 CYS cc_start: 0.8981 (t) cc_final: 0.8695 (t) REVERT: s 172 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7362 (mtt-85) REVERT: s 177 ASP cc_start: 0.7975 (t70) cc_final: 0.7760 (t70) REVERT: t 79 VAL cc_start: 0.7441 (t) cc_final: 0.6805 (p) REVERT: t 80 MET cc_start: 0.7830 (mmt) cc_final: 0.6820 (mmm) REVERT: t 86 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6115 (mt-10) REVERT: t 115 TYR cc_start: 0.8155 (p90) cc_final: 0.7821 (p90) REVERT: t 122 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7349 (mt-10) REVERT: u 3 TYR cc_start: 0.7134 (m-80) cc_final: 0.6183 (m-10) REVERT: u 6 SER cc_start: 0.8208 (p) cc_final: 0.7827 (m) REVERT: u 8 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6592 (mm-30) REVERT: u 80 PHE cc_start: 0.7815 (m-80) cc_final: 0.7412 (m-80) REVERT: v 4 ILE cc_start: 0.8751 (mt) cc_final: 0.8540 (mm) REVERT: v 38 ASP cc_start: 0.6743 (t70) cc_final: 0.6434 (t0) REVERT: v 76 ASN cc_start: 0.8172 (m-40) cc_final: 0.7898 (t160) REVERT: v 100 GLU cc_start: 0.7524 (tt0) cc_final: 0.6739 (mt-10) REVERT: v 105 SER cc_start: 0.8313 (t) cc_final: 0.7746 (m) REVERT: v 106 THR cc_start: 0.8047 (p) cc_final: 0.7552 (p) REVERT: v 110 THR cc_start: 0.8531 (p) cc_final: 0.8248 (m) REVERT: v 126 GLN cc_start: 0.7640 (tt0) cc_final: 0.7423 (tt0) REVERT: v 146 LYS cc_start: 0.7319 (tttt) cc_final: 0.7046 (ttmt) REVERT: v 147 LYS cc_start: 0.8499 (mttt) cc_final: 0.8277 (mmtm) REVERT: w 56 ASN cc_start: 0.7759 (t0) cc_final: 0.7352 (t0) REVERT: w 69 ILE cc_start: 0.8516 (mt) cc_final: 0.8280 (mm) REVERT: w 93 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7364 (mt-10) REVERT: w 115 THR cc_start: 0.8320 (m) cc_final: 0.8106 (p) REVERT: w 123 TRP cc_start: 0.8462 (p90) cc_final: 0.8245 (p90) REVERT: x 12 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7702 (tttp) REVERT: x 62 TYR cc_start: 0.7723 (m-80) cc_final: 0.6975 (m-80) REVERT: y 1 MET cc_start: 0.6321 (ptm) cc_final: 0.6028 (ptp) REVERT: y 2 ASN cc_start: 0.8168 (m-40) cc_final: 0.7635 (m110) REVERT: y 8 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7059 (mm-30) REVERT: y 23 LYS cc_start: 0.8523 (mttt) cc_final: 0.8070 (mmtp) REVERT: y 39 ASP cc_start: 0.6890 (p0) cc_final: 0.6645 (p0) REVERT: y 61 TYR cc_start: 0.9033 (p90) cc_final: 0.8577 (p90) REVERT: y 68 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6560 (mt-10) REVERT: y 111 ASP cc_start: 0.8632 (m-30) cc_final: 0.8162 (m-30) REVERT: y 114 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8156 (pp20) REVERT: z 25 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7599 (pp20) REVERT: z 42 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7507 (mpp80) REVERT: z 47 LYS cc_start: 0.7440 (tttt) cc_final: 0.7140 (tttt) outliers start: 40 outliers final: 8 residues processed: 1027 average time/residue: 1.6845 time to fit residues: 2037.1266 Evaluate side-chains 639 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 630 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 571 ASP Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain q residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 177 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 329 optimal weight: 30.0000 chunk 127 optimal weight: 0.0040 chunk 200 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 382 optimal weight: 4.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN o 136 GLN o 181 HIS o 341 GLN o 449 HIS o 531 ASN o 539 GLN o 671 ASN o 721 HIS o 780 ASN o 791 GLN o 792 ASN o 904 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1032 GLN o1082 HIS o1101 GLN o1163 HIS o1172 ASN o1182 GLN o1220 HIS o1462 GLN p 43 GLN p 245 GLN ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 518 HIS p 639 HIS p 699 HIS p 718 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 797 ASN p 838 GLN p 941 GLN p 948 GLN ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN q 260 GLN r 66 ASN r 129 GLN ** s 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 132 GLN t 46 GLN u 14 HIS v 131 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 36572 Z= 0.336 Angle : 0.674 13.135 49872 Z= 0.351 Chirality : 0.047 0.211 5552 Planarity : 0.005 0.079 6096 Dihedral : 16.871 179.805 5805 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer: Outliers : 4.20 % Allowed : 14.53 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 4137 helix: 1.31 (0.14), residues: 1395 sheet: 0.23 (0.20), residues: 648 loop : -0.22 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP o1192 HIS 0.008 0.001 HIS o 606 PHE 0.026 0.002 PHE u 119 TYR 0.023 0.002 TYR o 669 ARG 0.013 0.001 ARG u 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 645 time to evaluate : 3.920 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: S 105 LYS cc_start: 0.2019 (mmtm) cc_final: 0.1780 (tptp) REVERT: o 19 LYS cc_start: 0.7376 (mttp) cc_final: 0.6956 (mtpp) REVERT: o 30 GLU cc_start: 0.7214 (tt0) cc_final: 0.6583 (tt0) REVERT: o 51 ARG cc_start: 0.7812 (mpp80) cc_final: 0.7589 (mpp80) REVERT: o 67 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8142 (ttp80) REVERT: o 77 ASN cc_start: 0.7576 (t0) cc_final: 0.7098 (t0) REVERT: o 92 LYS cc_start: 0.8296 (mtpp) cc_final: 0.8038 (mttm) REVERT: o 151 LYS cc_start: 0.7647 (mmtp) cc_final: 0.7184 (mptm) REVERT: o 194 SER cc_start: 0.8640 (t) cc_final: 0.8129 (p) REVERT: o 197 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7058 (mt-10) REVERT: o 220 ARG cc_start: 0.8027 (tpt-90) cc_final: 0.7714 (tpt-90) REVERT: o 234 PHE cc_start: 0.8347 (t80) cc_final: 0.8004 (t80) REVERT: o 238 MET cc_start: 0.8015 (mtm) cc_final: 0.7716 (mtt) REVERT: o 305 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7559 (tm-30) REVERT: o 325 LEU cc_start: 0.8347 (mm) cc_final: 0.8128 (mt) REVERT: o 329 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.6918 (mtp) REVERT: o 347 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7445 (mp0) REVERT: o 417 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6733 (ttmm) REVERT: o 451 CYS cc_start: 0.6885 (m) cc_final: 0.6029 (p) REVERT: o 495 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6065 (p0) REVERT: o 508 SER cc_start: 0.6918 (t) cc_final: 0.6463 (p) REVERT: o 512 ARG cc_start: 0.6430 (ttt180) cc_final: 0.6142 (ttm170) REVERT: o 524 MET cc_start: 0.8454 (mmp) cc_final: 0.8050 (mmm) REVERT: o 573 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8464 (mttm) REVERT: o 691 ASP cc_start: 0.8315 (m-30) cc_final: 0.8084 (m-30) REVERT: o 700 GLN cc_start: 0.7688 (tt0) cc_final: 0.6660 (tp-100) REVERT: o 818 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7493 (mp0) REVERT: o 861 GLN cc_start: 0.7200 (tp40) cc_final: 0.6740 (mt0) REVERT: o 868 MET cc_start: 0.7600 (ptt) cc_final: 0.7261 (ptm) REVERT: o 936 GLU cc_start: 0.6625 (tt0) cc_final: 0.5665 (tm-30) REVERT: o 962 ASP cc_start: 0.6717 (m-30) cc_final: 0.6369 (m-30) REVERT: o 1015 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6206 (mm-30) REVERT: o 1063 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7510 (mm-30) REVERT: o 1104 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5824 (mt) REVERT: o 1146 GLN cc_start: 0.8090 (pp30) cc_final: 0.7795 (pp30) REVERT: o 1210 TRP cc_start: 0.7618 (m100) cc_final: 0.7256 (m100) REVERT: o 1216 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7780 (mp) REVERT: o 1247 PHE cc_start: 0.8751 (p90) cc_final: 0.8496 (p90) REVERT: o 1259 ILE cc_start: 0.8397 (mt) cc_final: 0.8106 (mm) REVERT: o 1262 MET cc_start: 0.7944 (tpp) cc_final: 0.7708 (tpp) REVERT: o 1284 PHE cc_start: 0.8420 (t80) cc_final: 0.7998 (t80) REVERT: o 1295 ASP cc_start: 0.8475 (m-30) cc_final: 0.8233 (m-30) REVERT: o 1337 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6389 (mm-30) REVERT: o 1339 ASP cc_start: 0.7143 (t0) cc_final: 0.6865 (m-30) REVERT: o 1388 PHE cc_start: 0.8261 (t80) cc_final: 0.7904 (t80) REVERT: o 1412 MET cc_start: 0.7598 (ttp) cc_final: 0.7063 (ttp) REVERT: o 1422 GLN cc_start: 0.7996 (mt0) cc_final: 0.6769 (mm110) REVERT: o 1423 ASP cc_start: 0.8116 (m-30) cc_final: 0.7282 (OUTLIER) REVERT: o 1428 MET cc_start: 0.7863 (ttm) cc_final: 0.7615 (ttm) REVERT: o 1472 ASP cc_start: 0.6587 (t0) cc_final: 0.6214 (m-30) REVERT: o 1484 MET cc_start: 0.5531 (ppp) cc_final: 0.5195 (ppp) REVERT: p 17 ILE cc_start: 0.8441 (mt) cc_final: 0.8172 (mm) REVERT: p 87 LYS cc_start: 0.7993 (tttt) cc_final: 0.7080 (tptt) REVERT: p 89 GLU cc_start: 0.7746 (tt0) cc_final: 0.7418 (mm-30) REVERT: p 169 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7750 (ttm110) REVERT: p 173 GLU cc_start: 0.8355 (tp30) cc_final: 0.8150 (tt0) REVERT: p 191 GLU cc_start: 0.7841 (mp0) cc_final: 0.7629 (mp0) REVERT: p 220 GLU cc_start: 0.7585 (pt0) cc_final: 0.7155 (pt0) REVERT: p 222 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6091 (mtp180) REVERT: p 239 MET cc_start: 0.8116 (ttm) cc_final: 0.7826 (ttm) REVERT: p 265 GLN cc_start: 0.8946 (pt0) cc_final: 0.8436 (pm20) REVERT: p 278 PHE cc_start: 0.7933 (m-80) cc_final: 0.7691 (m-80) REVERT: p 281 ASP cc_start: 0.6972 (m-30) cc_final: 0.6740 (m-30) REVERT: p 309 PHE cc_start: 0.9009 (t80) cc_final: 0.8335 (t80) REVERT: p 313 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7546 (tt0) REVERT: p 337 LYS cc_start: 0.7514 (tttm) cc_final: 0.7231 (tppp) REVERT: p 386 ASP cc_start: 0.8608 (m-30) cc_final: 0.8087 (m-30) REVERT: p 394 ASP cc_start: 0.7736 (m-30) cc_final: 0.7200 (m-30) REVERT: p 572 CYS cc_start: 0.8091 (m) cc_final: 0.7857 (t) REVERT: p 578 LYS cc_start: 0.8970 (mttm) cc_final: 0.8723 (mmtt) REVERT: p 582 GLN cc_start: 0.8307 (mm110) cc_final: 0.7964 (mm-40) REVERT: p 606 ASP cc_start: 0.7053 (t0) cc_final: 0.6602 (t0) REVERT: p 636 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7204 (mttp) REVERT: p 677 MET cc_start: 0.8716 (tpp) cc_final: 0.7783 (tpp) REVERT: p 683 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6237 (mm-40) REVERT: p 728 MET cc_start: 0.7669 (mtm) cc_final: 0.7383 (mtp) REVERT: p 733 MET cc_start: 0.8414 (ttm) cc_final: 0.8073 (ttm) REVERT: p 739 ASN cc_start: 0.7896 (p0) cc_final: 0.7396 (p0) REVERT: p 796 MET cc_start: 0.8791 (mtm) cc_final: 0.8363 (mtm) REVERT: p 841 ARG cc_start: 0.6485 (mmm-85) cc_final: 0.6232 (mmm-85) REVERT: p 930 GLN cc_start: 0.7444 (mt0) cc_final: 0.6903 (mt0) REVERT: p 952 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: p 1007 ASN cc_start: 0.7709 (m-40) cc_final: 0.7307 (m-40) REVERT: p 1026 GLU cc_start: 0.8487 (tt0) cc_final: 0.7962 (mt-10) REVERT: p 1054 MET cc_start: 0.8757 (mtm) cc_final: 0.8296 (mtt) REVERT: p 1089 MET cc_start: 0.7007 (mtp) cc_final: 0.6726 (mtp) REVERT: p 1121 LEU cc_start: 0.8645 (mm) cc_final: 0.8381 (mm) REVERT: p 1124 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7533 (pp) REVERT: p 1151 MET cc_start: 0.7894 (ptm) cc_final: 0.7644 (ptm) REVERT: p 1163 MET cc_start: 0.7759 (mtp) cc_final: 0.7549 (mtp) REVERT: q 27 ASP cc_start: 0.7736 (m-30) cc_final: 0.7393 (t0) REVERT: q 100 GLU cc_start: 0.7679 (tt0) cc_final: 0.7399 (tt0) REVERT: q 225 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8537 (tttt) REVERT: r 38 HIS cc_start: 0.7952 (t70) cc_final: 0.7534 (t70) REVERT: r 45 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7900 (ptpt) REVERT: r 61 PHE cc_start: 0.7704 (t80) cc_final: 0.7439 (t80) REVERT: r 62 MET cc_start: 0.9434 (mmm) cc_final: 0.9101 (mmm) REVERT: s 26 TYR cc_start: 0.8031 (m-80) cc_final: 0.7505 (m-80) REVERT: s 159 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7329 (tp) REVERT: s 195 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7593 (ptt180) REVERT: t 79 VAL cc_start: 0.7512 (t) cc_final: 0.7228 (p) REVERT: t 80 MET cc_start: 0.7497 (mmt) cc_final: 0.7243 (mmm) REVERT: t 82 GLU cc_start: 0.7660 (pp20) cc_final: 0.5948 (pp20) REVERT: t 83 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8011 (pp) REVERT: t 84 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7558 (mp0) REVERT: t 86 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6283 (mt-10) REVERT: t 116 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8079 (mt-10) REVERT: u 1 MET cc_start: 0.8270 (tpp) cc_final: 0.7991 (tmm) REVERT: u 63 ARG cc_start: 0.7097 (mtp85) cc_final: 0.6860 (mtp-110) REVERT: u 71 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7294 (mtmm) REVERT: u 80 PHE cc_start: 0.8119 (m-80) cc_final: 0.7371 (m-10) REVERT: u 104 MET cc_start: 0.7762 (tpp) cc_final: 0.7142 (tpp) REVERT: u 117 MET cc_start: 0.1979 (OUTLIER) cc_final: 0.1409 (mtp) REVERT: u 119 PHE cc_start: 0.8203 (t80) cc_final: 0.7372 (m-80) REVERT: v 4 ILE cc_start: 0.8909 (mt) cc_final: 0.8671 (mm) REVERT: v 36 LYS cc_start: 0.6936 (tppt) cc_final: 0.6625 (mmtt) REVERT: v 37 MET cc_start: 0.7740 (mtp) cc_final: 0.7422 (mtm) REVERT: v 38 ASP cc_start: 0.6834 (t70) cc_final: 0.6403 (t0) REVERT: v 76 ASN cc_start: 0.8150 (m-40) cc_final: 0.7884 (t160) REVERT: v 100 GLU cc_start: 0.7570 (tt0) cc_final: 0.6790 (mt-10) REVERT: v 126 GLN cc_start: 0.8013 (tt0) cc_final: 0.7726 (tt0) REVERT: v 146 LYS cc_start: 0.7400 (tttt) cc_final: 0.7110 (ttmt) REVERT: w 29 ASP cc_start: 0.8120 (t0) cc_final: 0.7869 (t0) REVERT: w 47 GLU cc_start: 0.7216 (pp20) cc_final: 0.6994 (pp20) REVERT: w 56 ASN cc_start: 0.7573 (t0) cc_final: 0.6968 (t0) REVERT: w 71 ASP cc_start: 0.8126 (m-30) cc_final: 0.7830 (m-30) REVERT: y 8 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7086 (mm-30) REVERT: y 23 LYS cc_start: 0.8375 (mttt) cc_final: 0.7974 (mmtp) REVERT: y 45 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7594 (tt) REVERT: y 70 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7782 (ttmm) REVERT: y 71 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7835 (tt) REVERT: y 93 ASP cc_start: 0.7679 (m-30) cc_final: 0.7176 (m-30) REVERT: z 15 MET cc_start: 0.6336 (mmm) cc_final: 0.5917 (mmm) REVERT: z 25 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7409 (pp20) REVERT: z 27 GLU cc_start: 0.8549 (mp0) cc_final: 0.8031 (mp0) REVERT: z 29 LYS cc_start: 0.8728 (pptt) cc_final: 0.8518 (pptt) REVERT: z 35 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8009 (ttm110) REVERT: z 37 ARG cc_start: 0.6533 (ptt90) cc_final: 0.6019 (ptt180) REVERT: z 42 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.6864 (mtt90) REVERT: z 47 LYS cc_start: 0.7547 (tttt) cc_final: 0.7275 (tttt) outliers start: 155 outliers final: 58 residues processed: 737 average time/residue: 1.5175 time to fit residues: 1335.4335 Evaluate side-chains 639 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 567 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 214 ILE Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1103 THR Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1117 VAL Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 489 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1069 ILE Chi-restraints excluded: chain p residue 1124 ILE Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 121 ASP Chi-restraints excluded: chain u residue 71 LYS Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 130 ASN Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 0.0010 chunk 118 optimal weight: 0.5980 chunk 318 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 383 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN o 181 HIS o 301 HIS o 485 ASN o 673 GLN o 723 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1182 GLN o1190 GLN o1220 HIS p 144 HIS ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 518 HIS p 755 GLN p 980 HIS p1021 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 ASN ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 36572 Z= 0.372 Angle : 0.639 11.797 49872 Z= 0.334 Chirality : 0.046 0.208 5552 Planarity : 0.005 0.058 6096 Dihedral : 16.703 178.313 5797 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.82 % Rotamer: Outliers : 4.66 % Allowed : 15.92 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4137 helix: 1.21 (0.14), residues: 1420 sheet: 0.29 (0.20), residues: 633 loop : -0.31 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP q 49 HIS 0.008 0.001 HIS S 152 PHE 0.035 0.002 PHE u 107 TYR 0.022 0.002 TYR q 231 ARG 0.006 0.001 ARG u 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 575 time to evaluate : 3.830 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: S 105 LYS cc_start: 0.1926 (mmtm) cc_final: 0.1687 (tptp) REVERT: o 19 LYS cc_start: 0.7628 (mttp) cc_final: 0.7015 (mtpp) REVERT: o 45 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6123 (pm20) REVERT: o 67 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8075 (ttp80) REVERT: o 77 ASN cc_start: 0.7638 (t0) cc_final: 0.7179 (t0) REVERT: o 92 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7973 (mttm) REVERT: o 146 ASP cc_start: 0.8415 (m-30) cc_final: 0.7905 (p0) REVERT: o 186 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: o 194 SER cc_start: 0.8554 (t) cc_final: 0.8091 (p) REVERT: o 197 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7186 (mt-10) REVERT: o 220 ARG cc_start: 0.8090 (tpt-90) cc_final: 0.7868 (tpt-90) REVERT: o 232 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: o 234 PHE cc_start: 0.8455 (t80) cc_final: 0.8142 (t80) REVERT: o 238 MET cc_start: 0.8173 (mtm) cc_final: 0.7702 (mtt) REVERT: o 273 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: o 286 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6943 (tp) REVERT: o 305 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7486 (tm-30) REVERT: o 329 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7223 (mtp) REVERT: o 336 LEU cc_start: 0.7515 (mm) cc_final: 0.7231 (mm) REVERT: o 347 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7109 (mm-30) REVERT: o 451 CYS cc_start: 0.6927 (m) cc_final: 0.6020 (p) REVERT: o 495 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6159 (p0) REVERT: o 508 SER cc_start: 0.6933 (t) cc_final: 0.6430 (p) REVERT: o 512 ARG cc_start: 0.6454 (ttt180) cc_final: 0.6073 (ttm170) REVERT: o 700 GLN cc_start: 0.7678 (tt0) cc_final: 0.6587 (tp-100) REVERT: o 775 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7728 (tppp) REVERT: o 818 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7310 (mp0) REVERT: o 861 GLN cc_start: 0.7282 (tp40) cc_final: 0.6755 (mt0) REVERT: o 868 MET cc_start: 0.7336 (ptt) cc_final: 0.7087 (ptm) REVERT: o 921 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7367 (mmm-85) REVERT: o 936 GLU cc_start: 0.6636 (tt0) cc_final: 0.5745 (tm-30) REVERT: o 962 ASP cc_start: 0.6725 (m-30) cc_final: 0.6383 (m-30) REVERT: o 1015 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6264 (mm-30) REVERT: o 1063 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7521 (mm-30) REVERT: o 1104 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5949 (mt) REVERT: o 1146 GLN cc_start: 0.8240 (pp30) cc_final: 0.7462 (pp30) REVERT: o 1210 TRP cc_start: 0.7663 (m100) cc_final: 0.7320 (m100) REVERT: o 1230 GLN cc_start: 0.9254 (mt0) cc_final: 0.8896 (mt0) REVERT: o 1233 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8985 (tp30) REVERT: o 1247 PHE cc_start: 0.8786 (p90) cc_final: 0.8512 (p90) REVERT: o 1259 ILE cc_start: 0.8334 (mt) cc_final: 0.8068 (mm) REVERT: o 1262 MET cc_start: 0.7903 (tpp) cc_final: 0.7587 (tpp) REVERT: o 1295 ASP cc_start: 0.8450 (m-30) cc_final: 0.8158 (m-30) REVERT: o 1318 LYS cc_start: 0.6260 (mtpt) cc_final: 0.5917 (mtpp) REVERT: o 1337 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6450 (mm-30) REVERT: o 1339 ASP cc_start: 0.7131 (t0) cc_final: 0.6851 (m-30) REVERT: o 1376 LYS cc_start: 0.6145 (ttmm) cc_final: 0.5666 (ttmt) REVERT: o 1388 PHE cc_start: 0.8151 (t80) cc_final: 0.7889 (t80) REVERT: o 1412 MET cc_start: 0.7436 (ttp) cc_final: 0.6909 (ttp) REVERT: o 1422 GLN cc_start: 0.7883 (mt0) cc_final: 0.6791 (mm110) REVERT: o 1423 ASP cc_start: 0.8276 (m-30) cc_final: 0.7469 (OUTLIER) REVERT: o 1428 MET cc_start: 0.7557 (ttm) cc_final: 0.7328 (ttm) REVERT: o 1472 ASP cc_start: 0.6837 (t0) cc_final: 0.6354 (m-30) REVERT: o 1484 MET cc_start: 0.5446 (ppp) cc_final: 0.5203 (ppp) REVERT: p 17 ILE cc_start: 0.8580 (mt) cc_final: 0.8273 (pt) REVERT: p 36 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: p 87 LYS cc_start: 0.8057 (tttt) cc_final: 0.7182 (tptt) REVERT: p 89 GLU cc_start: 0.7692 (tt0) cc_final: 0.7368 (mm-30) REVERT: p 173 GLU cc_start: 0.8386 (tp30) cc_final: 0.8109 (tt0) REVERT: p 191 GLU cc_start: 0.8180 (mp0) cc_final: 0.7933 (mp0) REVERT: p 220 GLU cc_start: 0.7223 (pt0) cc_final: 0.6846 (pt0) REVERT: p 265 GLN cc_start: 0.8909 (pt0) cc_final: 0.8228 (pm20) REVERT: p 278 PHE cc_start: 0.8160 (m-80) cc_final: 0.7862 (m-80) REVERT: p 281 ASP cc_start: 0.7075 (m-30) cc_final: 0.6798 (m-30) REVERT: p 299 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: p 309 PHE cc_start: 0.8993 (t80) cc_final: 0.8697 (t80) REVERT: p 310 VAL cc_start: 0.9169 (t) cc_final: 0.8859 (t) REVERT: p 312 GLN cc_start: 0.7490 (mp10) cc_final: 0.7041 (mp10) REVERT: p 313 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7589 (tt0) REVERT: p 335 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7236 (ttm110) REVERT: p 337 LYS cc_start: 0.7572 (tttm) cc_final: 0.7293 (tppp) REVERT: p 386 ASP cc_start: 0.8710 (m-30) cc_final: 0.8275 (m-30) REVERT: p 572 CYS cc_start: 0.8039 (m) cc_final: 0.7767 (t) REVERT: p 606 ASP cc_start: 0.7436 (t0) cc_final: 0.7116 (t0) REVERT: p 610 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6925 (ptm160) REVERT: p 710 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8306 (mt) REVERT: p 796 MET cc_start: 0.8834 (mtm) cc_final: 0.8533 (mtm) REVERT: p 930 GLN cc_start: 0.7543 (mt0) cc_final: 0.7216 (mt0) REVERT: p 1007 ASN cc_start: 0.7688 (m-40) cc_final: 0.7298 (m-40) REVERT: p 1089 MET cc_start: 0.7545 (mtp) cc_final: 0.6841 (mtp) REVERT: p 1121 LEU cc_start: 0.8674 (mm) cc_final: 0.8432 (mm) REVERT: p 1143 LYS cc_start: 0.6753 (tmtt) cc_final: 0.6429 (tptp) REVERT: q 27 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7199 (t0) REVERT: q 83 GLN cc_start: 0.8419 (mt0) cc_final: 0.8140 (mt0) REVERT: q 265 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.6928 (m170) REVERT: r 62 MET cc_start: 0.9379 (mmm) cc_final: 0.9085 (mmm) REVERT: s 26 TYR cc_start: 0.8149 (m-80) cc_final: 0.7640 (m-80) REVERT: s 121 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7714 (pmm) REVERT: s 159 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7404 (tp) REVERT: s 166 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6227 (mtm110) REVERT: s 172 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.6595 (mtt-85) REVERT: s 195 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7620 (ptt180) REVERT: t 79 VAL cc_start: 0.7540 (t) cc_final: 0.7083 (p) REVERT: t 80 MET cc_start: 0.7601 (mmt) cc_final: 0.7241 (mmm) REVERT: t 82 GLU cc_start: 0.7775 (pp20) cc_final: 0.6143 (pp20) REVERT: t 84 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7677 (mp0) REVERT: t 86 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6412 (mt-10) REVERT: t 95 LYS cc_start: 0.6094 (tttp) cc_final: 0.5774 (ttmm) REVERT: u 1 MET cc_start: 0.8148 (tpp) cc_final: 0.7836 (tmm) REVERT: u 63 ARG cc_start: 0.7253 (mtp85) cc_final: 0.7008 (mtp-110) REVERT: u 71 LYS cc_start: 0.7776 (mtmp) cc_final: 0.7491 (mtmp) REVERT: u 80 PHE cc_start: 0.8106 (m-80) cc_final: 0.7344 (m-10) REVERT: u 104 MET cc_start: 0.7678 (tpp) cc_final: 0.7080 (tpp) REVERT: u 117 MET cc_start: 0.1963 (OUTLIER) cc_final: 0.1197 (mtp) REVERT: u 119 PHE cc_start: 0.8293 (t80) cc_final: 0.7649 (m-80) REVERT: u 164 MET cc_start: 0.1853 (mmt) cc_final: 0.1558 (mpt) REVERT: v 4 ILE cc_start: 0.8922 (mt) cc_final: 0.8697 (mm) REVERT: v 37 MET cc_start: 0.7901 (mtp) cc_final: 0.7294 (mtp) REVERT: v 38 ASP cc_start: 0.6774 (t70) cc_final: 0.6511 (t0) REVERT: v 76 ASN cc_start: 0.8139 (m-40) cc_final: 0.7919 (t0) REVERT: v 84 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7276 (ptm-80) REVERT: v 100 GLU cc_start: 0.7654 (tt0) cc_final: 0.6988 (mt-10) REVERT: v 126 GLN cc_start: 0.7850 (tt0) cc_final: 0.7457 (tt0) REVERT: v 146 LYS cc_start: 0.7304 (tttt) cc_final: 0.7028 (ttmt) REVERT: w 18 GLN cc_start: 0.8679 (mm110) cc_final: 0.8476 (mm110) REVERT: w 29 ASP cc_start: 0.8363 (t0) cc_final: 0.8097 (t0) REVERT: w 41 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7289 (t0) REVERT: w 47 GLU cc_start: 0.7436 (pp20) cc_final: 0.7198 (pp20) REVERT: w 56 ASN cc_start: 0.8068 (t0) cc_final: 0.7762 (t0) REVERT: w 71 ASP cc_start: 0.8135 (m-30) cc_final: 0.7873 (m-30) REVERT: y 8 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7132 (mm-30) REVERT: y 23 LYS cc_start: 0.8410 (mttt) cc_final: 0.8097 (mmtp) REVERT: y 32 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7633 (mt) REVERT: y 70 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7859 (ttmm) REVERT: z 15 MET cc_start: 0.6339 (mmm) cc_final: 0.6029 (mmm) REVERT: z 25 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7322 (pp20) REVERT: z 27 GLU cc_start: 0.8489 (mp0) cc_final: 0.7911 (mp0) REVERT: z 28 ILE cc_start: 0.8954 (mt) cc_final: 0.8527 (mt) REVERT: z 29 LYS cc_start: 0.8817 (pptt) cc_final: 0.8537 (pptt) REVERT: z 35 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8188 (ttm110) REVERT: z 37 ARG cc_start: 0.6378 (ptt90) cc_final: 0.5941 (ptt180) REVERT: z 45 TYR cc_start: 0.8474 (m-80) cc_final: 0.8242 (m-80) REVERT: z 47 LYS cc_start: 0.7604 (tttt) cc_final: 0.7369 (tttt) outliers start: 172 outliers final: 87 residues processed: 690 average time/residue: 1.5708 time to fit residues: 1291.8870 Evaluate side-chains 645 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 538 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 232 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 327 ARG Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 360 ASP Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 811 ILE Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1035 GLU Chi-restraints excluded: chain o residue 1103 THR Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1117 VAL Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 299 GLU Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 489 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 610 ARG Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 265 HIS Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain s residue 121 MET Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain t residue 121 ASP Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 130 ASN Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 27 LYS Chi-restraints excluded: chain w residue 41 ASN Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 1.9990 chunk 287 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 384 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 364 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 27 ASN ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN o 181 HIS o 673 GLN o 723 ASN o1093 GLN o1182 GLN o1220 HIS p 98 HIS p 117 ASN ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1115 GLN ** p1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS t 46 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36572 Z= 0.229 Angle : 0.570 10.281 49872 Z= 0.300 Chirality : 0.043 0.192 5552 Planarity : 0.004 0.049 6096 Dihedral : 16.515 177.279 5797 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 4.34 % Allowed : 16.84 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4137 helix: 1.35 (0.14), residues: 1421 sheet: 0.31 (0.20), residues: 646 loop : -0.24 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP o 679 HIS 0.005 0.001 HIS o 84 PHE 0.038 0.001 PHE u 107 TYR 0.021 0.001 TYR r 67 ARG 0.009 0.000 ARG p 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 566 time to evaluate : 4.149 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: S 105 LYS cc_start: 0.2236 (mmtm) cc_final: 0.2011 (tptp) REVERT: o 19 LYS cc_start: 0.7583 (mttp) cc_final: 0.7021 (mtpp) REVERT: o 45 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6079 (pm20) REVERT: o 67 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8031 (ttp80) REVERT: o 77 ASN cc_start: 0.7628 (t0) cc_final: 0.7240 (t0) REVERT: o 92 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7804 (mttm) REVERT: o 146 ASP cc_start: 0.8409 (m-30) cc_final: 0.7898 (p0) REVERT: o 186 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: o 194 SER cc_start: 0.8580 (t) cc_final: 0.8159 (p) REVERT: o 197 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7175 (mt-10) REVERT: o 220 ARG cc_start: 0.8126 (tpt-90) cc_final: 0.7920 (tpt-90) REVERT: o 232 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: o 234 PHE cc_start: 0.8496 (t80) cc_final: 0.8172 (t80) REVERT: o 238 MET cc_start: 0.8174 (mtm) cc_final: 0.7704 (mtt) REVERT: o 271 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.6828 (ttm-80) REVERT: o 273 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: o 286 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6929 (tp) REVERT: o 305 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7476 (tm-30) REVERT: o 325 LEU cc_start: 0.8268 (mm) cc_final: 0.8030 (mt) REVERT: o 329 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6973 (mtp) REVERT: o 347 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7150 (mm-30) REVERT: o 451 CYS cc_start: 0.6914 (m) cc_final: 0.6031 (p) REVERT: o 495 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6150 (p0) REVERT: o 500 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8055 (mt-10) REVERT: o 508 SER cc_start: 0.7488 (t) cc_final: 0.6996 (p) REVERT: o 512 ARG cc_start: 0.6398 (ttt180) cc_final: 0.6149 (ttm-80) REVERT: o 612 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.6886 (p0) REVERT: o 700 GLN cc_start: 0.7597 (tt0) cc_final: 0.6498 (tp-100) REVERT: o 775 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8046 (tppp) REVERT: o 818 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7291 (mp0) REVERT: o 861 GLN cc_start: 0.7199 (tp40) cc_final: 0.6764 (mt0) REVERT: o 868 MET cc_start: 0.7559 (ptt) cc_final: 0.7275 (ptm) REVERT: o 883 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8010 (mt) REVERT: o 921 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7381 (mmm-85) REVERT: o 936 GLU cc_start: 0.6558 (tt0) cc_final: 0.5712 (tm-30) REVERT: o 962 ASP cc_start: 0.6729 (m-30) cc_final: 0.6350 (m-30) REVERT: o 1063 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7569 (mm-30) REVERT: o 1140 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7497 (m) REVERT: o 1146 GLN cc_start: 0.8288 (pp30) cc_final: 0.7518 (pp30) REVERT: o 1210 TRP cc_start: 0.7756 (m100) cc_final: 0.7451 (m100) REVERT: o 1218 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8229 (tpp80) REVERT: o 1227 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8275 (p) REVERT: o 1247 PHE cc_start: 0.8764 (p90) cc_final: 0.8530 (p90) REVERT: o 1259 ILE cc_start: 0.8252 (mt) cc_final: 0.7973 (mm) REVERT: o 1262 MET cc_start: 0.7937 (tpp) cc_final: 0.7641 (tpp) REVERT: o 1295 ASP cc_start: 0.8439 (m-30) cc_final: 0.8103 (m-30) REVERT: o 1318 LYS cc_start: 0.6257 (mtpt) cc_final: 0.5471 (mtmm) REVERT: o 1337 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6365 (mm-30) REVERT: o 1339 ASP cc_start: 0.7111 (t0) cc_final: 0.6851 (m-30) REVERT: o 1364 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5625 (tt0) REVERT: o 1376 LYS cc_start: 0.6396 (ttmm) cc_final: 0.5798 (ttmt) REVERT: o 1388 PHE cc_start: 0.8120 (t80) cc_final: 0.7895 (t80) REVERT: o 1412 MET cc_start: 0.7405 (ttp) cc_final: 0.6864 (ttp) REVERT: o 1422 GLN cc_start: 0.7953 (mt0) cc_final: 0.6820 (mm110) REVERT: o 1423 ASP cc_start: 0.8316 (m-30) cc_final: 0.7089 (OUTLIER) REVERT: o 1472 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6233 (m-30) REVERT: p 17 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8186 (pt) REVERT: p 87 LYS cc_start: 0.8047 (tttt) cc_final: 0.7133 (tptt) REVERT: p 89 GLU cc_start: 0.7620 (tt0) cc_final: 0.7325 (mm-30) REVERT: p 169 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7771 (ttm110) REVERT: p 173 GLU cc_start: 0.8419 (tp30) cc_final: 0.8193 (tt0) REVERT: p 191 GLU cc_start: 0.8105 (mp0) cc_final: 0.7209 (mt-10) REVERT: p 220 GLU cc_start: 0.7232 (pt0) cc_final: 0.6952 (pt0) REVERT: p 265 GLN cc_start: 0.8971 (pt0) cc_final: 0.8431 (pm20) REVERT: p 278 PHE cc_start: 0.8034 (m-80) cc_final: 0.7727 (m-80) REVERT: p 281 ASP cc_start: 0.7071 (m-30) cc_final: 0.6733 (m-30) REVERT: p 299 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: p 310 VAL cc_start: 0.9213 (t) cc_final: 0.8984 (t) REVERT: p 312 GLN cc_start: 0.7472 (mp10) cc_final: 0.7159 (mp10) REVERT: p 313 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7536 (tt0) REVERT: p 335 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.7130 (ttm110) REVERT: p 337 LYS cc_start: 0.7672 (tttm) cc_final: 0.7409 (tppp) REVERT: p 386 ASP cc_start: 0.8452 (m-30) cc_final: 0.8164 (m-30) REVERT: p 407 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5971 (mpp) REVERT: p 551 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: p 578 LYS cc_start: 0.8915 (mttm) cc_final: 0.8689 (mptm) REVERT: p 606 ASP cc_start: 0.7423 (t0) cc_final: 0.7093 (t0) REVERT: p 683 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6370 (mm-40) REVERT: p 796 MET cc_start: 0.8780 (mtm) cc_final: 0.8455 (mtm) REVERT: p 841 ARG cc_start: 0.6923 (mmm-85) cc_final: 0.6617 (mmm-85) REVERT: p 930 GLN cc_start: 0.7349 (mt0) cc_final: 0.7026 (mt0) REVERT: p 1007 ASN cc_start: 0.7601 (m-40) cc_final: 0.7228 (m-40) REVERT: p 1089 MET cc_start: 0.6902 (mtp) cc_final: 0.6677 (mtp) REVERT: p 1121 LEU cc_start: 0.8661 (mm) cc_final: 0.8390 (mm) REVERT: q 27 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7131 (t0) REVERT: q 83 GLN cc_start: 0.8387 (mt0) cc_final: 0.8128 (mt0) REVERT: r 62 MET cc_start: 0.9387 (mmm) cc_final: 0.9158 (mmm) REVERT: s 26 TYR cc_start: 0.8217 (m-80) cc_final: 0.7711 (m-80) REVERT: s 121 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7734 (pmm) REVERT: s 159 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7459 (tp) REVERT: s 166 ARG cc_start: 0.6651 (mtt180) cc_final: 0.6307 (mtm110) REVERT: s 195 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7830 (ptt180) REVERT: t 80 MET cc_start: 0.7569 (mmt) cc_final: 0.7147 (mmm) REVERT: t 82 GLU cc_start: 0.7858 (pp20) cc_final: 0.6678 (pp20) REVERT: t 84 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8085 (mp0) REVERT: t 86 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6671 (mt-10) REVERT: u 1 MET cc_start: 0.8012 (tpp) cc_final: 0.7710 (tmm) REVERT: u 10 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: u 53 ASN cc_start: 0.7432 (t0) cc_final: 0.7064 (p0) REVERT: u 80 PHE cc_start: 0.8160 (m-80) cc_final: 0.7364 (m-10) REVERT: u 104 MET cc_start: 0.7662 (tpp) cc_final: 0.7097 (tpp) REVERT: u 117 MET cc_start: 0.3267 (OUTLIER) cc_final: 0.2593 (mtp) REVERT: u 119 PHE cc_start: 0.8293 (t80) cc_final: 0.7726 (m-80) REVERT: v 4 ILE cc_start: 0.8910 (mt) cc_final: 0.8684 (mm) REVERT: v 38 ASP cc_start: 0.6772 (t70) cc_final: 0.6521 (m-30) REVERT: v 76 ASN cc_start: 0.8141 (m-40) cc_final: 0.7884 (t0) REVERT: v 100 GLU cc_start: 0.7744 (tt0) cc_final: 0.6881 (mt-10) REVERT: v 126 GLN cc_start: 0.7881 (tt0) cc_final: 0.7461 (tt0) REVERT: v 146 LYS cc_start: 0.7407 (tttt) cc_final: 0.7144 (ttmt) REVERT: w 18 GLN cc_start: 0.8769 (mm110) cc_final: 0.8488 (mm110) REVERT: w 29 ASP cc_start: 0.8433 (t0) cc_final: 0.8149 (t0) REVERT: w 41 ASN cc_start: 0.7608 (t0) cc_final: 0.7181 (t0) REVERT: w 47 GLU cc_start: 0.7516 (pp20) cc_final: 0.7266 (pp20) REVERT: w 56 ASN cc_start: 0.8095 (t0) cc_final: 0.7788 (t0) REVERT: w 71 ASP cc_start: 0.8118 (m-30) cc_final: 0.7886 (m-30) REVERT: y 8 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7212 (mm-30) REVERT: y 23 LYS cc_start: 0.8421 (mttt) cc_final: 0.8033 (mmtp) REVERT: y 70 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7637 (ttmm) REVERT: y 71 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7393 (pt) REVERT: y 102 GLU cc_start: 0.7461 (tt0) cc_final: 0.7099 (tt0) REVERT: z 15 MET cc_start: 0.6373 (mmm) cc_final: 0.5985 (mmm) REVERT: z 16 ILE cc_start: 0.8312 (mp) cc_final: 0.7902 (tp) REVERT: z 25 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7213 (pp20) REVERT: z 27 GLU cc_start: 0.8478 (mp0) cc_final: 0.7937 (mp0) REVERT: z 29 LYS cc_start: 0.8961 (pptt) cc_final: 0.8671 (pptt) REVERT: z 37 ARG cc_start: 0.6436 (ptt90) cc_final: 0.5994 (ptt180) REVERT: z 45 TYR cc_start: 0.8473 (m-80) cc_final: 0.8232 (m-80) REVERT: z 47 LYS cc_start: 0.7610 (tttt) cc_final: 0.7408 (tttt) outliers start: 160 outliers final: 66 residues processed: 670 average time/residue: 1.5529 time to fit residues: 1245.1867 Evaluate side-chains 627 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 537 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 232 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 327 ARG Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 1035 GLU Chi-restraints excluded: chain o residue 1103 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1434 GLU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 299 GLU Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 489 ILE Chi-restraints excluded: chain p residue 551 GLU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 87 ILE Chi-restraints excluded: chain s residue 121 MET Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 121 ASP Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 105 SER Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 0.0570 chunk 231 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 302 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 365 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1194 ASN o1220 HIS p 98 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36572 Z= 0.266 Angle : 0.584 13.942 49872 Z= 0.305 Chirality : 0.043 0.194 5552 Planarity : 0.004 0.059 6096 Dihedral : 16.407 176.174 5796 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 4.69 % Allowed : 17.00 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4137 helix: 1.39 (0.14), residues: 1409 sheet: 0.30 (0.20), residues: 641 loop : -0.26 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP q 49 HIS 0.005 0.001 HIS S 173 PHE 0.043 0.002 PHE u 107 TYR 0.022 0.002 TYR r 67 ARG 0.010 0.001 ARG z 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 556 time to evaluate : 4.237 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: o 19 LYS cc_start: 0.7580 (mttp) cc_final: 0.7024 (mtpp) REVERT: o 45 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: o 67 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8047 (ttp80) REVERT: o 77 ASN cc_start: 0.7595 (t0) cc_final: 0.7225 (t0) REVERT: o 92 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7601 (mttm) REVERT: o 146 ASP cc_start: 0.8424 (m-30) cc_final: 0.7904 (p0) REVERT: o 186 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7459 (mtm-85) REVERT: o 187 TYR cc_start: 0.8266 (m-80) cc_final: 0.7706 (m-10) REVERT: o 192 ARG cc_start: 0.7530 (ptt90) cc_final: 0.7163 (ptm160) REVERT: o 194 SER cc_start: 0.8537 (t) cc_final: 0.8059 (p) REVERT: o 197 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7220 (mt-10) REVERT: o 232 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6754 (tt0) REVERT: o 234 PHE cc_start: 0.8476 (t80) cc_final: 0.8155 (t80) REVERT: o 238 MET cc_start: 0.8133 (mtm) cc_final: 0.7618 (mtt) REVERT: o 271 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7056 (ttm-80) REVERT: o 273 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6793 (mp10) REVERT: o 305 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7533 (tm-30) REVERT: o 329 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7085 (mtp) REVERT: o 336 LEU cc_start: 0.7311 (mm) cc_final: 0.6938 (mm) REVERT: o 347 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7083 (mm-30) REVERT: o 451 CYS cc_start: 0.6998 (m) cc_final: 0.6083 (p) REVERT: o 495 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6092 (p0) REVERT: o 500 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8054 (mt-10) REVERT: o 508 SER cc_start: 0.7651 (t) cc_final: 0.7101 (p) REVERT: o 512 ARG cc_start: 0.6407 (ttt180) cc_final: 0.6164 (ttm-80) REVERT: o 612 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6884 (p0) REVERT: o 687 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8587 (tp) REVERT: o 700 GLN cc_start: 0.7442 (tt0) cc_final: 0.7187 (mt0) REVERT: o 775 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7823 (tppp) REVERT: o 818 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7266 (mp0) REVERT: o 861 GLN cc_start: 0.7319 (tp40) cc_final: 0.6731 (mt0) REVERT: o 868 MET cc_start: 0.7570 (ptt) cc_final: 0.7286 (ptm) REVERT: o 883 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7962 (mt) REVERT: o 921 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7338 (mmm-85) REVERT: o 936 GLU cc_start: 0.6655 (tt0) cc_final: 0.5931 (tm-30) REVERT: o 960 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6451 (ttm-80) REVERT: o 962 ASP cc_start: 0.6712 (m-30) cc_final: 0.6334 (m-30) REVERT: o 1063 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7802 (mm-30) REVERT: o 1104 LEU cc_start: 0.6344 (mt) cc_final: 0.6076 (mt) REVERT: o 1140 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7489 (m) REVERT: o 1146 GLN cc_start: 0.8345 (pp30) cc_final: 0.6457 (pp30) REVERT: o 1210 TRP cc_start: 0.7617 (m100) cc_final: 0.7343 (m100) REVERT: o 1227 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8194 (m) REVERT: o 1230 GLN cc_start: 0.9268 (mt0) cc_final: 0.9035 (mt0) REVERT: o 1247 PHE cc_start: 0.8757 (p90) cc_final: 0.8545 (p90) REVERT: o 1259 ILE cc_start: 0.8231 (mt) cc_final: 0.7960 (mm) REVERT: o 1262 MET cc_start: 0.7901 (tpp) cc_final: 0.7683 (tpp) REVERT: o 1332 GLN cc_start: 0.8072 (mt0) cc_final: 0.7716 (mt0) REVERT: o 1337 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6351 (mm-30) REVERT: o 1339 ASP cc_start: 0.7002 (t0) cc_final: 0.6720 (m-30) REVERT: o 1364 GLU cc_start: 0.6294 (mm-30) cc_final: 0.5505 (tt0) REVERT: o 1376 LYS cc_start: 0.6372 (ttmm) cc_final: 0.5761 (ttmt) REVERT: o 1388 PHE cc_start: 0.8133 (t80) cc_final: 0.7913 (t80) REVERT: o 1412 MET cc_start: 0.7457 (ttp) cc_final: 0.6909 (ttp) REVERT: o 1422 GLN cc_start: 0.7952 (mt0) cc_final: 0.6874 (mm110) REVERT: o 1423 ASP cc_start: 0.8242 (m-30) cc_final: 0.7087 (OUTLIER) REVERT: o 1472 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6222 (m-30) REVERT: p 17 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8185 (pt) REVERT: p 87 LYS cc_start: 0.8016 (tttt) cc_final: 0.7096 (tptt) REVERT: p 89 GLU cc_start: 0.7630 (tt0) cc_final: 0.7327 (mm-30) REVERT: p 169 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.7981 (ttm110) REVERT: p 173 GLU cc_start: 0.8395 (tp30) cc_final: 0.8091 (tt0) REVERT: p 191 GLU cc_start: 0.8135 (mp0) cc_final: 0.7144 (mt-10) REVERT: p 220 GLU cc_start: 0.7308 (pt0) cc_final: 0.7006 (pt0) REVERT: p 265 GLN cc_start: 0.8943 (pt0) cc_final: 0.8366 (pm20) REVERT: p 278 PHE cc_start: 0.8071 (m-80) cc_final: 0.7753 (m-80) REVERT: p 309 PHE cc_start: 0.9124 (t80) cc_final: 0.8621 (t80) REVERT: p 310 VAL cc_start: 0.9236 (t) cc_final: 0.8878 (t) REVERT: p 312 GLN cc_start: 0.7477 (mp10) cc_final: 0.7132 (mp10) REVERT: p 313 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7557 (tt0) REVERT: p 335 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7097 (ttm110) REVERT: p 337 LYS cc_start: 0.7729 (tttm) cc_final: 0.7402 (tppp) REVERT: p 386 ASP cc_start: 0.8456 (m-30) cc_final: 0.8175 (m-30) REVERT: p 516 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: p 551 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: p 576 ILE cc_start: 0.8690 (pp) cc_final: 0.7925 (pp) REVERT: p 606 ASP cc_start: 0.7503 (t0) cc_final: 0.7158 (t0) REVERT: p 683 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6761 (mm-40) REVERT: p 764 MET cc_start: 0.7434 (mtt) cc_final: 0.7180 (mtt) REVERT: p 796 MET cc_start: 0.8790 (mtm) cc_final: 0.8479 (mtm) REVERT: p 841 ARG cc_start: 0.7028 (mmm-85) cc_final: 0.6819 (mmm-85) REVERT: p 930 GLN cc_start: 0.7553 (mt0) cc_final: 0.7233 (mt0) REVERT: p 1007 ASN cc_start: 0.7615 (m-40) cc_final: 0.7255 (m-40) REVERT: p 1121 LEU cc_start: 0.8649 (mm) cc_final: 0.8407 (mm) REVERT: q 27 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7123 (t0) REVERT: q 83 GLN cc_start: 0.8381 (mt0) cc_final: 0.8136 (mt0) REVERT: q 265 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.6995 (m170) REVERT: r 38 HIS cc_start: 0.7914 (t70) cc_final: 0.7491 (t70) REVERT: r 62 MET cc_start: 0.9418 (mmm) cc_final: 0.9180 (mmm) REVERT: s 26 TYR cc_start: 0.8273 (m-80) cc_final: 0.7785 (m-80) REVERT: s 121 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7735 (pmm) REVERT: s 159 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7242 (tp) REVERT: s 166 ARG cc_start: 0.6762 (mtt180) cc_final: 0.6420 (mtm110) REVERT: s 172 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7660 (mpp80) REVERT: s 195 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7943 (ptt180) REVERT: t 82 GLU cc_start: 0.7932 (pp20) cc_final: 0.7079 (pp20) REVERT: t 84 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8131 (mp0) REVERT: t 86 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6799 (mt-10) REVERT: t 95 LYS cc_start: 0.6096 (tttp) cc_final: 0.5745 (ttmm) REVERT: u 1 MET cc_start: 0.8010 (tpp) cc_final: 0.7678 (tmm) REVERT: u 10 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: u 12 LEU cc_start: 0.8701 (tp) cc_final: 0.8429 (mm) REVERT: u 53 ASN cc_start: 0.7465 (t0) cc_final: 0.7091 (p0) REVERT: u 80 PHE cc_start: 0.8172 (m-80) cc_final: 0.7369 (m-10) REVERT: u 104 MET cc_start: 0.7731 (tpp) cc_final: 0.7206 (tpp) REVERT: u 117 MET cc_start: 0.3281 (OUTLIER) cc_final: 0.2602 (mtp) REVERT: u 119 PHE cc_start: 0.8277 (t80) cc_final: 0.7865 (m-80) REVERT: u 164 MET cc_start: 0.1842 (OUTLIER) cc_final: 0.1570 (mpt) REVERT: v 4 ILE cc_start: 0.8923 (mt) cc_final: 0.8705 (mm) REVERT: v 38 ASP cc_start: 0.6726 (t70) cc_final: 0.6453 (t0) REVERT: v 76 ASN cc_start: 0.8157 (m-40) cc_final: 0.7918 (t0) REVERT: v 100 GLU cc_start: 0.7741 (tt0) cc_final: 0.6903 (tt0) REVERT: v 126 GLN cc_start: 0.7713 (tt0) cc_final: 0.7420 (tt0) REVERT: v 146 LYS cc_start: 0.7399 (tttt) cc_final: 0.7134 (ttmt) REVERT: w 18 GLN cc_start: 0.8883 (mm110) cc_final: 0.8670 (mm110) REVERT: w 24 LEU cc_start: 0.7994 (mt) cc_final: 0.7777 (mt) REVERT: w 29 ASP cc_start: 0.8459 (t0) cc_final: 0.8150 (t0) REVERT: w 40 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6919 (mtt180) REVERT: w 41 ASN cc_start: 0.8078 (t0) cc_final: 0.7820 (t0) REVERT: w 56 ASN cc_start: 0.8133 (t0) cc_final: 0.7866 (t0) REVERT: w 122 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8575 (mtm-85) REVERT: y 8 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7153 (mm-30) REVERT: y 23 LYS cc_start: 0.8422 (mttt) cc_final: 0.8037 (mmtm) REVERT: y 70 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7874 (ttmm) REVERT: y 102 GLU cc_start: 0.7464 (tt0) cc_final: 0.7119 (tt0) REVERT: z 15 MET cc_start: 0.6399 (mmm) cc_final: 0.5995 (mmm) REVERT: z 16 ILE cc_start: 0.8322 (mp) cc_final: 0.7928 (tp) REVERT: z 25 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7174 (pp20) REVERT: z 27 GLU cc_start: 0.8475 (mp0) cc_final: 0.7936 (mp0) REVERT: z 29 LYS cc_start: 0.8965 (pptt) cc_final: 0.8725 (pptt) REVERT: z 35 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8104 (ttm110) REVERT: z 37 ARG cc_start: 0.6486 (ptt90) cc_final: 0.5969 (ptt180) REVERT: z 42 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7459 (mtt90) REVERT: z 45 TYR cc_start: 0.8453 (m-80) cc_final: 0.8230 (m-80) outliers start: 173 outliers final: 82 residues processed: 671 average time/residue: 1.5376 time to fit residues: 1236.9257 Evaluate side-chains 644 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 535 time to evaluate : 4.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 232 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 693 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 811 ILE Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1103 THR Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 489 ILE Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 551 GLU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 919 CYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1069 ILE Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 265 HIS Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 121 MET Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 164 MET Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 130 ASN Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 1.9990 chunk 366 optimal weight: 40.0000 chunk 80 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 407 optimal weight: 0.5980 chunk 338 optimal weight: 0.0170 chunk 188 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 172 ASN o 673 GLN o 723 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 98 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS u 28 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36572 Z= 0.279 Angle : 0.583 10.723 49872 Z= 0.304 Chirality : 0.043 0.193 5552 Planarity : 0.004 0.060 6096 Dihedral : 16.346 175.193 5796 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 4.26 % Allowed : 17.95 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 4137 helix: 1.36 (0.14), residues: 1408 sheet: 0.28 (0.20), residues: 627 loop : -0.31 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP q 49 HIS 0.018 0.001 HIS q 265 PHE 0.042 0.002 PHE u 107 TYR 0.020 0.001 TYR r 67 ARG 0.007 0.000 ARG z 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 546 time to evaluate : 3.935 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: o 19 LYS cc_start: 0.7594 (mttp) cc_final: 0.7086 (mtpp) REVERT: o 45 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: o 67 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7981 (ttp80) REVERT: o 77 ASN cc_start: 0.7637 (t0) cc_final: 0.7263 (t0) REVERT: o 92 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7558 (mttm) REVERT: o 146 ASP cc_start: 0.8431 (m-30) cc_final: 0.7906 (p0) REVERT: o 186 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: o 187 TYR cc_start: 0.8250 (m-80) cc_final: 0.7746 (m-10) REVERT: o 192 ARG cc_start: 0.7503 (ptt90) cc_final: 0.7253 (ptm160) REVERT: o 194 SER cc_start: 0.8507 (t) cc_final: 0.8014 (p) REVERT: o 197 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7282 (mt-10) REVERT: o 232 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: o 234 PHE cc_start: 0.8500 (t80) cc_final: 0.8171 (t80) REVERT: o 238 MET cc_start: 0.8108 (mtm) cc_final: 0.7617 (mtt) REVERT: o 271 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7130 (ttm-80) REVERT: o 273 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: o 305 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7517 (tm-30) REVERT: o 325 LEU cc_start: 0.8275 (mm) cc_final: 0.8068 (mt) REVERT: o 329 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6970 (mtp) REVERT: o 347 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7082 (mm-30) REVERT: o 451 CYS cc_start: 0.7048 (m) cc_final: 0.6096 (p) REVERT: o 495 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.5975 (p0) REVERT: o 500 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7958 (mt-10) REVERT: o 508 SER cc_start: 0.7601 (t) cc_final: 0.7152 (p) REVERT: o 512 ARG cc_start: 0.6421 (ttt180) cc_final: 0.6062 (ttm170) REVERT: o 517 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7730 (mp0) REVERT: o 612 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6888 (p0) REVERT: o 687 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8565 (tp) REVERT: o 775 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7822 (tppp) REVERT: o 818 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7285 (mp0) REVERT: o 861 GLN cc_start: 0.7323 (tp40) cc_final: 0.6729 (mt0) REVERT: o 868 MET cc_start: 0.7559 (ptt) cc_final: 0.7287 (ptm) REVERT: o 883 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7957 (mt) REVERT: o 921 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7448 (mmm-85) REVERT: o 936 GLU cc_start: 0.6724 (tt0) cc_final: 0.6112 (tm-30) REVERT: o 960 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6423 (ttm-80) REVERT: o 962 ASP cc_start: 0.6710 (m-30) cc_final: 0.6332 (m-30) REVERT: o 1063 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7800 (mm-30) REVERT: o 1104 LEU cc_start: 0.6275 (mt) cc_final: 0.5885 (mt) REVERT: o 1146 GLN cc_start: 0.8958 (pp30) cc_final: 0.8163 (pp30) REVERT: o 1153 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: o 1210 TRP cc_start: 0.7541 (m100) cc_final: 0.7303 (m100) REVERT: o 1218 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7797 (mmt180) REVERT: o 1227 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8167 (p) REVERT: o 1233 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8969 (tp30) REVERT: o 1247 PHE cc_start: 0.8779 (p90) cc_final: 0.8563 (p90) REVERT: o 1259 ILE cc_start: 0.8215 (mt) cc_final: 0.7960 (mm) REVERT: o 1263 ASN cc_start: 0.5981 (OUTLIER) cc_final: 0.5648 (p0) REVERT: o 1318 LYS cc_start: 0.6349 (mtpt) cc_final: 0.5504 (mttp) REVERT: o 1337 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6380 (mm-30) REVERT: o 1339 ASP cc_start: 0.6994 (t0) cc_final: 0.6718 (m-30) REVERT: o 1364 GLU cc_start: 0.6288 (mm-30) cc_final: 0.5593 (tt0) REVERT: o 1376 LYS cc_start: 0.6347 (ttmm) cc_final: 0.5799 (ttmt) REVERT: o 1388 PHE cc_start: 0.8155 (t80) cc_final: 0.7935 (t80) REVERT: o 1412 MET cc_start: 0.7455 (ttp) cc_final: 0.6995 (ttp) REVERT: o 1422 GLN cc_start: 0.7965 (mt0) cc_final: 0.6871 (mm110) REVERT: o 1423 ASP cc_start: 0.8238 (m-30) cc_final: 0.7072 (OUTLIER) REVERT: o 1472 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: p 17 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8255 (pt) REVERT: p 87 LYS cc_start: 0.8035 (tttt) cc_final: 0.7199 (tptt) REVERT: p 89 GLU cc_start: 0.7641 (tt0) cc_final: 0.7365 (mm-30) REVERT: p 173 GLU cc_start: 0.8421 (tp30) cc_final: 0.8133 (tt0) REVERT: p 191 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: p 220 GLU cc_start: 0.7298 (pt0) cc_final: 0.6994 (pt0) REVERT: p 265 GLN cc_start: 0.8896 (pt0) cc_final: 0.8205 (pm20) REVERT: p 278 PHE cc_start: 0.8086 (m-80) cc_final: 0.7813 (m-80) REVERT: p 281 ASP cc_start: 0.7708 (m-30) cc_final: 0.7482 (m-30) REVERT: p 309 PHE cc_start: 0.9109 (t80) cc_final: 0.8589 (t80) REVERT: p 310 VAL cc_start: 0.9238 (t) cc_final: 0.8885 (t) REVERT: p 312 GLN cc_start: 0.7500 (mp10) cc_final: 0.7168 (mp10) REVERT: p 313 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7580 (tt0) REVERT: p 335 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7299 (ttm110) REVERT: p 337 LYS cc_start: 0.7766 (tttm) cc_final: 0.7432 (tppp) REVERT: p 386 ASP cc_start: 0.8462 (m-30) cc_final: 0.8182 (m-30) REVERT: p 551 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: p 576 ILE cc_start: 0.8692 (pp) cc_final: 0.7942 (pp) REVERT: p 606 ASP cc_start: 0.7593 (t0) cc_final: 0.7268 (t0) REVERT: p 683 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6986 (mm-40) REVERT: p 764 MET cc_start: 0.7427 (mtt) cc_final: 0.7205 (mtt) REVERT: p 796 MET cc_start: 0.8796 (mtm) cc_final: 0.8476 (mtm) REVERT: p 817 GLN cc_start: 0.7919 (pt0) cc_final: 0.7095 (pm20) REVERT: p 841 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.7173 (mmm-85) REVERT: p 930 GLN cc_start: 0.7522 (mt0) cc_final: 0.7197 (mt0) REVERT: p 942 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7776 (pttt) REVERT: p 1007 ASN cc_start: 0.7705 (m-40) cc_final: 0.7327 (m110) REVERT: p 1121 LEU cc_start: 0.8595 (mm) cc_final: 0.8324 (mm) REVERT: q 27 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7122 (t0) REVERT: q 83 GLN cc_start: 0.8384 (mt0) cc_final: 0.8164 (mt0) REVERT: r 38 HIS cc_start: 0.8016 (t70) cc_final: 0.7793 (t70) REVERT: s 54 ARG cc_start: 0.7815 (ptm-80) cc_final: 0.7591 (ptt90) REVERT: s 73 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: s 121 MET cc_start: 0.8234 (ptm) cc_final: 0.7707 (pmm) REVERT: s 159 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7248 (tp) REVERT: s 166 ARG cc_start: 0.6692 (mtt180) cc_final: 0.6429 (mtm110) REVERT: s 172 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7673 (mpp80) REVERT: t 82 GLU cc_start: 0.7956 (pp20) cc_final: 0.7107 (pp20) REVERT: t 84 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8157 (mp0) REVERT: t 86 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6803 (mt-10) REVERT: t 95 LYS cc_start: 0.6104 (tttp) cc_final: 0.5782 (ttmm) REVERT: u 1 MET cc_start: 0.8015 (tpp) cc_final: 0.7671 (tmm) REVERT: u 10 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7623 (mm-30) REVERT: u 12 LEU cc_start: 0.8708 (tp) cc_final: 0.8435 (mm) REVERT: u 53 ASN cc_start: 0.7468 (t0) cc_final: 0.7086 (p0) REVERT: u 80 PHE cc_start: 0.8100 (m-80) cc_final: 0.7277 (m-10) REVERT: u 104 MET cc_start: 0.7736 (tpp) cc_final: 0.7220 (tpp) REVERT: u 117 MET cc_start: 0.3168 (OUTLIER) cc_final: 0.2565 (mtp) REVERT: u 164 MET cc_start: 0.1830 (mpp) cc_final: 0.1526 (mpt) REVERT: v 4 ILE cc_start: 0.8947 (mt) cc_final: 0.8728 (mm) REVERT: v 38 ASP cc_start: 0.6703 (t70) cc_final: 0.6472 (t0) REVERT: v 76 ASN cc_start: 0.8207 (m-40) cc_final: 0.7954 (t0) REVERT: v 100 GLU cc_start: 0.7735 (tt0) cc_final: 0.6882 (tt0) REVERT: v 126 GLN cc_start: 0.7738 (tt0) cc_final: 0.7368 (tt0) REVERT: v 146 LYS cc_start: 0.7391 (tttt) cc_final: 0.7127 (ttmt) REVERT: w 18 GLN cc_start: 0.8938 (mm110) cc_final: 0.8690 (mm110) REVERT: w 24 LEU cc_start: 0.7966 (mt) cc_final: 0.7736 (mt) REVERT: w 29 ASP cc_start: 0.8558 (t0) cc_final: 0.8262 (t0) REVERT: w 40 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7139 (mtt180) REVERT: w 41 ASN cc_start: 0.8049 (t0) cc_final: 0.7791 (t0) REVERT: w 56 ASN cc_start: 0.8152 (t0) cc_final: 0.7918 (t0) REVERT: w 122 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8545 (mtm-85) REVERT: y 8 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7154 (mm-30) REVERT: y 23 LYS cc_start: 0.8414 (mttt) cc_final: 0.8042 (mmtm) REVERT: y 70 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7863 (ttmm) REVERT: y 102 GLU cc_start: 0.7480 (tt0) cc_final: 0.7145 (tt0) REVERT: z 15 MET cc_start: 0.6431 (mmm) cc_final: 0.6013 (mmm) REVERT: z 16 ILE cc_start: 0.8321 (mp) cc_final: 0.7941 (tp) REVERT: z 25 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7193 (pp20) REVERT: z 27 GLU cc_start: 0.8487 (mp0) cc_final: 0.7992 (mp0) REVERT: z 29 LYS cc_start: 0.8996 (pptt) cc_final: 0.8738 (pptt) REVERT: z 35 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8003 (ttm110) REVERT: z 37 ARG cc_start: 0.6548 (ptt90) cc_final: 0.6028 (ptt180) REVERT: z 42 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7489 (mtt90) REVERT: z 45 TYR cc_start: 0.8447 (m-80) cc_final: 0.8221 (m-80) outliers start: 157 outliers final: 98 residues processed: 655 average time/residue: 1.5681 time to fit residues: 1228.9982 Evaluate side-chains 650 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 529 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 104 MET Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain o residue 215 LEU Chi-restraints excluded: chain o residue 232 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 693 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1103 THR Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1206 ARG Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 191 GLU Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 223 SER Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 489 ILE Chi-restraints excluded: chain p residue 551 GLU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain s residue 87 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain t residue 121 ASP Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 105 SER Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 52 LYS Chi-restraints excluded: chain y residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 232 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 230 optimal weight: 0.4980 chunk 342 optimal weight: 2.9990 chunk 227 optimal weight: 0.0170 chunk 405 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 247 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 172 ASN o 62 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 700 GLN o 723 ASN ** o1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1194 ASN p 98 HIS p 144 HIS ** p 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS r 47 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 GLN z 23 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36572 Z= 0.184 Angle : 0.560 10.820 49872 Z= 0.290 Chirality : 0.042 0.186 5552 Planarity : 0.004 0.052 6096 Dihedral : 16.246 174.909 5796 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 3.93 % Allowed : 18.66 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4137 helix: 1.47 (0.14), residues: 1407 sheet: 0.37 (0.20), residues: 618 loop : -0.27 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP o 679 HIS 0.005 0.001 HIS S 173 PHE 0.043 0.001 PHE u 107 TYR 0.024 0.001 TYR r 67 ARG 0.012 0.000 ARG p 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 549 time to evaluate : 4.840 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: o 19 LYS cc_start: 0.7592 (mttp) cc_final: 0.7086 (mtpp) REVERT: o 30 GLU cc_start: 0.7140 (tt0) cc_final: 0.6554 (tt0) REVERT: o 45 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: o 67 ARG cc_start: 0.8433 (ttp80) cc_final: 0.7975 (ttp80) REVERT: o 77 ASN cc_start: 0.7636 (t0) cc_final: 0.7289 (t0) REVERT: o 92 LYS cc_start: 0.7794 (mtpp) cc_final: 0.7561 (mttm) REVERT: o 146 ASP cc_start: 0.8453 (m-30) cc_final: 0.7924 (p0) REVERT: o 147 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6611 (mp) REVERT: o 186 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: o 187 TYR cc_start: 0.8253 (m-80) cc_final: 0.7793 (m-10) REVERT: o 194 SER cc_start: 0.8493 (t) cc_final: 0.8023 (p) REVERT: o 197 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7214 (mt-10) REVERT: o 232 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: o 234 PHE cc_start: 0.8513 (t80) cc_final: 0.8170 (t80) REVERT: o 238 MET cc_start: 0.8107 (mtm) cc_final: 0.7725 (mtt) REVERT: o 271 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7159 (ttm-80) REVERT: o 273 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6714 (mp10) REVERT: o 305 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7585 (tm-30) REVERT: o 329 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7139 (mtp) REVERT: o 347 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7050 (mm-30) REVERT: o 451 CYS cc_start: 0.7067 (m) cc_final: 0.6115 (p) REVERT: o 495 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.5829 (p0) REVERT: o 500 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7603 (mt-10) REVERT: o 508 SER cc_start: 0.7720 (t) cc_final: 0.7215 (p) REVERT: o 512 ARG cc_start: 0.6337 (ttt180) cc_final: 0.6076 (ttm-80) REVERT: o 517 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7591 (mp0) REVERT: o 612 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.6895 (p0) REVERT: o 818 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7289 (mp0) REVERT: o 861 GLN cc_start: 0.7297 (tp40) cc_final: 0.6684 (mt0) REVERT: o 868 MET cc_start: 0.7570 (ptt) cc_final: 0.7234 (ptm) REVERT: o 883 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7944 (mt) REVERT: o 921 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7467 (mmm-85) REVERT: o 936 GLU cc_start: 0.6704 (tt0) cc_final: 0.6116 (tm-30) REVERT: o 960 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6397 (ttm-80) REVERT: o 962 ASP cc_start: 0.6705 (m-30) cc_final: 0.6309 (m-30) REVERT: o 1063 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7780 (mm-30) REVERT: o 1146 GLN cc_start: 0.9088 (pp30) cc_final: 0.8170 (pp30) REVERT: o 1153 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: o 1210 TRP cc_start: 0.7424 (m100) cc_final: 0.7212 (m100) REVERT: o 1227 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8190 (p) REVERT: o 1259 ILE cc_start: 0.8193 (mt) cc_final: 0.7933 (mm) REVERT: o 1309 MET cc_start: 0.8691 (ptm) cc_final: 0.8361 (ttp) REVERT: o 1318 LYS cc_start: 0.6305 (mtpt) cc_final: 0.5598 (mttp) REVERT: o 1337 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6338 (mm-30) REVERT: o 1339 ASP cc_start: 0.6991 (t0) cc_final: 0.6728 (m-30) REVERT: o 1364 GLU cc_start: 0.6244 (mm-30) cc_final: 0.5494 (tt0) REVERT: o 1376 LYS cc_start: 0.6361 (ttmm) cc_final: 0.5711 (ttmt) REVERT: o 1388 PHE cc_start: 0.8171 (t80) cc_final: 0.7952 (t80) REVERT: o 1412 MET cc_start: 0.7461 (ttp) cc_final: 0.6948 (ttp) REVERT: o 1422 GLN cc_start: 0.7973 (mt0) cc_final: 0.6849 (mm110) REVERT: o 1423 ASP cc_start: 0.8132 (m-30) cc_final: 0.6812 (t0) REVERT: o 1472 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6216 (m-30) REVERT: p 17 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8189 (pt) REVERT: p 87 LYS cc_start: 0.8021 (tttt) cc_final: 0.7192 (tptt) REVERT: p 89 GLU cc_start: 0.7637 (tt0) cc_final: 0.7319 (mm-30) REVERT: p 169 ARG cc_start: 0.8067 (mtp-110) cc_final: 0.7771 (ttm110) REVERT: p 173 GLU cc_start: 0.8406 (tp30) cc_final: 0.8126 (tt0) REVERT: p 191 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: p 220 GLU cc_start: 0.7293 (pt0) cc_final: 0.7003 (pt0) REVERT: p 265 GLN cc_start: 0.8926 (pt0) cc_final: 0.8371 (pm20) REVERT: p 278 PHE cc_start: 0.8051 (m-80) cc_final: 0.7768 (m-80) REVERT: p 281 ASP cc_start: 0.7624 (m-30) cc_final: 0.7385 (m-30) REVERT: p 309 PHE cc_start: 0.9112 (t80) cc_final: 0.8400 (t80) REVERT: p 310 VAL cc_start: 0.9254 (t) cc_final: 0.8914 (t) REVERT: p 312 GLN cc_start: 0.7444 (mp10) cc_final: 0.7155 (mp10) REVERT: p 313 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7608 (tt0) REVERT: p 335 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.7280 (ttm110) REVERT: p 337 LYS cc_start: 0.7799 (tttm) cc_final: 0.7483 (tppp) REVERT: p 346 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7112 (mm-30) REVERT: p 386 ASP cc_start: 0.8450 (m-30) cc_final: 0.8174 (m-30) REVERT: p 438 ARG cc_start: 0.6641 (mmp-170) cc_final: 0.6235 (ttp-110) REVERT: p 551 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: p 576 ILE cc_start: 0.8657 (pp) cc_final: 0.7901 (pp) REVERT: p 606 ASP cc_start: 0.7595 (t0) cc_final: 0.7259 (t0) REVERT: p 683 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6689 (mm-40) REVERT: p 796 MET cc_start: 0.8755 (mtm) cc_final: 0.8428 (mtm) REVERT: p 817 GLN cc_start: 0.7904 (pt0) cc_final: 0.7149 (pm20) REVERT: p 930 GLN cc_start: 0.7457 (mt0) cc_final: 0.6781 (mt0) REVERT: p 1007 ASN cc_start: 0.7753 (m-40) cc_final: 0.7409 (m110) REVERT: p 1121 LEU cc_start: 0.8648 (mm) cc_final: 0.8441 (mm) REVERT: q 27 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7078 (t0) REVERT: q 83 GLN cc_start: 0.8358 (mt0) cc_final: 0.8151 (mt0) REVERT: r 38 HIS cc_start: 0.8077 (t70) cc_final: 0.7607 (t70) REVERT: r 62 MET cc_start: 0.9388 (mmm) cc_final: 0.9100 (mmm) REVERT: s 121 MET cc_start: 0.8333 (ptm) cc_final: 0.7761 (pmm) REVERT: s 159 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7208 (tp) REVERT: s 166 ARG cc_start: 0.6676 (mtt180) cc_final: 0.6381 (mtm110) REVERT: s 172 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7772 (mpp80) REVERT: t 82 GLU cc_start: 0.8000 (pp20) cc_final: 0.6980 (pp20) REVERT: t 84 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8128 (mp0) REVERT: t 86 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6794 (mt-10) REVERT: t 95 LYS cc_start: 0.6108 (tttp) cc_final: 0.5805 (ttmm) REVERT: u 1 MET cc_start: 0.8033 (tpp) cc_final: 0.7610 (tmm) REVERT: u 8 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: u 10 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7636 (mm-30) REVERT: u 12 LEU cc_start: 0.8718 (tp) cc_final: 0.8446 (mm) REVERT: u 53 ASN cc_start: 0.7739 (t0) cc_final: 0.7426 (p0) REVERT: u 80 PHE cc_start: 0.8085 (m-80) cc_final: 0.7246 (m-10) REVERT: u 104 MET cc_start: 0.7720 (tpp) cc_final: 0.7294 (tpp) REVERT: u 117 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2592 (mtp) REVERT: u 164 MET cc_start: 0.2278 (OUTLIER) cc_final: 0.1899 (mpt) REVERT: v 4 ILE cc_start: 0.8895 (mt) cc_final: 0.8688 (mm) REVERT: v 38 ASP cc_start: 0.6650 (t70) cc_final: 0.6351 (t0) REVERT: v 76 ASN cc_start: 0.8208 (m-40) cc_final: 0.7948 (t0) REVERT: v 100 GLU cc_start: 0.7689 (tt0) cc_final: 0.6934 (tt0) REVERT: v 124 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7636 (ttp80) REVERT: v 126 GLN cc_start: 0.7718 (tt0) cc_final: 0.7480 (tt0) REVERT: v 146 LYS cc_start: 0.7344 (tttt) cc_final: 0.7044 (ttmt) REVERT: w 18 GLN cc_start: 0.8953 (mm110) cc_final: 0.8700 (mm110) REVERT: w 29 ASP cc_start: 0.8618 (t0) cc_final: 0.8339 (t0) REVERT: w 40 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6422 (mtm180) REVERT: w 41 ASN cc_start: 0.8031 (t0) cc_final: 0.7799 (t0) REVERT: w 122 ARG cc_start: 0.8793 (mtm-85) cc_final: 0.8552 (mtm-85) REVERT: y 8 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7328 (mm-30) REVERT: y 23 LYS cc_start: 0.8393 (mttt) cc_final: 0.8051 (mmtp) REVERT: y 70 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7645 (ttmm) REVERT: y 71 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7432 (pt) REVERT: y 102 GLU cc_start: 0.7443 (tt0) cc_final: 0.7143 (tt0) REVERT: z 15 MET cc_start: 0.6434 (mmm) cc_final: 0.6014 (mmm) REVERT: z 16 ILE cc_start: 0.8363 (mp) cc_final: 0.7981 (tp) REVERT: z 25 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7179 (pp20) REVERT: z 27 GLU cc_start: 0.8494 (mp0) cc_final: 0.7942 (mp0) REVERT: z 29 LYS cc_start: 0.8969 (pptt) cc_final: 0.8715 (pptt) REVERT: z 35 ARG cc_start: 0.8444 (ttm110) cc_final: 0.7888 (ttm110) REVERT: z 37 ARG cc_start: 0.6539 (ptt90) cc_final: 0.6063 (ptt180) REVERT: z 42 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7440 (mtt90) REVERT: z 45 TYR cc_start: 0.8449 (m-80) cc_final: 0.8238 (m-80) REVERT: z 52 LEU cc_start: 0.7677 (mm) cc_final: 0.7385 (mt) outliers start: 145 outliers final: 74 residues processed: 643 average time/residue: 1.6442 time to fit residues: 1274.5707 Evaluate side-chains 625 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 527 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 232 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 693 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1206 ARG Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 191 GLU Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 551 GLU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 265 HIS Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 87 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain t residue 121 ASP Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 164 MET Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 105 SER Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 37 optimal weight: 0.0040 chunk 318 optimal weight: 6.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 172 ASN o 62 GLN o 152 ASN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 HIS p 144 HIS ** p 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS r 47 GLN s 210 GLN u 28 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 GLN z 23 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36572 Z= 0.251 Angle : 0.582 11.574 49872 Z= 0.301 Chirality : 0.043 0.188 5552 Planarity : 0.004 0.048 6096 Dihedral : 16.185 174.385 5796 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.30 % Favored : 95.53 % Rotamer: Outliers : 3.80 % Allowed : 19.39 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4137 helix: 1.43 (0.14), residues: 1411 sheet: 0.32 (0.20), residues: 635 loop : -0.29 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 679 HIS 0.021 0.001 HIS q 265 PHE 0.043 0.001 PHE u 107 TYR 0.022 0.001 TYR r 67 ARG 0.011 0.000 ARG p 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 532 time to evaluate : 3.278 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: o 19 LYS cc_start: 0.7622 (mttp) cc_final: 0.7084 (mtpp) REVERT: o 45 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: o 67 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7977 (ttp80) REVERT: o 77 ASN cc_start: 0.7642 (t0) cc_final: 0.7279 (t0) REVERT: o 92 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7559 (mttm) REVERT: o 146 ASP cc_start: 0.8439 (m-30) cc_final: 0.7887 (p0) REVERT: o 147 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6692 (mp) REVERT: o 186 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: o 192 ARG cc_start: 0.7314 (ptm160) cc_final: 0.7039 (tmm160) REVERT: o 194 SER cc_start: 0.8504 (t) cc_final: 0.7872 (p) REVERT: o 197 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7872 (mt-10) REVERT: o 232 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: o 234 PHE cc_start: 0.8549 (t80) cc_final: 0.8216 (t80) REVERT: o 238 MET cc_start: 0.8089 (mtm) cc_final: 0.7714 (mtt) REVERT: o 271 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7645 (ttm-80) REVERT: o 273 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6765 (mp10) REVERT: o 305 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7620 (tm-30) REVERT: o 329 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7153 (mtp) REVERT: o 347 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7059 (mm-30) REVERT: o 451 CYS cc_start: 0.7086 (m) cc_final: 0.6128 (p) REVERT: o 495 ASP cc_start: 0.6325 (OUTLIER) cc_final: 0.5844 (p0) REVERT: o 500 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7648 (mt-10) REVERT: o 508 SER cc_start: 0.7673 (t) cc_final: 0.7217 (p) REVERT: o 512 ARG cc_start: 0.6356 (ttt180) cc_final: 0.6091 (ttm-80) REVERT: o 517 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7578 (mp0) REVERT: o 612 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6909 (p0) REVERT: o 818 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7288 (mp0) REVERT: o 861 GLN cc_start: 0.7304 (tp40) cc_final: 0.6702 (mt0) REVERT: o 868 MET cc_start: 0.7586 (ptt) cc_final: 0.7248 (ptm) REVERT: o 883 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7952 (mt) REVERT: o 921 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7441 (mmm-85) REVERT: o 936 GLU cc_start: 0.6738 (tt0) cc_final: 0.6102 (tm-30) REVERT: o 960 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6409 (ttm-80) REVERT: o 962 ASP cc_start: 0.6704 (m-30) cc_final: 0.6313 (m-30) REVERT: o 1063 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7776 (mm-30) REVERT: o 1104 LEU cc_start: 0.6014 (mt) cc_final: 0.5793 (mt) REVERT: o 1146 GLN cc_start: 0.9124 (pp30) cc_final: 0.8342 (pp30) REVERT: o 1227 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8141 (m) REVERT: o 1230 GLN cc_start: 0.9271 (mt0) cc_final: 0.9016 (mt0) REVERT: o 1259 ILE cc_start: 0.8228 (mt) cc_final: 0.7983 (mm) REVERT: o 1279 MET cc_start: 0.7652 (mtt) cc_final: 0.7408 (mtp) REVERT: o 1309 MET cc_start: 0.8776 (ptm) cc_final: 0.8285 (ttp) REVERT: o 1318 LYS cc_start: 0.6331 (mtpt) cc_final: 0.5573 (mtmm) REVERT: o 1337 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6334 (mm-30) REVERT: o 1364 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5491 (tt0) REVERT: o 1376 LYS cc_start: 0.6416 (ttmm) cc_final: 0.5762 (ttmt) REVERT: o 1388 PHE cc_start: 0.8134 (t80) cc_final: 0.7911 (t80) REVERT: o 1412 MET cc_start: 0.7399 (ttp) cc_final: 0.6881 (ttp) REVERT: o 1422 GLN cc_start: 0.7952 (mt0) cc_final: 0.6889 (mm110) REVERT: o 1423 ASP cc_start: 0.8132 (m-30) cc_final: 0.6973 (t0) REVERT: o 1472 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6220 (m-30) REVERT: p 17 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8220 (pt) REVERT: p 57 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6982 (ttm110) REVERT: p 61 ASP cc_start: 0.7548 (t0) cc_final: 0.7085 (m-30) REVERT: p 87 LYS cc_start: 0.7994 (tttt) cc_final: 0.7158 (tptt) REVERT: p 89 GLU cc_start: 0.7649 (tt0) cc_final: 0.7331 (mm-30) REVERT: p 169 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7991 (ttm110) REVERT: p 173 GLU cc_start: 0.8385 (tp30) cc_final: 0.8052 (tt0) REVERT: p 191 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: p 220 GLU cc_start: 0.7309 (pt0) cc_final: 0.7063 (pt0) REVERT: p 265 GLN cc_start: 0.8923 (pt0) cc_final: 0.8272 (pm20) REVERT: p 281 ASP cc_start: 0.7636 (m-30) cc_final: 0.7413 (m-30) REVERT: p 309 PHE cc_start: 0.9110 (t80) cc_final: 0.8425 (t80) REVERT: p 310 VAL cc_start: 0.9257 (t) cc_final: 0.8909 (t) REVERT: p 312 GLN cc_start: 0.7377 (mp10) cc_final: 0.7032 (mp10) REVERT: p 313 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7786 (tt0) REVERT: p 335 ARG cc_start: 0.7547 (ttp-110) cc_final: 0.7278 (ttm110) REVERT: p 337 LYS cc_start: 0.7845 (tttm) cc_final: 0.7543 (tppp) REVERT: p 346 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7208 (mm-30) REVERT: p 386 ASP cc_start: 0.8460 (m-30) cc_final: 0.8176 (m-30) REVERT: p 438 ARG cc_start: 0.6644 (mmp-170) cc_final: 0.6256 (ttp-110) REVERT: p 551 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: p 576 ILE cc_start: 0.8689 (pp) cc_final: 0.7949 (pp) REVERT: p 606 ASP cc_start: 0.7603 (t0) cc_final: 0.7286 (t0) REVERT: p 683 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6903 (mm-40) REVERT: p 796 MET cc_start: 0.8776 (mtm) cc_final: 0.8459 (mtm) REVERT: p 817 GLN cc_start: 0.7924 (pt0) cc_final: 0.7179 (pm20) REVERT: p 930 GLN cc_start: 0.7508 (mt0) cc_final: 0.7166 (mt0) REVERT: p 1007 ASN cc_start: 0.7752 (m-40) cc_final: 0.7414 (m110) REVERT: q 27 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7074 (t0) REVERT: q 83 GLN cc_start: 0.8380 (mt0) cc_final: 0.8170 (mt0) REVERT: r 38 HIS cc_start: 0.7944 (t70) cc_final: 0.7730 (t70) REVERT: r 62 MET cc_start: 0.9344 (mmm) cc_final: 0.9096 (mmm) REVERT: s 121 MET cc_start: 0.8389 (ptm) cc_final: 0.7788 (pmm) REVERT: s 159 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7222 (tp) REVERT: s 166 ARG cc_start: 0.6677 (mtt180) cc_final: 0.6394 (mtm110) REVERT: s 172 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7745 (mpp80) REVERT: t 82 GLU cc_start: 0.8004 (pp20) cc_final: 0.7182 (pp20) REVERT: t 86 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7190 (mm-30) REVERT: t 95 LYS cc_start: 0.6109 (tttp) cc_final: 0.5874 (ttmm) REVERT: u 1 MET cc_start: 0.7982 (tpp) cc_final: 0.7460 (tmm) REVERT: u 10 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7641 (mm-30) REVERT: u 12 LEU cc_start: 0.8725 (tp) cc_final: 0.8454 (mm) REVERT: u 53 ASN cc_start: 0.7746 (t0) cc_final: 0.7414 (p0) REVERT: u 80 PHE cc_start: 0.8011 (m-80) cc_final: 0.7185 (m-10) REVERT: u 104 MET cc_start: 0.7593 (tpp) cc_final: 0.7121 (tpp) REVERT: u 117 MET cc_start: 0.3204 (OUTLIER) cc_final: 0.2615 (mtp) REVERT: u 164 MET cc_start: 0.2267 (OUTLIER) cc_final: 0.1872 (mpt) REVERT: v 4 ILE cc_start: 0.8903 (mt) cc_final: 0.8695 (mm) REVERT: v 38 ASP cc_start: 0.6734 (t70) cc_final: 0.6373 (t0) REVERT: v 76 ASN cc_start: 0.8216 (m-40) cc_final: 0.7964 (t0) REVERT: v 100 GLU cc_start: 0.7696 (tt0) cc_final: 0.6946 (tt0) REVERT: v 124 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7620 (ttp80) REVERT: v 146 LYS cc_start: 0.7333 (tttt) cc_final: 0.7034 (ttmt) REVERT: w 18 GLN cc_start: 0.8920 (mm110) cc_final: 0.8675 (mm110) REVERT: w 29 ASP cc_start: 0.8626 (t0) cc_final: 0.8345 (t0) REVERT: w 40 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6288 (mtt180) REVERT: w 41 ASN cc_start: 0.8102 (t0) cc_final: 0.7815 (t0) REVERT: w 45 GLN cc_start: 0.8882 (mt0) cc_final: 0.8045 (mp10) REVERT: w 122 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8441 (mtm-85) REVERT: y 8 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7108 (mm-30) REVERT: y 23 LYS cc_start: 0.8395 (mttt) cc_final: 0.8044 (mmtp) REVERT: y 70 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7648 (ttmm) REVERT: y 71 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7437 (pt) REVERT: y 102 GLU cc_start: 0.7464 (tt0) cc_final: 0.7173 (tt0) REVERT: z 15 MET cc_start: 0.6487 (mmm) cc_final: 0.6071 (mmm) REVERT: z 16 ILE cc_start: 0.8363 (mp) cc_final: 0.7980 (tp) REVERT: z 25 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7189 (pp20) REVERT: z 27 GLU cc_start: 0.8460 (mp0) cc_final: 0.7951 (mp0) REVERT: z 29 LYS cc_start: 0.8984 (pptt) cc_final: 0.8702 (pptt) REVERT: z 35 ARG cc_start: 0.8464 (ttm110) cc_final: 0.7958 (ttm110) REVERT: z 37 ARG cc_start: 0.6561 (ptt90) cc_final: 0.6089 (ptt180) REVERT: z 42 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7451 (mtt90) REVERT: z 45 TYR cc_start: 0.8427 (m-80) cc_final: 0.8199 (m-80) outliers start: 140 outliers final: 86 residues processed: 623 average time/residue: 1.5749 time to fit residues: 1169.7372 Evaluate side-chains 627 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 518 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 104 MET Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 232 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 693 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1206 ARG Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 191 GLU Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 368 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 551 GLU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 164 MET Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 105 SER Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 10.0000 chunk 388 optimal weight: 3.9990 chunk 354 optimal weight: 0.1980 chunk 378 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 172 ASN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN o 673 GLN o 723 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 144 HIS ** p 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS s 210 GLN u 28 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 GLN z 23 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36572 Z= 0.264 Angle : 0.591 12.053 49872 Z= 0.305 Chirality : 0.043 0.190 5552 Planarity : 0.004 0.044 6096 Dihedral : 16.126 173.572 5796 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 3.90 % Allowed : 19.31 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 4137 helix: 1.38 (0.14), residues: 1409 sheet: 0.21 (0.20), residues: 665 loop : -0.30 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP o1210 HIS 0.014 0.001 HIS q 265 PHE 0.045 0.002 PHE u 107 TYR 0.024 0.002 TYR r 67 ARG 0.009 0.000 ARG p 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 528 time to evaluate : 4.107 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: o 19 LYS cc_start: 0.7679 (mttp) cc_final: 0.7121 (mtpp) REVERT: o 45 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: o 67 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7976 (ttp80) REVERT: o 77 ASN cc_start: 0.7647 (t0) cc_final: 0.7271 (t0) REVERT: o 92 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7567 (mttm) REVERT: o 146 ASP cc_start: 0.8547 (m-30) cc_final: 0.8026 (p0) REVERT: o 186 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: o 194 SER cc_start: 0.8352 (t) cc_final: 0.7902 (p) REVERT: o 196 LEU cc_start: 0.8644 (mm) cc_final: 0.8393 (mm) REVERT: o 197 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7724 (mt-10) REVERT: o 234 PHE cc_start: 0.8569 (t80) cc_final: 0.8222 (t80) REVERT: o 238 MET cc_start: 0.8079 (mtm) cc_final: 0.7697 (mtt) REVERT: o 271 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7634 (ttm-80) REVERT: o 273 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: o 305 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7627 (tm-30) REVERT: o 329 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: o 347 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7071 (mm-30) REVERT: o 451 CYS cc_start: 0.7054 (m) cc_final: 0.6073 (p) REVERT: o 495 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.5920 (p0) REVERT: o 500 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7626 (mt-10) REVERT: o 508 SER cc_start: 0.7612 (t) cc_final: 0.7147 (p) REVERT: o 517 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7559 (mp0) REVERT: o 612 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.6924 (p0) REVERT: o 687 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8562 (tp) REVERT: o 775 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8077 (tppp) REVERT: o 818 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7281 (mp0) REVERT: o 861 GLN cc_start: 0.7315 (tp40) cc_final: 0.6680 (mt0) REVERT: o 868 MET cc_start: 0.7594 (ptt) cc_final: 0.7255 (ptm) REVERT: o 883 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7866 (mt) REVERT: o 921 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7409 (mmm-85) REVERT: o 936 GLU cc_start: 0.6732 (tt0) cc_final: 0.6140 (tm-30) REVERT: o 960 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6395 (ttm-80) REVERT: o 962 ASP cc_start: 0.6701 (m-30) cc_final: 0.6310 (m-30) REVERT: o 1063 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7800 (mm-30) REVERT: o 1146 GLN cc_start: 0.9160 (pp30) cc_final: 0.8247 (pp30) REVERT: o 1153 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7788 (mmm-85) REVERT: o 1196 TYR cc_start: 0.8280 (m-80) cc_final: 0.7944 (m-80) REVERT: o 1210 TRP cc_start: 0.8036 (m100) cc_final: 0.7826 (m100) REVERT: o 1227 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8106 (m) REVERT: o 1230 GLN cc_start: 0.9282 (mt0) cc_final: 0.9016 (mt0) REVERT: o 1233 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9010 (tp30) REVERT: o 1247 PHE cc_start: 0.8922 (p90) cc_final: 0.8663 (p90) REVERT: o 1259 ILE cc_start: 0.8186 (mt) cc_final: 0.7948 (mm) REVERT: o 1279 MET cc_start: 0.7639 (mtt) cc_final: 0.7384 (mtp) REVERT: o 1309 MET cc_start: 0.8773 (ptm) cc_final: 0.8260 (ttp) REVERT: o 1318 LYS cc_start: 0.6203 (mtpt) cc_final: 0.5526 (mtmm) REVERT: o 1337 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6383 (mm-30) REVERT: o 1364 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5492 (tt0) REVERT: o 1376 LYS cc_start: 0.6393 (ttmm) cc_final: 0.5803 (ttmt) REVERT: o 1388 PHE cc_start: 0.8141 (t80) cc_final: 0.7914 (t80) REVERT: o 1412 MET cc_start: 0.7404 (ttp) cc_final: 0.6785 (ttp) REVERT: o 1422 GLN cc_start: 0.7882 (mt0) cc_final: 0.6783 (mm110) REVERT: o 1423 ASP cc_start: 0.8047 (m-30) cc_final: 0.6783 (t0) REVERT: o 1472 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6212 (m-30) REVERT: p 17 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8240 (pt) REVERT: p 61 ASP cc_start: 0.7493 (t0) cc_final: 0.7045 (m-30) REVERT: p 87 LYS cc_start: 0.7987 (tttt) cc_final: 0.7160 (tptt) REVERT: p 89 GLU cc_start: 0.7657 (tt0) cc_final: 0.7334 (mm-30) REVERT: p 169 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7996 (ttm110) REVERT: p 173 GLU cc_start: 0.8387 (tp30) cc_final: 0.8053 (tt0) REVERT: p 191 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: p 220 GLU cc_start: 0.7302 (pt0) cc_final: 0.7030 (pt0) REVERT: p 265 GLN cc_start: 0.8910 (pt0) cc_final: 0.8413 (pm20) REVERT: p 281 ASP cc_start: 0.7615 (m-30) cc_final: 0.7382 (m-30) REVERT: p 306 ASP cc_start: 0.8432 (m-30) cc_final: 0.8195 (m-30) REVERT: p 309 PHE cc_start: 0.9045 (t80) cc_final: 0.8392 (t80) REVERT: p 310 VAL cc_start: 0.9245 (t) cc_final: 0.8860 (t) REVERT: p 312 GLN cc_start: 0.7499 (mp10) cc_final: 0.7116 (mp10) REVERT: p 313 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7597 (tt0) REVERT: p 335 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7271 (ttm110) REVERT: p 337 LYS cc_start: 0.7834 (tttm) cc_final: 0.7542 (tppp) REVERT: p 346 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7259 (mm-30) REVERT: p 386 ASP cc_start: 0.8458 (m-30) cc_final: 0.8179 (m-30) REVERT: p 438 ARG cc_start: 0.6517 (mmp-170) cc_final: 0.6120 (ttp-110) REVERT: p 551 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: p 576 ILE cc_start: 0.8754 (pp) cc_final: 0.7988 (pp) REVERT: p 606 ASP cc_start: 0.7614 (t0) cc_final: 0.7312 (t0) REVERT: p 683 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7125 (mm-40) REVERT: p 796 MET cc_start: 0.8791 (mtm) cc_final: 0.8465 (mtm) REVERT: p 817 GLN cc_start: 0.7922 (pt0) cc_final: 0.7213 (pm20) REVERT: p 841 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7228 (mmm-85) REVERT: p 930 GLN cc_start: 0.7501 (mt0) cc_final: 0.7160 (mt0) REVERT: p 1007 ASN cc_start: 0.7737 (m-40) cc_final: 0.7403 (m110) REVERT: q 27 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7085 (t0) REVERT: q 83 GLN cc_start: 0.8358 (mt0) cc_final: 0.8145 (mt0) REVERT: r 62 MET cc_start: 0.9376 (mmm) cc_final: 0.9097 (mmm) REVERT: s 121 MET cc_start: 0.8418 (ptm) cc_final: 0.7817 (pmm) REVERT: s 159 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7231 (tp) REVERT: s 166 ARG cc_start: 0.6693 (mtt180) cc_final: 0.6402 (mtm110) REVERT: s 172 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6967 (mpp80) REVERT: t 82 GLU cc_start: 0.7698 (pp20) cc_final: 0.7214 (pp20) REVERT: t 84 GLU cc_start: 0.6830 (mp0) cc_final: 0.6505 (mp0) REVERT: t 86 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7124 (mm-30) REVERT: u 1 MET cc_start: 0.7998 (tpp) cc_final: 0.7499 (tmm) REVERT: u 10 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7646 (mm-30) REVERT: u 12 LEU cc_start: 0.8725 (tp) cc_final: 0.8448 (mm) REVERT: u 44 PHE cc_start: 0.8178 (m-80) cc_final: 0.7213 (m-80) REVERT: u 53 ASN cc_start: 0.7727 (t0) cc_final: 0.7375 (p0) REVERT: u 80 PHE cc_start: 0.7984 (m-80) cc_final: 0.7152 (m-10) REVERT: u 104 MET cc_start: 0.7537 (tpp) cc_final: 0.6956 (tpt) REVERT: u 117 MET cc_start: 0.3222 (OUTLIER) cc_final: 0.2635 (mtp) REVERT: u 164 MET cc_start: 0.2271 (OUTLIER) cc_final: 0.1872 (mpt) REVERT: v 4 ILE cc_start: 0.8910 (mt) cc_final: 0.8700 (mm) REVERT: v 38 ASP cc_start: 0.6763 (t70) cc_final: 0.6392 (t0) REVERT: v 76 ASN cc_start: 0.8220 (m-40) cc_final: 0.7968 (t0) REVERT: v 100 GLU cc_start: 0.7703 (tt0) cc_final: 0.6955 (tt0) REVERT: v 124 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7623 (ttp80) REVERT: v 146 LYS cc_start: 0.7334 (tttt) cc_final: 0.7035 (ttmt) REVERT: w 18 GLN cc_start: 0.8959 (mm110) cc_final: 0.8744 (mm110) REVERT: w 24 LEU cc_start: 0.8636 (mt) cc_final: 0.8314 (mt) REVERT: w 29 ASP cc_start: 0.8648 (t0) cc_final: 0.8362 (t0) REVERT: w 40 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6697 (mtt180) REVERT: w 45 GLN cc_start: 0.8883 (mt0) cc_final: 0.8032 (mp10) REVERT: w 122 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8340 (mtm-85) REVERT: x 41 LYS cc_start: 0.8421 (mttp) cc_final: 0.8085 (mmtt) REVERT: y 8 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7252 (mm-30) REVERT: y 23 LYS cc_start: 0.8380 (mttt) cc_final: 0.8021 (mmtm) REVERT: y 70 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7649 (ttmm) REVERT: y 71 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7436 (pt) REVERT: y 102 GLU cc_start: 0.7469 (tt0) cc_final: 0.7172 (tt0) REVERT: z 15 MET cc_start: 0.6418 (mmm) cc_final: 0.5989 (mmm) REVERT: z 16 ILE cc_start: 0.8363 (mp) cc_final: 0.7976 (tp) REVERT: z 25 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7192 (pp20) REVERT: z 27 GLU cc_start: 0.8463 (mp0) cc_final: 0.7984 (mp0) REVERT: z 29 LYS cc_start: 0.8975 (pptt) cc_final: 0.8694 (pptt) REVERT: z 37 ARG cc_start: 0.6628 (ptt90) cc_final: 0.6180 (ptt180) REVERT: z 42 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7500 (mtt90) outliers start: 144 outliers final: 83 residues processed: 623 average time/residue: 1.5969 time to fit residues: 1184.2506 Evaluate side-chains 621 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 514 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 104 MET Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 693 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1206 ARG Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1255 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 191 GLU Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 489 ILE Chi-restraints excluded: chain p residue 551 GLU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 268 GLN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain s residue 195 ARG Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain t residue 121 ASP Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 164 MET Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 105 SER Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.0020 chunk 399 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 419 optimal weight: 0.0470 chunk 386 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 204 optimal weight: 0.9980 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 673 GLN o 723 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 144 HIS ** p 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS r 47 GLN s 210 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 41 ASN w 74 GLN z 23 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36572 Z= 0.199 Angle : 0.583 12.438 49872 Z= 0.300 Chirality : 0.042 0.187 5552 Planarity : 0.004 0.045 6096 Dihedral : 16.054 173.271 5796 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.67 % Rotamer: Outliers : 2.90 % Allowed : 20.44 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4137 helix: 1.46 (0.14), residues: 1402 sheet: 0.27 (0.20), residues: 668 loop : -0.28 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP o1210 HIS 0.014 0.001 HIS r 38 PHE 0.042 0.001 PHE u 107 TYR 0.027 0.001 TYR r 67 ARG 0.010 0.000 ARG p 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 524 time to evaluate : 3.978 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: o 19 LYS cc_start: 0.7611 (mttp) cc_final: 0.7054 (mtpp) REVERT: o 45 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: o 67 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7973 (ttp80) REVERT: o 77 ASN cc_start: 0.7621 (t0) cc_final: 0.7270 (t0) REVERT: o 92 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7560 (mttm) REVERT: o 146 ASP cc_start: 0.8452 (m-30) cc_final: 0.7930 (p0) REVERT: o 147 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6833 (mp) REVERT: o 186 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7664 (mtm-85) REVERT: o 194 SER cc_start: 0.8430 (t) cc_final: 0.7848 (p) REVERT: o 197 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7995 (mt-10) REVERT: o 234 PHE cc_start: 0.8572 (t80) cc_final: 0.8231 (t80) REVERT: o 238 MET cc_start: 0.8135 (mtm) cc_final: 0.7728 (mtt) REVERT: o 271 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7636 (ttm-80) REVERT: o 273 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: o 305 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7608 (tm-30) REVERT: o 329 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7146 (mtp) REVERT: o 347 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7051 (mm-30) REVERT: o 451 CYS cc_start: 0.7080 (m) cc_final: 0.6091 (p) REVERT: o 495 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.5850 (p0) REVERT: o 500 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7478 (mt-10) REVERT: o 508 SER cc_start: 0.7657 (t) cc_final: 0.7193 (p) REVERT: o 612 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.6935 (p0) REVERT: o 687 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8563 (tp) REVERT: o 775 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8121 (tppp) REVERT: o 818 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7277 (mp0) REVERT: o 861 GLN cc_start: 0.7305 (tp40) cc_final: 0.6685 (mt0) REVERT: o 868 MET cc_start: 0.7554 (ptt) cc_final: 0.7247 (ptm) REVERT: o 883 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7848 (mt) REVERT: o 921 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7282 (mmm-85) REVERT: o 936 GLU cc_start: 0.6715 (tt0) cc_final: 0.6138 (tm-30) REVERT: o 960 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6408 (ttm-80) REVERT: o 962 ASP cc_start: 0.6695 (m-30) cc_final: 0.6297 (m-30) REVERT: o 1063 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7789 (mm-30) REVERT: o 1146 GLN cc_start: 0.9187 (pp30) cc_final: 0.8394 (pp30) REVERT: o 1153 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7804 (mmm-85) REVERT: o 1196 TYR cc_start: 0.8242 (m-80) cc_final: 0.7886 (m-80) REVERT: o 1227 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8079 (m) REVERT: o 1230 GLN cc_start: 0.9286 (mt0) cc_final: 0.9040 (mt0) REVERT: o 1247 PHE cc_start: 0.8894 (p90) cc_final: 0.8623 (p90) REVERT: o 1259 ILE cc_start: 0.8196 (mt) cc_final: 0.7957 (mm) REVERT: o 1279 MET cc_start: 0.7494 (mtt) cc_final: 0.7280 (mtp) REVERT: o 1309 MET cc_start: 0.8708 (ptm) cc_final: 0.8231 (ttp) REVERT: o 1337 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6324 (mm-30) REVERT: o 1364 GLU cc_start: 0.6237 (mm-30) cc_final: 0.5469 (tt0) REVERT: o 1376 LYS cc_start: 0.6371 (ttmm) cc_final: 0.5723 (ttmt) REVERT: o 1388 PHE cc_start: 0.8141 (t80) cc_final: 0.7915 (t80) REVERT: o 1412 MET cc_start: 0.7412 (ttp) cc_final: 0.6946 (ttp) REVERT: o 1422 GLN cc_start: 0.7882 (mt0) cc_final: 0.6774 (mm110) REVERT: o 1423 ASP cc_start: 0.8025 (m-30) cc_final: 0.6775 (t0) REVERT: o 1472 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6188 (m-30) REVERT: p 17 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8190 (pt) REVERT: p 61 ASP cc_start: 0.7489 (t0) cc_final: 0.7024 (m-30) REVERT: p 87 LYS cc_start: 0.8017 (tttt) cc_final: 0.7194 (tptt) REVERT: p 89 GLU cc_start: 0.7656 (tt0) cc_final: 0.7307 (mm-30) REVERT: p 169 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.7993 (ttm110) REVERT: p 173 GLU cc_start: 0.8413 (tp30) cc_final: 0.8129 (tt0) REVERT: p 191 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: p 220 GLU cc_start: 0.7365 (pt0) cc_final: 0.7120 (pt0) REVERT: p 265 GLN cc_start: 0.8888 (pt0) cc_final: 0.8382 (pm20) REVERT: p 281 ASP cc_start: 0.7601 (m-30) cc_final: 0.7368 (m-30) REVERT: p 309 PHE cc_start: 0.8985 (t80) cc_final: 0.8391 (t80) REVERT: p 310 VAL cc_start: 0.9249 (t) cc_final: 0.8869 (t) REVERT: p 312 GLN cc_start: 0.7640 (mp10) cc_final: 0.7190 (mp10) REVERT: p 313 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7735 (tt0) REVERT: p 335 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7263 (ttm110) REVERT: p 337 LYS cc_start: 0.7805 (tttm) cc_final: 0.7550 (tppp) REVERT: p 346 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7138 (mm-30) REVERT: p 386 ASP cc_start: 0.8454 (m-30) cc_final: 0.8158 (m-30) REVERT: p 438 ARG cc_start: 0.6509 (mmp-170) cc_final: 0.6165 (ttp80) REVERT: p 606 ASP cc_start: 0.7613 (t0) cc_final: 0.7310 (t0) REVERT: p 683 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7114 (mm-40) REVERT: p 796 MET cc_start: 0.8771 (mtm) cc_final: 0.8453 (mtm) REVERT: p 817 GLN cc_start: 0.7835 (pt0) cc_final: 0.7172 (pm20) REVERT: p 841 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7385 (mmm-85) REVERT: p 930 GLN cc_start: 0.7450 (mt0) cc_final: 0.7103 (mt0) REVERT: p 942 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8157 (pttp) REVERT: p 1007 ASN cc_start: 0.7703 (m-40) cc_final: 0.7389 (m110) REVERT: q 27 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7051 (t0) REVERT: q 83 GLN cc_start: 0.8338 (mt0) cc_final: 0.8133 (mt0) REVERT: r 62 MET cc_start: 0.9397 (mmm) cc_final: 0.9135 (mmm) REVERT: s 121 MET cc_start: 0.8442 (ptm) cc_final: 0.7909 (pmm) REVERT: s 159 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7212 (tp) REVERT: s 166 ARG cc_start: 0.6777 (mtt180) cc_final: 0.6436 (mtm110) REVERT: s 172 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7766 (mpp80) REVERT: t 82 GLU cc_start: 0.7860 (pp20) cc_final: 0.7216 (pp20) REVERT: t 84 GLU cc_start: 0.7232 (mp0) cc_final: 0.6527 (mp0) REVERT: t 86 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7153 (mm-30) REVERT: u 1 MET cc_start: 0.7996 (tpp) cc_final: 0.7478 (tmm) REVERT: u 10 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7644 (mm-30) REVERT: u 12 LEU cc_start: 0.8726 (tp) cc_final: 0.8452 (mm) REVERT: u 44 PHE cc_start: 0.8169 (m-80) cc_final: 0.7256 (m-80) REVERT: u 53 ASN cc_start: 0.7725 (t0) cc_final: 0.7385 (p0) REVERT: u 80 PHE cc_start: 0.7973 (m-80) cc_final: 0.7128 (m-10) REVERT: u 117 MET cc_start: 0.3226 (OUTLIER) cc_final: 0.2650 (mtp) REVERT: u 164 MET cc_start: 0.2260 (OUTLIER) cc_final: 0.1862 (mpt) REVERT: v 4 ILE cc_start: 0.8938 (mt) cc_final: 0.8737 (mm) REVERT: v 38 ASP cc_start: 0.6741 (t70) cc_final: 0.6385 (t0) REVERT: v 76 ASN cc_start: 0.8216 (m-40) cc_final: 0.7960 (t0) REVERT: v 100 GLU cc_start: 0.7694 (tt0) cc_final: 0.6942 (tt0) REVERT: v 124 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7734 (ttp80) REVERT: v 146 LYS cc_start: 0.7341 (tttt) cc_final: 0.7053 (ttmt) REVERT: w 18 GLN cc_start: 0.8943 (mm110) cc_final: 0.8742 (mm110) REVERT: w 29 ASP cc_start: 0.8634 (t0) cc_final: 0.8337 (t0) REVERT: w 40 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6664 (mtt180) REVERT: w 45 GLN cc_start: 0.8916 (mt0) cc_final: 0.8058 (mp10) REVERT: w 122 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8326 (mtm-85) REVERT: x 41 LYS cc_start: 0.8344 (mttp) cc_final: 0.8042 (mmtt) REVERT: y 8 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7164 (mm-30) REVERT: y 23 LYS cc_start: 0.8349 (mttt) cc_final: 0.8016 (mmtm) REVERT: y 70 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7633 (ttmm) REVERT: y 71 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7437 (pt) REVERT: y 102 GLU cc_start: 0.7448 (tt0) cc_final: 0.7191 (tt0) REVERT: z 15 MET cc_start: 0.6483 (mmm) cc_final: 0.6138 (mmm) REVERT: z 16 ILE cc_start: 0.8350 (mp) cc_final: 0.7983 (tp) REVERT: z 25 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7170 (pp20) REVERT: z 27 GLU cc_start: 0.8438 (mp0) cc_final: 0.7944 (mp0) REVERT: z 29 LYS cc_start: 0.8977 (pptt) cc_final: 0.8691 (pptt) REVERT: z 37 ARG cc_start: 0.6620 (ptt90) cc_final: 0.6168 (ptt180) REVERT: z 42 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7503 (mtt90) outliers start: 107 outliers final: 68 residues processed: 592 average time/residue: 1.6251 time to fit residues: 1147.0830 Evaluate side-chains 598 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 506 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 273 GLN Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 693 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 921 ARG Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1206 ARG Chi-restraints excluded: chain o residue 1227 THR Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1305 SER Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 191 GLU Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 265 HIS Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain u residue 117 MET Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 164 MET Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 1.9990 chunk 355 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 334 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 673 GLN o 723 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 144 HIS ** p 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS s 210 GLN u 28 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 GLN z 23 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099610 restraints weight = 48196.535| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.25 r_work: 0.3170 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36572 Z= 0.329 Angle : 0.625 12.327 49872 Z= 0.321 Chirality : 0.044 0.199 5552 Planarity : 0.004 0.058 6096 Dihedral : 16.027 172.622 5796 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.33 % Rotamer: Outliers : 3.09 % Allowed : 20.34 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4137 helix: 1.34 (0.14), residues: 1402 sheet: 0.16 (0.20), residues: 665 loop : -0.35 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP o1210 HIS 0.040 0.001 HIS q 265 PHE 0.041 0.002 PHE u 107 TYR 0.028 0.002 TYR r 67 ARG 0.016 0.001 ARG z 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18970.19 seconds wall clock time: 333 minutes 42.16 seconds (20022.16 seconds total)