Starting phenix.real_space_refine on Thu Feb 22 14:15:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of4_12869/02_2024/7of4_12869_updated.pdb" } resolution = 2.7 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= -0.000 sd= 0.002 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 3 6.06 5 P 1528 5.49 5 Mg 89 5.21 5 S 282 5.16 5 C 57795 2.51 5 N 18272 2.21 5 O 22353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 100322 Number of models: 1 Model: "" Number of chains: 60 Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 333 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "5" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3199 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 359} Chain: "6" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2723 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 651 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 31075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1463, 31075 Classifications: {'RNA': 1463} Modifications used: {'rna2p_pur': 159, 'rna2p_pyr': 118, 'rna3p': 3, 'rna3p_pur': 612, 'rna3p_pyr': 571} Link IDs: {'rna2p': 276, 'rna3p': 1186} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "C" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3313 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 19, 'TRANS': 402} Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1842 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain: "E" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2405 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 24, 'TRANS': 280} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1568 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 16, 'TRANS': 174} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1731 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 18, 'TRANS': 189} Chain breaks: 4 Chain: "e" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1599 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 2 Chain: "f" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 834 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1011 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 14, 'TRANS': 105} Chain: "r" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} Chain breaks: 1 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 150 Unusual residues: {' MG': 86, 'GTP': 2} Classifications: {'undetermined': 88} Link IDs: {None: 87} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" 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 264 SG CYS 0 110 134.114 40.289 126.578 1.00 77.59 S ATOM 286 SG CYS 0 113 137.456 41.568 125.081 1.00 80.23 S ATOM 366 SG CYS 0 123 134.464 43.428 124.497 1.00 74.20 S ATOM 389 SG CYS 0 126 134.802 39.895 122.872 1.00 77.99 S ATOM 2605 SG CYS 4 76 57.357 110.883 167.656 1.00 79.21 S ATOM 2628 SG CYS 4 79 61.075 110.130 167.391 1.00 76.05 S ATOM 2752 SG CYS 4 92 58.438 107.373 166.863 1.00 74.81 S ATOM 55608 SG CYS I 64 80.949 114.322 198.619 1.00 81.20 S ATOM 96084 SG CYS r 70 80.393 110.355 198.853 1.00 77.09 S ATOM 96105 SG CYS r 73 83.539 112.193 198.610 1.00 77.80 S ATOM 96399 SG CYS r 108 80.616 112.000 195.604 1.00 77.11 S Time building chain proxies: 38.64, per 1000 atoms: 0.39 Number of scatterers: 100322 At special positions: 0 Unit cell: (225.75, 238.35, 228.9, 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 3 29.99 S 282 16.00 P 1528 15.00 Mg 89 11.99 O 22353 8.00 N 18272 7.00 C 57795 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=0, symmetry=0 Time building additional restraints: 38.33 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " Number of angles added : 15 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 273 helices and 79 sheets defined 41.7% alpha, 14.3% beta 405 base pairs and 746 stacking pairs defined. Time for finding SS restraints: 59.45 Creating SS restraints... Processing helix chain '0' and resid 86 through 96 Processing helix chain '0' and resid 123 through 146 Processing helix chain '0' and resid 166 through 171 removed outlier: 5.598A pdb=" N GLY 0 171 " --> pdb=" O GLU 0 167 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 73 removed outlier: 3.909A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Proline residue: 2 73 - end of helix Processing helix chain '2' and resid 74 through 86 Processing helix chain '3' and resid 107 through 114 removed outlier: 3.620A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.681A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 146 removed outlier: 3.911A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.821A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 3.646A pdb=" N HIS 3 181 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 177 through 182' Processing helix chain '5' and resid 35 through 40 removed outlier: 5.104A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 3.780A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) Proline residue: 5 53 - end of helix Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.036A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 4.208A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 4.066A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 4.943A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.048A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.298A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 78 removed outlier: 3.759A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 5.319A pdb=" N VAL 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 118 through 126 Processing helix chain '6' and resid 131 through 143 Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 308 Processing helix chain '6' and resid 324 through 333 Processing helix chain '6' and resid 362 through 370 removed outlier: 4.924A pdb=" N LEU 6 366 " --> pdb=" O PRO 6 362 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 3.889A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 4.056A pdb=" N THR 7 59 " --> pdb=" O GLN 7 55 " (cutoff:3.500A) Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.928A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 3.897A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU 7 191 " --> pdb=" O SER 7 187 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 186 through 191' Processing helix chain '7' and resid 195 through 213 Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 248 Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 4.129A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 4.865A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 155 through 164 removed outlier: 4.943A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 removed outlier: 3.758A pdb=" N LEU 8 168 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE 8 169 " --> pdb=" O PRO 8 166 " (cutoff:3.500A) Proline residue: 8 170 - end of helix No H-bonds generated for 'chain '8' and resid 165 through 170' Processing helix chain '9' and resid 27 through 35 removed outlier: 5.671A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.542A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 97 through 106 Processing helix chain '9' and resid 113 through 118 removed outlier: 4.650A pdb=" N TYR 9 117 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 Processing helix chain 'C' and resid 154 through 169 Proline residue: C 169 - end of helix Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 214 through 229 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 232 through 242 removed outlier: 4.639A pdb=" N HIS C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 290 removed outlier: 4.345A pdb=" N GLN C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.139A pdb=" N ILE C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 366 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 404 Processing helix chain 'C' and resid 406 through 413 removed outlier: 4.498A pdb=" N SER C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.636A pdb=" N VAL C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Proline residue: C 424 - end of helix No H-bonds generated for 'chain 'C' and resid 419 through 424' Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 473 through 482 Processing helix chain 'C' and resid 503 through 515 Proline residue: C 515 - end of helix Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.656A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.610A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.629A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.831A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.350A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.568A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 109 removed outlier: 4.815A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.262A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.591A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.788A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.057A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.878A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.640A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 85 through 90 removed outlier: 3.991A pdb=" N ARG H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Proline residue: H 90 - end of helix No H-bonds generated for 'chain 'H' and resid 85 through 90' Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 133 through 147 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.547A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.929A pdb=" N LEU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Proline residue: I 66 - end of helix No H-bonds generated for 'chain 'I' and resid 61 through 66' Processing helix chain 'I' and resid 77 through 93 Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.786A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix removed outlier: 4.302A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.659A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 33 through 43 Proline residue: J 37 - end of helix removed outlier: 3.884A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.270A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.834A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.999A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.004A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.936A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 154 through 159 removed outlier: 5.542A pdb=" N THR K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 167 Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 124 through 131 removed outlier: 4.552A pdb=" N ARG L 128 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 124 through 131' Processing helix chain 'L' and resid 134 through 142 removed outlier: 5.303A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 20 Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.683A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.605A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.593A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 3.572A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.814A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.070A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 Processing helix chain 'N' and resid 68 through 74 removed outlier: 4.732A pdb=" N ILE N 72 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 183 removed outlier: 3.931A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.536A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.348A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.370A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 4.984A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.335A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.909A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 117 removed outlier: 4.560A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 156 through 169 Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.126A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 107 removed outlier: 3.835A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 194 removed outlier: 4.679A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.578A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.738A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.336A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 290 Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.837A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.545A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 80 removed outlier: 4.398A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 4.649A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.689A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.900A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.624A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.129A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.602A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 116 through 121 removed outlier: 4.704A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 120 Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.842A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 25 Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 35 removed outlier: 5.597A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 3.970A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 Processing helix chain 'X' and resid 197 through 204 removed outlier: 3.734A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.695A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.634A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 5.677A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.740A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.586A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.737A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 removed outlier: 4.985A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.384A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.428A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 48' Processing helix chain 'Z' and resid 49 through 57 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 Processing helix chain 'a' and resid 68 through 73 removed outlier: 4.093A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS a 73 " --> pdb=" O TYR a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.677A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 119 through 124' Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.578A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 50 removed outlier: 3.652A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.422A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.881A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 Processing helix chain 'c' and resid 84 through 94 removed outlier: 5.326A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.700A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.897A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 48 through 54 removed outlier: 4.378A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 130 Processing helix chain 'd' and resid 133 through 155 Proline residue: d 138 - end of helix Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.589A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 5.123A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.565A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 removed outlier: 4.660A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS e 143 " --> pdb=" O GLU e 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 138 through 143' Processing helix chain 'e' and resid 183 through 197 removed outlier: 4.089A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER e 196 " --> pdb=" O LEU e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.517A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.612A pdb=" N LEU f 178 " --> pdb=" O ILE f 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.461A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 65 through 78 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.177A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 133 Proline residue: h 133 - end of helix Processing helix chain 'h' and resid 138 through 147 removed outlier: 4.554A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 4.109A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 removed outlier: 3.956A pdb=" N ARG j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 107 Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.577A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.515A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'l' and resid 114 through 135 removed outlier: 4.527A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 51 removed outlier: 4.109A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.836A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.070A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 72 through 77 removed outlier: 4.933A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 124 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 174 through 190 removed outlier: 4.061A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.019A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 64 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.342A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 144 Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 70 through 76 Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.483A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 Processing helix chain 'r' and resid 178 through 183 removed outlier: 3.931A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 's' and resid 55 through 74 removed outlier: 5.474A pdb=" N GLU s 74 " --> pdb=" O VAL s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.683A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 155 Processing helix chain 's' and resid 164 through 193 removed outlier: 4.323A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 267 through 272 removed outlier: 4.332A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 Processing helix chain 's' and resid 318 through 344 removed outlier: 4.301A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.238A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 Processing sheet with id= 1, first strand: chain '0' and resid 155 through 159 Processing sheet with id= 2, first strand: chain '1' and resid 17 through 22 removed outlier: 5.854A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 41 through 46 removed outlier: 5.958A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 122 through 125 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain '4' and resid 66 through 69 removed outlier: 6.894A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '5' and resid 126 through 130 removed outlier: 5.217A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '5' and resid 208 through 214 removed outlier: 4.672A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '5' and resid 230 through 233 removed outlier: 6.536A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '5' and resid 350 through 353 removed outlier: 8.527A pdb=" N ARG 5 350 " --> pdb=" O LEU 5 382 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '6' and resid 183 through 187 removed outlier: 4.619A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS 6 174 " --> pdb=" O THR 6 205 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '6' and resid 231 through 234 removed outlier: 6.610A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 310 through 314 removed outlier: 8.288A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 213 through 221 removed outlier: 5.071A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '7' and resid 77 through 82 removed outlier: 4.604A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '7' and resid 164 through 167 removed outlier: 6.987A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 217 through 221 removed outlier: 4.734A pdb=" N LYS 7 253 " --> pdb=" O SER 7 264 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 281 through 286 removed outlier: 5.405A pdb=" N ILE 7 294 " --> pdb=" O LEU 7 286 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '9' and resid 42 through 45 removed outlier: 3.666A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 133 through 136 removed outlier: 4.364A pdb=" N GLN C 96 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER C 135 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 138 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS C 106 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 332 through 339 removed outlier: 3.645A pdb=" N THR C 333 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 350 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY C 301 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 463 through 468 removed outlier: 3.550A pdb=" N GLU C 486 " --> pdb=" O ARG C 499 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 97 through 102 Processing sheet with id= 23, first strand: chain 'D' and resid 128 through 131 removed outlier: 3.828A pdb=" N GLN D 128 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 190 through 194 removed outlier: 4.078A pdb=" N THR D 191 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.297A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 27, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.755A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 175 through 181 removed outlier: 3.512A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 265 through 269 removed outlier: 4.395A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 31, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 32, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.037A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 34, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.126A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'J' and resid 18 through 25 removed outlier: 3.570A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.236A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 77 through 81 removed outlier: 7.315A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 39, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 40, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 41, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 42, first strand: chain 'N' and resid 93 through 97 removed outlier: 6.124A pdb=" N GLY N 93 " --> pdb=" O ALA N 156 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA N 156 " --> pdb=" O GLY N 93 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.569A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 41 through 44 removed outlier: 4.254A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'P' and resid 80 through 85 Processing sheet with id= 46, first strand: chain 'Q' and resid 129 through 135 removed outlier: 4.426A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Q' and resid 139 through 142 removed outlier: 3.824A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 49, first strand: chain 'S' and resid 112 through 117 removed outlier: 3.939A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 51, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.098A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.959A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.350A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.954A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 132 through 135 removed outlier: 7.341A pdb=" N GLU V 132 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG V 152 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 81 through 84 removed outlier: 4.531A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 97 through 103 Processing sheet with id= 59, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.163A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.075A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 62, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.221A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'a' and resid 44 through 52 removed outlier: 5.521A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL a 65 " --> pdb=" O ASN a 44 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'b' and resid 61 through 68 removed outlier: 4.198A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 66, first strand: chain 'c' and resid 269 through 275 removed outlier: 3.813A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'd' and resid 212 through 218 removed outlier: 3.867A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 175 through 178 removed outlier: 3.859A pdb=" N TRP e 178 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.059A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 44 through 55 removed outlier: 3.733A pdb=" N LYS e 230 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU e 48 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE e 232 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA e 236 " --> pdb=" O CYS e 52 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.805A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR f 125 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS f 94 " --> pdb=" O SER f 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER f 185 " --> pdb=" O HIS f 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR f 96 " --> pdb=" O ARG f 183 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG f 183 " --> pdb=" O THR f 96 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.418A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'k' and resid 51 through 56 removed outlier: 4.155A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'm' and resid 53 through 56 Processing sheet with id= 75, first strand: chain 'p' and resid 78 through 82 Processing sheet with id= 76, first strand: chain 'r' and resid 35 through 42 removed outlier: 4.264A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 's' and resid 90 through 93 Processing sheet with id= 78, first strand: chain 's' and resid 112 through 116 removed outlier: 6.242A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 's' and resid 241 through 244 removed outlier: 6.615A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) 2680 hydrogen bonds defined for protein. 7950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 990 hydrogen bonds 1678 hydrogen bond angles 0 basepair planarities 405 basepair parallelities 746 stacking parallelities Total time for adding SS restraints: 80.37 Time building geometry restraints manager: 41.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 24755 1.33 - 1.46: 30811 1.46 - 1.58: 46647 1.58 - 1.70: 3035 1.70 - 1.83: 445 Bond restraints: 105693 Sorted by residual: bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.489 1.332 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" N3 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 1.492 1.349 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 1.492 1.350 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N3 OMU A3039 " pdb=" C4 OMU A3039 " ideal model delta sigma weight residual 1.455 1.330 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C2 OMG A3040 " pdb=" N3 OMG A3040 " ideal model delta sigma weight residual 1.466 1.343 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 105688 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.11: 10569 106.11 - 113.59: 60827 113.59 - 121.07: 50102 121.07 - 128.55: 26146 128.55 - 136.03: 2546 Bond angle restraints: 150190 Sorted by residual: angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 108.29 125.54 -17.25 3.00e+00 1.11e-01 3.31e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C8 OMG A2815 " ideal model delta sigma weight residual 142.82 126.00 16.82 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C8 OMG A3040 " ideal model delta sigma weight residual 142.82 128.06 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 108.29 122.67 -14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" PA GTP A3387 " pdb=" O3A GTP A3387 " pdb=" PB GTP A3387 " ideal model delta sigma weight residual 120.50 133.21 -12.71 3.00e+00 1.11e-01 1.80e+01 ... (remaining 150185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 61215 35.77 - 71.54: 3463 71.54 - 107.31: 500 107.31 - 143.09: 26 143.09 - 178.86: 38 Dihedral angle restraints: 65242 sinusoidal: 41027 harmonic: 24215 Sorted by residual: dihedral pdb=" O4' C A3170 " pdb=" C1' C A3170 " pdb=" N1 C A3170 " pdb=" C2 C A3170 " ideal model delta sinusoidal sigma weight residual -160.00 18.22 -178.22 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual -160.00 17.73 -177.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1689 " pdb=" C1' C A1689 " pdb=" N1 C A1689 " pdb=" C2 C A1689 " ideal model delta sinusoidal sigma weight residual 200.00 24.90 175.10 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 65239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 15923 0.059 - 0.118: 1530 0.118 - 0.177: 179 0.177 - 0.235: 8 0.235 - 0.294: 3 Chirality restraints: 17643 Sorted by residual: chirality pdb=" P G A3036 " pdb=" OP1 G A3036 " pdb=" OP2 G A3036 " pdb=" O5' G A3036 " both_signs ideal model delta sigma weight residual True 2.41 -2.70 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' A A2693 " pdb=" C4' A A2693 " pdb=" O3' A A2693 " pdb=" C2' A A2693 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3* GTP A3387 " pdb=" C2* GTP A3387 " pdb=" C4* GTP A3387 " pdb=" O3* GTP A3387 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 17640 not shown) Planarity restraints: 13626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " 0.026 2.00e-02 2.50e+03 5.61e-01 7.09e+03 pdb=" C4' OMG A3040 " 0.441 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.598 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.555 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.194 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.881 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.256 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.867 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2815 " 0.052 2.00e-02 2.50e+03 5.60e-01 7.06e+03 pdb=" C4' OMG A2815 " 0.420 2.00e-02 2.50e+03 pdb=" O4' OMG A2815 " 0.550 2.00e-02 2.50e+03 pdb=" C3' OMG A2815 " -0.597 2.00e-02 2.50e+03 pdb=" O3' OMG A2815 " -0.574 2.00e-02 2.50e+03 pdb=" C2' OMG A2815 " -0.198 2.00e-02 2.50e+03 pdb=" O2' OMG A2815 " 0.937 2.00e-02 2.50e+03 pdb=" C1' OMG A2815 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG A2815 " -0.827 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMU A3039 " -0.037 2.00e-02 2.50e+03 5.33e-01 6.40e+03 pdb=" C4' OMU A3039 " 0.432 2.00e-02 2.50e+03 pdb=" O4' OMU A3039 " 0.606 2.00e-02 2.50e+03 pdb=" C3' OMU A3039 " -0.569 2.00e-02 2.50e+03 pdb=" O3' OMU A3039 " -0.454 2.00e-02 2.50e+03 pdb=" C2' OMU A3039 " -0.225 2.00e-02 2.50e+03 pdb=" O2' OMU A3039 " 0.818 2.00e-02 2.50e+03 pdb=" C1' OMU A3039 " 0.259 2.00e-02 2.50e+03 pdb=" N1 OMU A3039 " -0.830 2.00e-02 2.50e+03 ... (remaining 13623 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 385 2.38 - 3.01: 57429 3.01 - 3.64: 169037 3.64 - 4.27: 272559 4.27 - 4.90: 410382 Nonbonded interactions: 909792 Sorted by model distance: nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3314 " model vdw 1.751 2.170 nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3314 " model vdw 1.796 2.170 nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3338 " model vdw 1.820 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3338 " model vdw 1.821 2.170 nonbonded pdb=" O3G GTP C 601 " pdb="MG MG C 602 " model vdw 1.825 2.170 ... (remaining 909787 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 13.030 Check model and map are aligned: 1.140 Set scattering table: 0.700 Process input model: 316.110 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.280 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 348.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 105693 Z= 0.269 Angle : 0.546 17.249 150190 Z= 0.278 Chirality : 0.038 0.294 17643 Planarity : 0.009 0.561 13626 Dihedral : 19.420 178.857 49562 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.20 (0.09), residues: 8170 helix: 1.97 (0.10), residues: 2828 sheet: -0.44 (0.15), residues: 1058 loop : 0.45 (0.10), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP h 156 HIS 0.015 0.001 HIS S 76 PHE 0.017 0.001 PHE F 106 TYR 0.021 0.001 TYR F 280 ARG 0.014 0.000 ARG I 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1487 time to evaluate : 7.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 178 ASP cc_start: 0.8296 (t0) cc_final: 0.8064 (t0) REVERT: 1 26 THR cc_start: 0.9015 (m) cc_final: 0.8749 (p) REVERT: 6 274 LYS cc_start: 0.8629 (tttm) cc_final: 0.8379 (mtpm) REVERT: 6 330 ILE cc_start: 0.9499 (mt) cc_final: 0.9261 (mt) REVERT: 7 49 ASN cc_start: 0.9214 (m-40) cc_final: 0.9004 (m110) REVERT: 7 231 GLN cc_start: 0.8479 (pm20) cc_final: 0.7374 (pm20) REVERT: 7 232 HIS cc_start: 0.8724 (m-70) cc_final: 0.8130 (m-70) REVERT: 9 66 THR cc_start: 0.9093 (p) cc_final: 0.8635 (p) REVERT: C 134 TRP cc_start: 0.6288 (p90) cc_final: 0.5961 (p90) REVERT: C 394 CYS cc_start: 0.8993 (m) cc_final: 0.8667 (m) REVERT: C 507 TYR cc_start: 0.9179 (t80) cc_final: 0.8779 (t80) REVERT: H 93 ASN cc_start: 0.9333 (m-40) cc_final: 0.9117 (m110) REVERT: H 113 SER cc_start: 0.9010 (m) cc_final: 0.8283 (t) REVERT: I 48 MET cc_start: 0.8844 (mmm) cc_final: 0.8350 (mmm) REVERT: I 108 ASP cc_start: 0.8993 (m-30) cc_final: 0.8319 (m-30) REVERT: I 119 HIS cc_start: 0.7918 (t70) cc_final: 0.7540 (t70) REVERT: I 120 LYS cc_start: 0.8343 (tmtt) cc_final: 0.7861 (tmmm) REVERT: I 156 SER cc_start: 0.6490 (t) cc_final: 0.5404 (t) REVERT: J 53 PHE cc_start: 0.8682 (t80) cc_final: 0.8398 (t80) REVERT: J 90 PHE cc_start: 0.7811 (t80) cc_final: 0.7192 (t80) REVERT: K 34 MET cc_start: 0.8732 (mtp) cc_final: 0.8344 (mtm) REVERT: K 52 ASP cc_start: 0.8002 (t0) cc_final: 0.7593 (t0) REVERT: K 99 ASP cc_start: 0.8672 (t0) cc_final: 0.8422 (t0) REVERT: K 135 GLU cc_start: 0.7675 (tp30) cc_final: 0.7336 (tp30) REVERT: N 104 MET cc_start: 0.8939 (tmm) cc_final: 0.8692 (tmm) REVERT: N 197 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8493 (tttm) REVERT: N 201 ASP cc_start: 0.8313 (m-30) cc_final: 0.8047 (m-30) REVERT: P 114 LYS cc_start: 0.9403 (ptmt) cc_final: 0.9121 (ptmm) REVERT: P 156 ASP cc_start: 0.9139 (m-30) cc_final: 0.8777 (p0) REVERT: Q 184 ASP cc_start: 0.8458 (m-30) cc_final: 0.8195 (m-30) REVERT: R 147 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8727 (mm-40) REVERT: U 109 ASP cc_start: 0.8542 (t0) cc_final: 0.8329 (t0) REVERT: V 119 GLN cc_start: 0.9351 (mt0) cc_final: 0.8953 (mt0) REVERT: W 60 TYR cc_start: 0.8955 (t80) cc_final: 0.8730 (t80) REVERT: W 71 ARG cc_start: 0.8483 (ttt90) cc_final: 0.8119 (ttt90) REVERT: W 147 MET cc_start: 0.8843 (tpt) cc_final: 0.8619 (tpt) REVERT: Y 143 ASP cc_start: 0.8406 (t0) cc_final: 0.8205 (t0) REVERT: c 67 ASP cc_start: 0.8809 (t0) cc_final: 0.8598 (t0) REVERT: c 238 MET cc_start: 0.9112 (tpp) cc_final: 0.8868 (mmm) REVERT: d 121 SER cc_start: 0.8886 (m) cc_final: 0.8336 (t) REVERT: d 184 SER cc_start: 0.9113 (t) cc_final: 0.8658 (p) REVERT: d 217 HIS cc_start: 0.9022 (t-90) cc_final: 0.8799 (t-90) REVERT: e 123 MET cc_start: 0.7274 (tmm) cc_final: 0.6888 (ptt) REVERT: e 258 ASP cc_start: 0.7801 (m-30) cc_final: 0.7528 (p0) REVERT: e 278 ASP cc_start: 0.5177 (m-30) cc_final: 0.3949 (p0) REVERT: f 102 LEU cc_start: 0.8201 (tp) cc_final: 0.7819 (pt) REVERT: f 109 TYR cc_start: 0.7901 (t80) cc_final: 0.7548 (t80) REVERT: g 116 ASP cc_start: 0.8612 (t0) cc_final: 0.8317 (t70) REVERT: h 103 HIS cc_start: 0.8556 (m-70) cc_final: 0.8073 (m90) REVERT: h 125 ASP cc_start: 0.9078 (m-30) cc_final: 0.8549 (m-30) REVERT: i 45 ASP cc_start: 0.8439 (t0) cc_final: 0.8116 (t0) REVERT: i 58 ASP cc_start: 0.8501 (m-30) cc_final: 0.8231 (m-30) REVERT: j 45 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8081 (mt-10) REVERT: j 81 SER cc_start: 0.9193 (m) cc_final: 0.8832 (p) REVERT: j 97 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8182 (mmpt) REVERT: k 31 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8197 (mtp180) REVERT: k 43 ARG cc_start: 0.8400 (mtm110) cc_final: 0.7873 (mtm110) REVERT: k 46 ASN cc_start: 0.7580 (m-40) cc_final: 0.7369 (t0) REVERT: k 64 VAL cc_start: 0.8839 (t) cc_final: 0.8605 (m) REVERT: l 117 TYR cc_start: 0.8956 (t80) cc_final: 0.7238 (m-10) REVERT: l 119 ARG cc_start: 0.8402 (ttm170) cc_final: 0.7796 (tpt170) REVERT: l 120 ARG cc_start: 0.6440 (ttp-170) cc_final: 0.6029 (tpt90) REVERT: l 134 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8793 (tptp) REVERT: o 35 MET cc_start: 0.8688 (ttm) cc_final: 0.8315 (ttp) REVERT: o 51 MET cc_start: 0.8476 (mtm) cc_final: 0.8274 (mtp) REVERT: p 149 ASP cc_start: 0.8520 (t0) cc_final: 0.7953 (t0) REVERT: p 152 GLN cc_start: 0.9006 (tp40) cc_final: 0.8405 (tp40) REVERT: q 41 ASP cc_start: 0.8278 (p0) cc_final: 0.7814 (p0) REVERT: q 44 ASP cc_start: 0.8825 (t0) cc_final: 0.8537 (t0) REVERT: r 39 VAL cc_start: 0.8676 (t) cc_final: 0.8243 (m) REVERT: s 89 MET cc_start: 0.9232 (mmm) cc_final: 0.8897 (mmt) outliers start: 0 outliers final: 3 residues processed: 1487 average time/residue: 1.8604 time to fit residues: 3752.1099 Evaluate side-chains 1099 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1096 time to evaluate : 7.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain r residue 183 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 809 optimal weight: 50.0000 chunk 726 optimal weight: 3.9990 chunk 403 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 751 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 457 optimal weight: 9.9990 chunk 559 optimal weight: 5.9990 chunk 870 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 0 170 GLN 3 154 GLN ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 177 ASN C 232 ASN C 304 ASN C 380 HIS D 156 ASN D 165 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 136 ASN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN L 143 ASN ** M 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 202 GLN O 91 GLN O 154 GLN P 176 GLN Q 139 GLN Q 261 ASN S 84 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN T 201 GLN U 23 ASN V 78 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN Y 183 GLN b 27 GLN c 123 GLN c 172 ASN d 77 HIS d 131 ASN d 154 ASN d 167 HIS e 156 ASN f 61 HIS g 155 GLN h 119 GLN ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 16 GLN p 176 HIS p 184 ASN r 146 GLN r 148 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 105693 Z= 0.523 Angle : 0.701 14.919 150190 Z= 0.359 Chirality : 0.046 0.307 17643 Planarity : 0.006 0.136 13626 Dihedral : 21.283 179.912 32016 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 9.66 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.06 (0.09), residues: 8170 helix: 1.74 (0.10), residues: 2845 sheet: -0.45 (0.15), residues: 1067 loop : 0.44 (0.10), residues: 4258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Z 81 HIS 0.012 0.001 HIS N 149 PHE 0.026 0.002 PHE I 173 TYR 0.027 0.002 TYR d 88 ARG 0.012 0.001 ARG J 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1093 time to evaluate : 7.186 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: 0 178 ASP cc_start: 0.8306 (t0) cc_final: 0.8072 (t0) REVERT: 1 26 THR cc_start: 0.9043 (m) cc_final: 0.8713 (p) REVERT: 4 74 LYS cc_start: 0.9319 (mtpm) cc_final: 0.9117 (mtpp) REVERT: 6 116 ASN cc_start: 0.8916 (t0) cc_final: 0.8659 (t0) REVERT: 6 330 ILE cc_start: 0.9538 (mt) cc_final: 0.9304 (mt) REVERT: 7 49 ASN cc_start: 0.9199 (m-40) cc_final: 0.8989 (m110) REVERT: 7 162 TYR cc_start: 0.9136 (m-80) cc_final: 0.8656 (m-80) REVERT: 9 117 TYR cc_start: 0.7933 (m-80) cc_final: 0.7337 (m-80) REVERT: C 134 TRP cc_start: 0.6489 (p90) cc_final: 0.6189 (p90) REVERT: H 93 ASN cc_start: 0.9326 (m-40) cc_final: 0.9113 (m110) REVERT: I 48 MET cc_start: 0.8884 (mmm) cc_final: 0.8438 (mmm) REVERT: I 107 GLU cc_start: 0.8542 (pp20) cc_final: 0.8323 (pp20) REVERT: I 108 ASP cc_start: 0.8707 (m-30) cc_final: 0.8455 (m-30) REVERT: I 119 HIS cc_start: 0.8081 (t70) cc_final: 0.7815 (t70) REVERT: I 120 LYS cc_start: 0.8438 (tmtt) cc_final: 0.7819 (tmmt) REVERT: J 53 PHE cc_start: 0.8675 (t80) cc_final: 0.8472 (t80) REVERT: J 103 GLN cc_start: 0.6487 (tt0) cc_final: 0.4170 (tt0) REVERT: K 34 MET cc_start: 0.8683 (mtp) cc_final: 0.8326 (mtm) REVERT: K 52 ASP cc_start: 0.8027 (t0) cc_final: 0.7627 (t0) REVERT: K 99 ASP cc_start: 0.8704 (t0) cc_final: 0.8416 (t0) REVERT: K 135 GLU cc_start: 0.7848 (tp30) cc_final: 0.7493 (tp30) REVERT: N 104 MET cc_start: 0.8982 (tmm) cc_final: 0.8737 (tmm) REVERT: N 114 ASP cc_start: 0.8248 (t0) cc_final: 0.8013 (t0) REVERT: N 117 ASN cc_start: 0.9015 (m-40) cc_final: 0.8756 (m-40) REVERT: N 148 ASP cc_start: 0.8146 (t70) cc_final: 0.7730 (t0) REVERT: N 197 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8497 (tttm) REVERT: N 201 ASP cc_start: 0.8335 (m-30) cc_final: 0.8039 (m-30) REVERT: O 155 ASP cc_start: 0.8106 (m-30) cc_final: 0.7689 (m-30) REVERT: P 134 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8269 (tm-30) REVERT: Q 184 ASP cc_start: 0.8520 (m-30) cc_final: 0.8281 (m-30) REVERT: R 147 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8677 (mm-40) REVERT: U 103 GLN cc_start: 0.7894 (mp10) cc_final: 0.7634 (mp10) REVERT: U 149 SER cc_start: 0.9235 (p) cc_final: 0.9033 (p) REVERT: V 91 LEU cc_start: 0.9501 (mm) cc_final: 0.9223 (mm) REVERT: W 57 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: W 147 MET cc_start: 0.8908 (tpt) cc_final: 0.8527 (tpt) REVERT: Y 70 ASP cc_start: 0.7884 (t0) cc_final: 0.7057 (t0) REVERT: Y 115 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9302 (tp) REVERT: Z 38 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8015 (mtm-85) REVERT: Z 131 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: c 67 ASP cc_start: 0.8903 (t0) cc_final: 0.8631 (t0) REVERT: c 238 MET cc_start: 0.9178 (tpp) cc_final: 0.8952 (mmm) REVERT: c 240 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9168 (tt) REVERT: d 121 SER cc_start: 0.8920 (m) cc_final: 0.8663 (t) REVERT: d 124 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7513 (ttp80) REVERT: d 154 ASN cc_start: 0.8345 (t0) cc_final: 0.8106 (t0) REVERT: d 184 SER cc_start: 0.9090 (t) cc_final: 0.8539 (p) REVERT: d 217 HIS cc_start: 0.9088 (t-90) cc_final: 0.8796 (t-90) REVERT: e 123 MET cc_start: 0.7421 (tmm) cc_final: 0.7052 (ptt) REVERT: e 133 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3664 (mt) REVERT: e 169 ASP cc_start: 0.7037 (t70) cc_final: 0.6804 (t70) REVERT: e 278 ASP cc_start: 0.4812 (m-30) cc_final: 0.3201 (p0) REVERT: f 102 LEU cc_start: 0.8260 (tp) cc_final: 0.7795 (pt) REVERT: f 178 LEU cc_start: 0.7740 (tt) cc_final: 0.7352 (tm) REVERT: g 81 ASN cc_start: 0.8157 (p0) cc_final: 0.7885 (p0) REVERT: g 116 ASP cc_start: 0.8652 (t0) cc_final: 0.8401 (t0) REVERT: h 86 TRP cc_start: 0.9123 (p-90) cc_final: 0.8609 (p-90) REVERT: h 116 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7830 (mtp85) REVERT: h 124 ARG cc_start: 0.8262 (ttp80) cc_final: 0.8021 (ttp80) REVERT: h 125 ASP cc_start: 0.9049 (m-30) cc_final: 0.8776 (m-30) REVERT: h 137 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7484 (ptt90) REVERT: i 45 ASP cc_start: 0.8471 (t0) cc_final: 0.8182 (t0) REVERT: j 97 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8065 (mmmm) REVERT: j 100 GLU cc_start: 0.8616 (pp20) cc_final: 0.8373 (OUTLIER) REVERT: j 101 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: k 19 GLN cc_start: 0.8166 (tm130) cc_final: 0.7701 (tm-30) REVERT: l 119 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8145 (mtp85) REVERT: l 120 ARG cc_start: 0.6633 (ttp-170) cc_final: 0.5997 (tpp80) REVERT: o 35 MET cc_start: 0.8872 (ttm) cc_final: 0.8513 (ttt) REVERT: p 47 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8907 (mttt) REVERT: q 41 ASP cc_start: 0.8450 (p0) cc_final: 0.8047 (p0) REVERT: q 125 MET cc_start: 0.9202 (mmm) cc_final: 0.8996 (mmm) REVERT: s 66 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.6850 (t60) REVERT: s 89 MET cc_start: 0.9213 (mmm) cc_final: 0.8876 (mmm) outliers start: 155 outliers final: 58 residues processed: 1166 average time/residue: 1.7747 time to fit residues: 2855.1924 Evaluate side-chains 1078 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1009 time to evaluate : 7.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 61 LYS Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 150 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 101 GLU Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain s residue 66 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 483 optimal weight: 0.3980 chunk 270 optimal weight: 5.9990 chunk 724 optimal weight: 0.6980 chunk 593 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 872 optimal weight: 3.9990 chunk 942 optimal weight: 5.9990 chunk 776 optimal weight: 1.9990 chunk 865 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 699 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN 7 45 ASN 7 287 GLN 9 90 GLN C 177 ASN C 232 ASN C 304 ASN D 156 ASN E 336 ASN H 100 GLN I 100 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN K 56 HIS L 33 GLN L 142 GLN M 26 ASN M 276 ASN N 98 HIS N 202 GLN O 150 GLN P 176 GLN Q 261 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN T 151 GLN T 201 GLN V 119 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN Y 183 GLN a 46 ASN d 131 ASN d 211 GLN d 220 GLN g 155 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 35 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 146 GLN r 148 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 105693 Z= 0.179 Angle : 0.588 14.300 150190 Z= 0.304 Chirality : 0.038 0.272 17643 Planarity : 0.004 0.126 13626 Dihedral : 21.270 179.938 32010 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.19 % Allowed : 11.68 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.20 (0.09), residues: 8170 helix: 1.88 (0.10), residues: 2836 sheet: -0.39 (0.15), residues: 1062 loop : 0.51 (0.10), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 81 HIS 0.007 0.001 HIS S 76 PHE 0.029 0.001 PHE 6 273 TYR 0.030 0.001 TYR d 88 ARG 0.009 0.000 ARG O 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1108 time to evaluate : 7.411 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: 0 128 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7843 (tm-30) REVERT: 0 178 ASP cc_start: 0.8205 (t0) cc_final: 0.7998 (t0) REVERT: 1 26 THR cc_start: 0.9022 (m) cc_final: 0.8744 (p) REVERT: 2 88 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8415 (ttpp) REVERT: 6 116 ASN cc_start: 0.8948 (t0) cc_final: 0.8557 (t0) REVERT: 6 330 ILE cc_start: 0.9426 (mt) cc_final: 0.9200 (mt) REVERT: 7 45 ASN cc_start: 0.9326 (m-40) cc_final: 0.8909 (m110) REVERT: 7 49 ASN cc_start: 0.9237 (m-40) cc_final: 0.9026 (m110) REVERT: 7 162 TYR cc_start: 0.9061 (m-80) cc_final: 0.8618 (m-80) REVERT: 7 232 HIS cc_start: 0.8756 (m-70) cc_final: 0.8094 (m-70) REVERT: 9 103 ASP cc_start: 0.5478 (t0) cc_final: 0.5039 (t0) REVERT: 9 117 TYR cc_start: 0.7756 (m-80) cc_final: 0.7544 (m-80) REVERT: 9 120 GLU cc_start: 0.8263 (pt0) cc_final: 0.7844 (pt0) REVERT: D 161 ASP cc_start: 0.8126 (m-30) cc_final: 0.7756 (m-30) REVERT: H 84 GLU cc_start: 0.7948 (tt0) cc_final: 0.7312 (tt0) REVERT: H 89 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8121 (mtt-85) REVERT: H 122 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6352 (ttm110) REVERT: H 141 GLU cc_start: 0.8236 (pp20) cc_final: 0.7495 (pp20) REVERT: H 142 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: I 48 MET cc_start: 0.8861 (mmm) cc_final: 0.8482 (mmm) REVERT: I 95 MET cc_start: 0.8855 (ppp) cc_final: 0.8122 (pmm) REVERT: I 96 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7248 (mm) REVERT: I 119 HIS cc_start: 0.8083 (t70) cc_final: 0.7855 (t70) REVERT: I 155 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8294 (m) REVERT: J 115 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7168 (tptt) REVERT: K 34 MET cc_start: 0.8619 (mtp) cc_final: 0.8194 (mtm) REVERT: K 52 ASP cc_start: 0.7972 (t0) cc_final: 0.7607 (t0) REVERT: K 99 ASP cc_start: 0.8606 (t0) cc_final: 0.8340 (t0) REVERT: K 135 GLU cc_start: 0.7756 (tp30) cc_final: 0.7377 (tp30) REVERT: K 144 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: N 104 MET cc_start: 0.9031 (tmm) cc_final: 0.8806 (tmm) REVERT: N 114 ASP cc_start: 0.8207 (t0) cc_final: 0.7960 (t0) REVERT: N 117 ASN cc_start: 0.8980 (m-40) cc_final: 0.8700 (m-40) REVERT: N 148 ASP cc_start: 0.7878 (t70) cc_final: 0.7507 (t0) REVERT: N 149 HIS cc_start: 0.6073 (m90) cc_final: 0.5526 (m90) REVERT: N 197 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8485 (tttm) REVERT: N 201 ASP cc_start: 0.8276 (m-30) cc_final: 0.8020 (m-30) REVERT: O 155 ASP cc_start: 0.8028 (m-30) cc_final: 0.7662 (m-30) REVERT: P 114 LYS cc_start: 0.9326 (ptmm) cc_final: 0.9019 (ptpp) REVERT: P 134 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8309 (tm-30) REVERT: P 159 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8608 (mtmm) REVERT: R 147 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8656 (mm-40) REVERT: U 103 GLN cc_start: 0.7873 (mp10) cc_final: 0.7586 (mp10) REVERT: U 126 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8169 (tm) REVERT: V 23 MET cc_start: 0.8862 (mmm) cc_final: 0.8258 (mmm) REVERT: V 91 LEU cc_start: 0.9497 (mm) cc_final: 0.9214 (mm) REVERT: V 111 SER cc_start: 0.9238 (m) cc_final: 0.8776 (p) REVERT: W 147 MET cc_start: 0.8896 (tpt) cc_final: 0.8586 (tpt) REVERT: Y 70 ASP cc_start: 0.7501 (t0) cc_final: 0.6670 (t0) REVERT: Y 183 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: Z 131 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: b 49 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7890 (mtm110) REVERT: c 67 ASP cc_start: 0.8822 (t0) cc_final: 0.8535 (t0) REVERT: c 238 MET cc_start: 0.9067 (tpp) cc_final: 0.8829 (mmm) REVERT: c 240 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9164 (tt) REVERT: d 121 SER cc_start: 0.8908 (m) cc_final: 0.8291 (t) REVERT: d 124 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7403 (ttp80) REVERT: d 125 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8778 (mp) REVERT: d 154 ASN cc_start: 0.8306 (t0) cc_final: 0.7858 (t0) REVERT: d 184 SER cc_start: 0.9045 (t) cc_final: 0.8507 (p) REVERT: d 217 HIS cc_start: 0.9105 (t-90) cc_final: 0.8790 (t-90) REVERT: e 123 MET cc_start: 0.7374 (tmm) cc_final: 0.6929 (ptt) REVERT: e 154 ASP cc_start: 0.7886 (p0) cc_final: 0.7625 (p0) REVERT: e 169 ASP cc_start: 0.6879 (t70) cc_final: 0.6614 (t70) REVERT: e 278 ASP cc_start: 0.4741 (m-30) cc_final: 0.3237 (p0) REVERT: f 102 LEU cc_start: 0.8174 (tp) cc_final: 0.7720 (pt) REVERT: f 178 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7419 (tm) REVERT: g 116 ASP cc_start: 0.8521 (t0) cc_final: 0.8304 (t0) REVERT: h 86 TRP cc_start: 0.9035 (p-90) cc_final: 0.8232 (p-90) REVERT: h 116 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7840 (mtp85) REVERT: i 45 ASP cc_start: 0.8385 (t0) cc_final: 0.8109 (t0) REVERT: k 26 ASN cc_start: 0.8100 (p0) cc_final: 0.7696 (p0) REVERT: k 85 GLU cc_start: 0.8468 (mp0) cc_final: 0.8243 (mp0) REVERT: l 117 TYR cc_start: 0.8762 (t80) cc_final: 0.8545 (t80) REVERT: l 119 ARG cc_start: 0.8554 (ttm170) cc_final: 0.7982 (mtp85) REVERT: l 120 ARG cc_start: 0.6599 (ttp-170) cc_final: 0.6002 (tpp80) REVERT: l 134 LYS cc_start: 0.9237 (tppp) cc_final: 0.8558 (tptp) REVERT: o 35 MET cc_start: 0.8764 (ttm) cc_final: 0.8348 (ttt) REVERT: p 124 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8893 (ptpp) REVERT: p 149 ASP cc_start: 0.8389 (t0) cc_final: 0.7889 (t0) REVERT: q 41 ASP cc_start: 0.8396 (p0) cc_final: 0.7953 (p0) REVERT: q 44 ASP cc_start: 0.9027 (t0) cc_final: 0.8771 (t0) REVERT: s 66 TRP cc_start: 0.7952 (OUTLIER) cc_final: 0.6797 (t60) REVERT: s 89 MET cc_start: 0.9253 (mmm) cc_final: 0.8897 (mmt) outliers start: 161 outliers final: 53 residues processed: 1179 average time/residue: 1.7749 time to fit residues: 2883.0419 Evaluate side-chains 1090 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1023 time to evaluate : 7.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain Y residue 183 GLN Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 167 ASP Chi-restraints excluded: chain f residue 150 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 95 ARG Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain s residue 66 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 861 optimal weight: 6.9990 chunk 655 optimal weight: 9.9990 chunk 452 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 416 optimal weight: 2.9990 chunk 585 optimal weight: 1.9990 chunk 875 optimal weight: 9.9990 chunk 926 optimal weight: 0.9980 chunk 457 optimal weight: 9.9990 chunk 829 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN 9 90 GLN C 232 ASN C 261 GLN D 156 ASN F 257 GLN H 93 ASN H 100 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS O 150 GLN P 176 GLN Q 261 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 151 GLN T 201 GLN V 119 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN Y 147 GLN d 131 ASN d 211 GLN d 220 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 105693 Z= 0.231 Angle : 0.586 14.225 150190 Z= 0.303 Chirality : 0.039 0.268 17643 Planarity : 0.004 0.126 13626 Dihedral : 21.140 179.815 32010 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.03 % Allowed : 13.13 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.25 (0.09), residues: 8170 helix: 1.91 (0.10), residues: 2834 sheet: -0.31 (0.15), residues: 1084 loop : 0.53 (0.10), residues: 4252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP q 143 HIS 0.007 0.001 HIS S 76 PHE 0.023 0.001 PHE I 173 TYR 0.024 0.001 TYR f 59 ARG 0.010 0.000 ARG Z 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1062 time to evaluate : 7.448 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: 0 128 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: 0 178 ASP cc_start: 0.8165 (t0) cc_final: 0.7948 (t0) REVERT: 1 26 THR cc_start: 0.9040 (m) cc_final: 0.8750 (p) REVERT: 2 88 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8371 (ttpp) REVERT: 6 116 ASN cc_start: 0.8981 (t0) cc_final: 0.8567 (t0) REVERT: 6 330 ILE cc_start: 0.9426 (mt) cc_final: 0.9214 (mt) REVERT: 7 49 ASN cc_start: 0.9253 (m-40) cc_final: 0.9029 (m110) REVERT: 7 162 TYR cc_start: 0.9072 (m-80) cc_final: 0.8677 (m-80) REVERT: 7 232 HIS cc_start: 0.8758 (m-70) cc_final: 0.8037 (m-70) REVERT: 9 103 ASP cc_start: 0.5606 (t0) cc_final: 0.5387 (t0) REVERT: 9 120 GLU cc_start: 0.8313 (pt0) cc_final: 0.8083 (pt0) REVERT: C 114 MET cc_start: 0.7715 (ttm) cc_final: 0.7480 (ttm) REVERT: C 410 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8893 (mm) REVERT: D 161 ASP cc_start: 0.8138 (m-30) cc_final: 0.7609 (m-30) REVERT: H 84 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: H 138 LYS cc_start: 0.8380 (tmmm) cc_final: 0.8016 (tmmm) REVERT: I 48 MET cc_start: 0.8838 (mmm) cc_final: 0.8438 (mmm) REVERT: I 95 MET cc_start: 0.8357 (ppp) cc_final: 0.8146 (ppp) REVERT: I 108 ASP cc_start: 0.8850 (m-30) cc_final: 0.8274 (m-30) REVERT: I 119 HIS cc_start: 0.8106 (t70) cc_final: 0.7847 (t-90) REVERT: I 126 PHE cc_start: 0.8845 (m-80) cc_final: 0.8474 (m-80) REVERT: I 128 ASN cc_start: 0.8450 (m-40) cc_final: 0.8170 (m-40) REVERT: J 53 PHE cc_start: 0.8488 (t80) cc_final: 0.8221 (t80) REVERT: J 66 LEU cc_start: 0.9228 (tp) cc_final: 0.8535 (pp) REVERT: K 34 MET cc_start: 0.8674 (mtp) cc_final: 0.8288 (mtm) REVERT: K 52 ASP cc_start: 0.8000 (t0) cc_final: 0.7621 (t0) REVERT: K 99 ASP cc_start: 0.8560 (t0) cc_final: 0.8294 (t0) REVERT: K 135 GLU cc_start: 0.7783 (tp30) cc_final: 0.7455 (tp30) REVERT: N 104 MET cc_start: 0.9060 (tmm) cc_final: 0.8851 (tmm) REVERT: N 114 ASP cc_start: 0.8254 (t0) cc_final: 0.7725 (t0) REVERT: N 117 ASN cc_start: 0.8988 (m-40) cc_final: 0.8717 (m-40) REVERT: N 148 ASP cc_start: 0.7814 (t70) cc_final: 0.7380 (t0) REVERT: N 149 HIS cc_start: 0.6125 (m90) cc_final: 0.5490 (m90) REVERT: N 197 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8471 (tttm) REVERT: N 201 ASP cc_start: 0.8316 (m-30) cc_final: 0.8040 (m-30) REVERT: O 58 LYS cc_start: 0.8907 (mptm) cc_final: 0.8687 (mptm) REVERT: P 58 LEU cc_start: 0.9303 (mt) cc_final: 0.8972 (mt) REVERT: P 114 LYS cc_start: 0.9365 (ptmm) cc_final: 0.9101 (ptpp) REVERT: P 134 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8357 (tm-30) REVERT: P 142 ASN cc_start: 0.9144 (m110) cc_final: 0.8935 (m110) REVERT: P 159 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8591 (mtmm) REVERT: Q 270 MET cc_start: 0.8785 (mmp) cc_final: 0.8457 (mmt) REVERT: R 147 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8622 (mm-40) REVERT: T 126 ASP cc_start: 0.7913 (t0) cc_final: 0.7630 (t0) REVERT: U 103 GLN cc_start: 0.7932 (mp10) cc_final: 0.7670 (mp10) REVERT: V 23 MET cc_start: 0.8876 (mmm) cc_final: 0.8303 (mmm) REVERT: V 91 LEU cc_start: 0.9522 (mm) cc_final: 0.9237 (mm) REVERT: V 111 SER cc_start: 0.9215 (m) cc_final: 0.8797 (p) REVERT: W 57 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: W 147 MET cc_start: 0.8921 (tpt) cc_final: 0.8429 (tpt) REVERT: Y 115 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9302 (tp) REVERT: Y 157 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8621 (mm-40) REVERT: Z 131 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: c 67 ASP cc_start: 0.8824 (t0) cc_final: 0.8543 (t0) REVERT: c 238 MET cc_start: 0.9064 (tpp) cc_final: 0.8844 (mmm) REVERT: c 240 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9172 (tt) REVERT: d 121 SER cc_start: 0.8876 (m) cc_final: 0.8486 (t) REVERT: d 124 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7339 (ttp80) REVERT: d 154 ASN cc_start: 0.8320 (t0) cc_final: 0.7830 (t0) REVERT: d 184 SER cc_start: 0.9077 (t) cc_final: 0.8563 (p) REVERT: e 123 MET cc_start: 0.7468 (tmm) cc_final: 0.7134 (ptt) REVERT: e 133 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3639 (mt) REVERT: e 154 ASP cc_start: 0.7880 (p0) cc_final: 0.7620 (p0) REVERT: e 169 ASP cc_start: 0.6944 (t70) cc_final: 0.6683 (t70) REVERT: e 205 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6994 (mm) REVERT: f 102 LEU cc_start: 0.8229 (tp) cc_final: 0.7767 (pt) REVERT: f 178 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7226 (tm) REVERT: g 81 ASN cc_start: 0.8048 (p0) cc_final: 0.7846 (p0) REVERT: h 86 TRP cc_start: 0.8866 (p-90) cc_final: 0.8590 (p-90) REVERT: h 116 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8067 (mtp85) REVERT: h 120 MET cc_start: 0.8083 (tpp) cc_final: 0.7649 (mmm) REVERT: i 45 ASP cc_start: 0.8380 (t0) cc_final: 0.8093 (t0) REVERT: k 17 ARG cc_start: 0.8066 (ppp80) cc_final: 0.7609 (ptt90) REVERT: k 19 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7989 (tm-30) REVERT: k 26 ASN cc_start: 0.8042 (p0) cc_final: 0.7770 (p0) REVERT: k 65 ASP cc_start: 0.7539 (t0) cc_final: 0.6978 (p0) REVERT: k 85 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8181 (mp0) REVERT: l 119 ARG cc_start: 0.8553 (ttm170) cc_final: 0.7723 (tpt-90) REVERT: l 120 ARG cc_start: 0.6598 (ttp-170) cc_final: 0.6037 (tpp80) REVERT: o 35 MET cc_start: 0.8816 (ttm) cc_final: 0.8418 (ttt) REVERT: p 47 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9019 (mttt) REVERT: p 124 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8897 (ptpp) REVERT: p 149 ASP cc_start: 0.8450 (t0) cc_final: 0.7970 (t0) REVERT: p 183 MET cc_start: 0.8746 (ttm) cc_final: 0.8499 (ttt) REVERT: q 41 ASP cc_start: 0.8429 (p0) cc_final: 0.7994 (p0) REVERT: q 44 ASP cc_start: 0.8980 (t0) cc_final: 0.8740 (t0) REVERT: s 66 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.6818 (t60) REVERT: s 89 MET cc_start: 0.9269 (mmm) cc_final: 0.8904 (mmt) outliers start: 149 outliers final: 71 residues processed: 1131 average time/residue: 1.7678 time to fit residues: 2763.9186 Evaluate side-chains 1098 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1012 time to evaluate : 7.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 5 residue 194 LYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 124 GLU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 103 GLN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 66 ASN Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 167 ASP Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 150 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 772 optimal weight: 4.9990 chunk 526 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 690 optimal weight: 0.9990 chunk 382 optimal weight: 9.9990 chunk 791 optimal weight: 5.9990 chunk 640 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 473 optimal weight: 0.3980 chunk 832 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN ** 2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 9 90 GLN C 232 ASN D 156 ASN H 93 ASN H 100 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN M 219 ASN N 98 HIS N 202 GLN O 27 HIS O 150 GLN P 142 ASN P 176 GLN Q 261 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 151 GLN T 201 GLN V 119 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN a 46 ASN d 131 ASN d 211 GLN d 220 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 ASN q 142 ASN r 146 GLN r 148 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 105693 Z= 0.240 Angle : 0.586 14.192 150190 Z= 0.303 Chirality : 0.039 0.305 17643 Planarity : 0.004 0.126 13626 Dihedral : 21.092 179.966 32010 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.22 % Allowed : 13.71 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.25 (0.09), residues: 8170 helix: 1.91 (0.10), residues: 2841 sheet: -0.29 (0.15), residues: 1102 loop : 0.53 (0.10), residues: 4227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP q 143 HIS 0.007 0.001 HIS S 76 PHE 0.024 0.001 PHE I 173 TYR 0.021 0.001 TYR 5 176 ARG 0.015 0.000 ARG V 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1048 time to evaluate : 7.208 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: 0 128 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: 0 178 ASP cc_start: 0.8153 (t0) cc_final: 0.7933 (t0) REVERT: 1 26 THR cc_start: 0.9043 (m) cc_final: 0.8759 (p) REVERT: 2 88 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8335 (ttpp) REVERT: 6 116 ASN cc_start: 0.9001 (t0) cc_final: 0.8549 (t0) REVERT: 6 148 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8745 (mmmm) REVERT: 7 45 ASN cc_start: 0.9335 (m-40) cc_final: 0.8908 (m110) REVERT: 7 49 ASN cc_start: 0.9263 (m-40) cc_final: 0.9050 (m110) REVERT: 7 162 TYR cc_start: 0.9099 (m-80) cc_final: 0.8649 (m-80) REVERT: 7 232 HIS cc_start: 0.8780 (m-70) cc_final: 0.7926 (m-70) REVERT: 8 139 MET cc_start: 0.5757 (ppp) cc_final: 0.5524 (ppp) REVERT: 9 120 GLU cc_start: 0.8262 (pt0) cc_final: 0.8002 (pt0) REVERT: C 410 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8912 (mm) REVERT: D 161 ASP cc_start: 0.8019 (m-30) cc_final: 0.7611 (m-30) REVERT: H 122 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6315 (ttm110) REVERT: H 138 LYS cc_start: 0.8241 (tmmm) cc_final: 0.7979 (tmmm) REVERT: I 48 MET cc_start: 0.8808 (mmm) cc_final: 0.8488 (mmm) REVERT: I 95 MET cc_start: 0.8419 (ppp) cc_final: 0.8192 (ppp) REVERT: I 108 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: I 119 HIS cc_start: 0.8107 (t70) cc_final: 0.7866 (t-90) REVERT: I 123 MET cc_start: 0.8652 (ttp) cc_final: 0.8279 (tmm) REVERT: I 155 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8463 (m) REVERT: J 53 PHE cc_start: 0.8391 (t80) cc_final: 0.8124 (t80) REVERT: J 66 LEU cc_start: 0.9226 (tp) cc_final: 0.8540 (pp) REVERT: K 34 MET cc_start: 0.8669 (mtp) cc_final: 0.8293 (mtm) REVERT: K 52 ASP cc_start: 0.7997 (t0) cc_final: 0.7621 (t0) REVERT: K 99 ASP cc_start: 0.8554 (t0) cc_final: 0.8295 (t0) REVERT: K 135 GLU cc_start: 0.7771 (tp30) cc_final: 0.7444 (tp30) REVERT: L 43 ASN cc_start: 0.8374 (t0) cc_final: 0.8098 (t0) REVERT: N 114 ASP cc_start: 0.8253 (t0) cc_final: 0.7828 (t0) REVERT: N 117 ASN cc_start: 0.8992 (m-40) cc_final: 0.8751 (m-40) REVERT: N 148 ASP cc_start: 0.7814 (t70) cc_final: 0.7338 (t0) REVERT: N 149 HIS cc_start: 0.6132 (m90) cc_final: 0.5358 (m90) REVERT: N 201 ASP cc_start: 0.8308 (m-30) cc_final: 0.8049 (m-30) REVERT: O 155 ASP cc_start: 0.7916 (m-30) cc_final: 0.7637 (m-30) REVERT: P 114 LYS cc_start: 0.9373 (ptmm) cc_final: 0.9116 (ptpp) REVERT: P 134 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8384 (tm-30) REVERT: P 142 ASN cc_start: 0.8934 (m-40) cc_final: 0.8649 (m-40) REVERT: P 159 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8646 (mtmm) REVERT: R 147 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8649 (mm-40) REVERT: T 126 ASP cc_start: 0.7963 (t0) cc_final: 0.7654 (t0) REVERT: U 103 GLN cc_start: 0.7962 (mp10) cc_final: 0.7679 (mp10) REVERT: U 132 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7951 (tt0) REVERT: U 136 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7686 (tp-100) REVERT: V 91 LEU cc_start: 0.9540 (mm) cc_final: 0.9249 (mm) REVERT: V 111 SER cc_start: 0.9199 (m) cc_final: 0.8744 (p) REVERT: W 57 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: W 147 MET cc_start: 0.8924 (tpt) cc_final: 0.8425 (tpt) REVERT: Y 115 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9282 (tp) REVERT: Y 157 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8555 (mm-40) REVERT: Z 131 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: c 67 ASP cc_start: 0.8821 (t0) cc_final: 0.8576 (t0) REVERT: c 238 MET cc_start: 0.9057 (tpp) cc_final: 0.8844 (mmm) REVERT: c 240 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9179 (tt) REVERT: d 121 SER cc_start: 0.8900 (m) cc_final: 0.8517 (t) REVERT: d 124 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7462 (ttp80) REVERT: d 154 ASN cc_start: 0.8363 (t0) cc_final: 0.7968 (t0) REVERT: d 184 SER cc_start: 0.9091 (t) cc_final: 0.8568 (p) REVERT: e 123 MET cc_start: 0.7505 (tmm) cc_final: 0.7140 (ptt) REVERT: e 133 LEU cc_start: 0.3868 (OUTLIER) cc_final: 0.3660 (mt) REVERT: e 154 ASP cc_start: 0.7914 (p0) cc_final: 0.7620 (p0) REVERT: e 169 ASP cc_start: 0.7002 (t70) cc_final: 0.6746 (t70) REVERT: e 205 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6909 (mm) REVERT: e 278 ASP cc_start: 0.4317 (m-30) cc_final: 0.2599 (OUTLIER) REVERT: f 102 LEU cc_start: 0.8233 (tp) cc_final: 0.7769 (pt) REVERT: f 178 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7241 (tm) REVERT: g 116 ASP cc_start: 0.8604 (t0) cc_final: 0.8363 (t0) REVERT: h 86 TRP cc_start: 0.8835 (p-90) cc_final: 0.8628 (p-90) REVERT: h 116 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7966 (mtp85) REVERT: h 142 GLU cc_start: 0.7543 (tp30) cc_final: 0.7323 (tp30) REVERT: h 156 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.7670 (m100) REVERT: i 45 ASP cc_start: 0.8374 (t0) cc_final: 0.8100 (t0) REVERT: j 98 LEU cc_start: 0.8908 (pp) cc_final: 0.8608 (pp) REVERT: k 19 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7854 (tm-30) REVERT: k 65 ASP cc_start: 0.7447 (t0) cc_final: 0.6760 (t0) REVERT: k 85 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: l 119 ARG cc_start: 0.8575 (ttm170) cc_final: 0.7881 (ttt-90) REVERT: l 120 ARG cc_start: 0.6602 (ttp-170) cc_final: 0.6076 (tpp80) REVERT: o 35 MET cc_start: 0.8829 (ttm) cc_final: 0.8420 (ttt) REVERT: p 124 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8902 (ptpp) REVERT: p 149 ASP cc_start: 0.8464 (t0) cc_final: 0.7988 (t0) REVERT: p 183 MET cc_start: 0.8812 (ttm) cc_final: 0.8567 (ttt) REVERT: q 41 ASP cc_start: 0.8428 (p0) cc_final: 0.7978 (p0) REVERT: q 44 ASP cc_start: 0.8847 (t0) cc_final: 0.8619 (t0) REVERT: s 66 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.6831 (t60) REVERT: s 89 MET cc_start: 0.9263 (mmm) cc_final: 0.8925 (mmm) outliers start: 163 outliers final: 82 residues processed: 1128 average time/residue: 1.7546 time to fit residues: 2747.1679 Evaluate side-chains 1111 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1013 time to evaluate : 7.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 5 residue 194 LYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 66 ASN Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 167 ASP Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 150 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 122 LYS Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 95 ARG Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 118 LYS Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 160 ARG Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 311 optimal weight: 5.9990 chunk 834 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 927 optimal weight: 7.9990 chunk 770 optimal weight: 9.9990 chunk 429 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 306 optimal weight: 0.0970 chunk 487 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 232 ASN C 304 ASN D 156 ASN F 257 GLN H 93 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS N 138 HIS N 202 GLN O 150 GLN P 176 GLN Q 261 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 151 GLN T 201 GLN V 119 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 225 ASN d 131 ASN d 220 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN k 26 ASN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 105693 Z= 0.344 Angle : 0.620 14.080 150190 Z= 0.320 Chirality : 0.041 0.318 17643 Planarity : 0.005 0.129 13626 Dihedral : 21.067 179.994 32010 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 14.58 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.21 (0.09), residues: 8170 helix: 1.89 (0.10), residues: 2829 sheet: -0.26 (0.15), residues: 1098 loop : 0.49 (0.10), residues: 4243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP q 143 HIS 0.007 0.001 HIS S 76 PHE 0.022 0.001 PHE I 126 TYR 0.022 0.001 TYR f 109 ARG 0.013 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1022 time to evaluate : 7.334 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: 0 128 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: 0 178 ASP cc_start: 0.8165 (t0) cc_final: 0.7943 (t0) REVERT: 1 26 THR cc_start: 0.9045 (m) cc_final: 0.8752 (p) REVERT: 2 88 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8369 (ttpp) REVERT: 4 69 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8143 (mtpt) REVERT: 6 107 LYS cc_start: 0.9381 (mttp) cc_final: 0.9141 (mttp) REVERT: 6 116 ASN cc_start: 0.9023 (t0) cc_final: 0.8587 (t0) REVERT: 6 148 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8791 (mmmm) REVERT: 7 49 ASN cc_start: 0.9249 (m-40) cc_final: 0.9028 (m110) REVERT: 7 162 TYR cc_start: 0.9097 (m-80) cc_final: 0.8696 (m-80) REVERT: 7 232 HIS cc_start: 0.8806 (m-70) cc_final: 0.8028 (m-70) REVERT: 8 139 MET cc_start: 0.5711 (ppp) cc_final: 0.5438 (ppp) REVERT: 9 64 ASP cc_start: 0.8177 (t0) cc_final: 0.7970 (t0) REVERT: 9 83 GLU cc_start: 0.7813 (tp30) cc_final: 0.7390 (tp30) REVERT: 9 120 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: C 410 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8923 (mm) REVERT: D 161 ASP cc_start: 0.8021 (m-30) cc_final: 0.7316 (m-30) REVERT: H 122 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6372 (ttm110) REVERT: H 138 LYS cc_start: 0.8235 (tmmm) cc_final: 0.7830 (tmmm) REVERT: I 48 MET cc_start: 0.8816 (mmm) cc_final: 0.8478 (mmm) REVERT: I 95 MET cc_start: 0.8440 (ppp) cc_final: 0.8150 (ppp) REVERT: I 108 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: I 115 GLN cc_start: 0.9342 (mt0) cc_final: 0.8844 (tt0) REVERT: I 119 HIS cc_start: 0.8175 (t70) cc_final: 0.7928 (t-90) REVERT: I 123 MET cc_start: 0.8682 (ttp) cc_final: 0.8214 (tmm) REVERT: I 144 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7348 (mm) REVERT: K 34 MET cc_start: 0.8658 (mtp) cc_final: 0.8298 (mtm) REVERT: K 52 ASP cc_start: 0.8021 (t0) cc_final: 0.7653 (t0) REVERT: K 99 ASP cc_start: 0.8584 (t0) cc_final: 0.8326 (t0) REVERT: K 135 GLU cc_start: 0.7811 (tp30) cc_final: 0.7484 (tp30) REVERT: K 157 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8127 (mp0) REVERT: L 43 ASN cc_start: 0.8411 (t0) cc_final: 0.8150 (t0) REVERT: N 114 ASP cc_start: 0.8385 (t0) cc_final: 0.8070 (t0) REVERT: N 148 ASP cc_start: 0.7801 (t70) cc_final: 0.7307 (t70) REVERT: N 149 HIS cc_start: 0.6111 (m90) cc_final: 0.5209 (m90) REVERT: N 201 ASP cc_start: 0.8306 (m-30) cc_final: 0.8049 (m-30) REVERT: O 58 LYS cc_start: 0.8987 (mptm) cc_final: 0.8755 (mptm) REVERT: P 58 LEU cc_start: 0.9324 (mt) cc_final: 0.9016 (mt) REVERT: P 114 LYS cc_start: 0.9386 (ptmm) cc_final: 0.9090 (ptpp) REVERT: P 134 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8445 (tm-30) REVERT: P 142 ASN cc_start: 0.9020 (m-40) cc_final: 0.8709 (m-40) REVERT: P 159 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8624 (mtmm) REVERT: R 147 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8646 (mm-40) REVERT: T 126 ASP cc_start: 0.8021 (t0) cc_final: 0.7700 (t0) REVERT: U 103 GLN cc_start: 0.8033 (mp10) cc_final: 0.7733 (mp10) REVERT: V 91 LEU cc_start: 0.9560 (mm) cc_final: 0.9269 (mm) REVERT: W 57 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: W 109 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6958 (ptt90) REVERT: W 147 MET cc_start: 0.8925 (tpt) cc_final: 0.8427 (tpt) REVERT: Y 70 ASP cc_start: 0.7647 (t0) cc_final: 0.7436 (t0) REVERT: Y 115 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9291 (tp) REVERT: Y 157 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8634 (mm-40) REVERT: Z 131 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: c 67 ASP cc_start: 0.8873 (t0) cc_final: 0.8647 (t0) REVERT: c 238 MET cc_start: 0.9094 (tpp) cc_final: 0.8874 (mmm) REVERT: c 240 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9172 (tt) REVERT: d 121 SER cc_start: 0.8937 (m) cc_final: 0.8269 (t) REVERT: d 124 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7603 (ttp80) REVERT: d 125 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8671 (mp) REVERT: d 154 ASN cc_start: 0.8392 (t0) cc_final: 0.7886 (t0) REVERT: d 184 SER cc_start: 0.9113 (t) cc_final: 0.8585 (p) REVERT: e 123 MET cc_start: 0.7502 (tmm) cc_final: 0.7125 (ptt) REVERT: e 133 LEU cc_start: 0.3872 (OUTLIER) cc_final: 0.3668 (mt) REVERT: e 154 ASP cc_start: 0.7895 (p0) cc_final: 0.7559 (p0) REVERT: e 169 ASP cc_start: 0.6834 (t70) cc_final: 0.6510 (t70) REVERT: e 205 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6870 (mm) REVERT: f 102 LEU cc_start: 0.8243 (tp) cc_final: 0.7794 (pt) REVERT: f 178 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7323 (tm) REVERT: g 81 ASN cc_start: 0.7957 (p0) cc_final: 0.7714 (p0) REVERT: g 116 ASP cc_start: 0.8581 (t0) cc_final: 0.8296 (t0) REVERT: h 142 GLU cc_start: 0.7589 (tp30) cc_final: 0.7288 (tp30) REVERT: h 156 TRP cc_start: 0.8129 (OUTLIER) cc_final: 0.7753 (m100) REVERT: i 45 ASP cc_start: 0.8396 (t0) cc_final: 0.8124 (t0) REVERT: k 19 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7823 (tm-30) REVERT: k 65 ASP cc_start: 0.7150 (t0) cc_final: 0.6147 (t0) REVERT: l 119 ARG cc_start: 0.8599 (ttm170) cc_final: 0.7892 (ttt-90) REVERT: l 120 ARG cc_start: 0.6661 (ttp-170) cc_final: 0.6170 (tpp80) REVERT: o 35 MET cc_start: 0.8860 (ttm) cc_final: 0.8367 (ttt) REVERT: p 47 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9118 (mttt) REVERT: p 113 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7288 (tm-30) REVERT: p 124 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8909 (ptpp) REVERT: p 149 ASP cc_start: 0.8460 (t0) cc_final: 0.7992 (t0) REVERT: q 41 ASP cc_start: 0.8435 (p0) cc_final: 0.8027 (p0) REVERT: q 128 MET cc_start: 0.9051 (tpt) cc_final: 0.8713 (mmt) REVERT: s 51 MET cc_start: 0.8460 (tpp) cc_final: 0.8155 (tpt) REVERT: s 66 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.6915 (t60) REVERT: s 89 MET cc_start: 0.9244 (mmm) cc_final: 0.8938 (mmm) outliers start: 167 outliers final: 83 residues processed: 1104 average time/residue: 1.7639 time to fit residues: 2696.7592 Evaluate side-chains 1094 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 991 time to evaluate : 7.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 4 residue 69 LYS Chi-restraints excluded: chain 5 residue 194 LYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 150 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 95 ARG Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 118 LYS Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 160 ARG Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 894 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 528 optimal weight: 6.9990 chunk 677 optimal weight: 0.1980 chunk 524 optimal weight: 0.8980 chunk 781 optimal weight: 9.9990 chunk 518 optimal weight: 0.7980 chunk 924 optimal weight: 8.9990 chunk 578 optimal weight: 0.7980 chunk 563 optimal weight: 2.9990 chunk 426 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 232 ASN C 304 ASN D 156 ASN H 93 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS N 202 GLN O 150 GLN P 176 GLN Q 261 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 151 GLN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN Y 183 GLN c 42 GLN d 131 ASN d 220 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 85 ASN k 26 ASN k 72 HIS q 142 ASN r 146 GLN r 148 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 105693 Z= 0.163 Angle : 0.585 14.406 150190 Z= 0.301 Chirality : 0.037 0.321 17643 Planarity : 0.004 0.121 13626 Dihedral : 21.051 179.632 32010 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 1.92 % Allowed : 15.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.27 (0.09), residues: 8170 helix: 1.96 (0.10), residues: 2825 sheet: -0.26 (0.15), residues: 1097 loop : 0.52 (0.10), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP q 143 HIS 0.005 0.001 HIS S 76 PHE 0.020 0.001 PHE k 68 TYR 0.024 0.001 TYR C 426 ARG 0.014 0.000 ARG h 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1074 time to evaluate : 7.332 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: 0 128 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: 0 178 ASP cc_start: 0.8111 (t0) cc_final: 0.7890 (t0) REVERT: 1 26 THR cc_start: 0.8969 (m) cc_final: 0.8681 (p) REVERT: 2 88 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8333 (ttpp) REVERT: 6 116 ASN cc_start: 0.9044 (t0) cc_final: 0.8588 (t0) REVERT: 6 148 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8778 (mmmm) REVERT: 7 45 ASN cc_start: 0.9318 (m-40) cc_final: 0.8896 (m110) REVERT: 7 49 ASN cc_start: 0.9239 (m-40) cc_final: 0.9036 (m110) REVERT: 7 162 TYR cc_start: 0.9056 (m-80) cc_final: 0.8566 (m-80) REVERT: 7 232 HIS cc_start: 0.8815 (m-70) cc_final: 0.8605 (m90) REVERT: 8 139 MET cc_start: 0.5720 (ppp) cc_final: 0.5325 (ppp) REVERT: 9 64 ASP cc_start: 0.8121 (t0) cc_final: 0.7868 (t0) REVERT: 9 120 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: C 410 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8863 (mm) REVERT: D 161 ASP cc_start: 0.7895 (m-30) cc_final: 0.7332 (m-30) REVERT: H 100 GLN cc_start: 0.8114 (mt0) cc_final: 0.7799 (pm20) REVERT: H 122 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6264 (ttm110) REVERT: I 48 MET cc_start: 0.8716 (mmm) cc_final: 0.8392 (mmm) REVERT: I 95 MET cc_start: 0.8357 (ppp) cc_final: 0.8136 (ppp) REVERT: I 108 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: I 115 GLN cc_start: 0.9363 (mt0) cc_final: 0.8848 (tt0) REVERT: I 123 MET cc_start: 0.8667 (ttp) cc_final: 0.8315 (tmm) REVERT: J 107 GLU cc_start: 0.8580 (pm20) cc_final: 0.8281 (pm20) REVERT: K 34 MET cc_start: 0.8613 (mtp) cc_final: 0.8206 (mtm) REVERT: K 52 ASP cc_start: 0.7976 (t0) cc_final: 0.7617 (t0) REVERT: K 99 ASP cc_start: 0.8510 (t0) cc_final: 0.8307 (t0) REVERT: K 157 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8079 (mp0) REVERT: L 118 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.7012 (mmm-85) REVERT: N 114 ASP cc_start: 0.8197 (t0) cc_final: 0.7905 (t0) REVERT: N 148 ASP cc_start: 0.7857 (t70) cc_final: 0.7501 (t0) REVERT: N 149 HIS cc_start: 0.5974 (m90) cc_final: 0.5051 (m90) REVERT: P 58 LEU cc_start: 0.9293 (mt) cc_final: 0.8963 (mt) REVERT: P 114 LYS cc_start: 0.9374 (ptmm) cc_final: 0.9120 (ptpp) REVERT: P 134 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8367 (tm-30) REVERT: P 142 ASN cc_start: 0.8974 (m-40) cc_final: 0.8704 (m-40) REVERT: P 159 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8707 (mtmm) REVERT: R 147 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8632 (mm-40) REVERT: T 126 ASP cc_start: 0.8012 (t0) cc_final: 0.7665 (t0) REVERT: U 103 GLN cc_start: 0.7994 (mp10) cc_final: 0.7691 (mp10) REVERT: U 136 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7393 (tp-100) REVERT: V 23 MET cc_start: 0.8792 (mmm) cc_final: 0.8387 (mmp) REVERT: V 82 GLN cc_start: 0.8891 (mp10) cc_final: 0.8527 (mp10) REVERT: V 91 LEU cc_start: 0.9554 (mm) cc_final: 0.9290 (mm) REVERT: V 111 SER cc_start: 0.9214 (m) cc_final: 0.8768 (p) REVERT: W 147 MET cc_start: 0.8918 (tpt) cc_final: 0.8541 (tpt) REVERT: Y 70 ASP cc_start: 0.7402 (t0) cc_final: 0.7177 (t0) REVERT: Y 157 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8499 (mm-40) REVERT: Y 161 GLU cc_start: 0.7583 (pm20) cc_final: 0.7376 (pm20) REVERT: Z 131 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: c 67 ASP cc_start: 0.8840 (t0) cc_final: 0.8609 (t0) REVERT: d 121 SER cc_start: 0.8890 (m) cc_final: 0.8148 (t) REVERT: d 124 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7571 (ttp80) REVERT: d 125 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8646 (mp) REVERT: d 154 ASN cc_start: 0.8343 (t0) cc_final: 0.7808 (t0) REVERT: d 184 SER cc_start: 0.9104 (t) cc_final: 0.8622 (p) REVERT: e 123 MET cc_start: 0.7503 (tmm) cc_final: 0.7126 (ptt) REVERT: e 154 ASP cc_start: 0.7885 (p0) cc_final: 0.7563 (p0) REVERT: e 169 ASP cc_start: 0.7122 (t70) cc_final: 0.6816 (t70) REVERT: e 205 LEU cc_start: 0.7372 (pt) cc_final: 0.7003 (mm) REVERT: e 278 ASP cc_start: 0.4264 (m-30) cc_final: 0.2538 (p0) REVERT: f 95 LEU cc_start: 0.5913 (mt) cc_final: 0.5709 (mt) REVERT: f 102 LEU cc_start: 0.8248 (tp) cc_final: 0.7799 (pt) REVERT: f 178 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7290 (tm) REVERT: g 81 ASN cc_start: 0.7992 (p0) cc_final: 0.7763 (p0) REVERT: g 116 ASP cc_start: 0.8514 (t0) cc_final: 0.8190 (t70) REVERT: h 116 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: h 120 MET cc_start: 0.7837 (tpp) cc_final: 0.7316 (mpp) REVERT: h 142 GLU cc_start: 0.7554 (tp30) cc_final: 0.7347 (tp30) REVERT: i 45 ASP cc_start: 0.8319 (t0) cc_final: 0.8045 (t0) REVERT: k 19 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7679 (tm-30) REVERT: l 119 ARG cc_start: 0.8559 (ttm170) cc_final: 0.7847 (ttt-90) REVERT: l 120 ARG cc_start: 0.6593 (ttp-170) cc_final: 0.6107 (tpp80) REVERT: o 35 MET cc_start: 0.8812 (ttm) cc_final: 0.8396 (ttt) REVERT: p 47 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9140 (mttt) REVERT: p 113 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7574 (tm-30) REVERT: p 124 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8896 (ptpp) REVERT: p 149 ASP cc_start: 0.8455 (t0) cc_final: 0.7980 (t0) REVERT: s 51 MET cc_start: 0.8454 (tpp) cc_final: 0.8186 (tpt) REVERT: s 66 TRP cc_start: 0.8037 (OUTLIER) cc_final: 0.6819 (t60) REVERT: s 89 MET cc_start: 0.9283 (mmm) cc_final: 0.8943 (mmm) outliers start: 141 outliers final: 66 residues processed: 1142 average time/residue: 1.7516 time to fit residues: 2772.7748 Evaluate side-chains 1083 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1005 time to evaluate : 7.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 72 HIS Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 118 LYS Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 571 optimal weight: 2.9990 chunk 369 optimal weight: 0.0970 chunk 552 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 587 optimal weight: 6.9990 chunk 629 optimal weight: 8.9990 chunk 456 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 726 optimal weight: 1.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN 5 146 HIS 9 90 GLN C 160 HIS C 232 ASN C 304 ASN D 156 ASN F 257 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS N 138 HIS O 150 GLN P 176 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 109 ASN T 151 GLN T 201 GLN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN c 42 GLN d 131 ASN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN h 85 ASN h 147 ASN k 26 ASN q 142 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 105693 Z= 0.312 Angle : 0.623 14.347 150190 Z= 0.320 Chirality : 0.040 0.374 17643 Planarity : 0.005 0.126 13626 Dihedral : 20.969 179.980 32010 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 1.74 % Allowed : 16.53 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.26 (0.09), residues: 8170 helix: 1.92 (0.10), residues: 2826 sheet: -0.27 (0.15), residues: 1104 loop : 0.53 (0.10), residues: 4240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP q 143 HIS 0.015 0.001 HIS C 160 PHE 0.019 0.001 PHE J 90 TYR 0.022 0.001 TYR f 59 ARG 0.015 0.000 ARG J 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1008 time to evaluate : 7.373 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: 0 128 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: 0 178 ASP cc_start: 0.8133 (t0) cc_final: 0.7909 (t0) REVERT: 1 26 THR cc_start: 0.8994 (m) cc_final: 0.8753 (p) REVERT: 2 88 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8405 (ttpp) REVERT: 4 69 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8136 (mtpt) REVERT: 6 107 LYS cc_start: 0.9391 (mttp) cc_final: 0.9155 (mttp) REVERT: 6 116 ASN cc_start: 0.9044 (t0) cc_final: 0.8583 (t0) REVERT: 6 148 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8791 (mmmm) REVERT: 6 305 LYS cc_start: 0.9233 (tppp) cc_final: 0.8969 (tmmt) REVERT: 7 45 ASN cc_start: 0.9339 (m-40) cc_final: 0.8956 (m110) REVERT: 7 49 ASN cc_start: 0.9225 (m-40) cc_final: 0.9013 (m110) REVERT: 7 231 GLN cc_start: 0.8912 (pm20) cc_final: 0.8073 (pp30) REVERT: 7 232 HIS cc_start: 0.8834 (m-70) cc_final: 0.8075 (m-70) REVERT: 9 64 ASP cc_start: 0.8105 (t0) cc_final: 0.7872 (t0) REVERT: 9 120 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: C 410 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8899 (mm) REVERT: D 161 ASP cc_start: 0.7985 (m-30) cc_final: 0.7720 (m-30) REVERT: H 93 ASN cc_start: 0.9214 (m-40) cc_final: 0.8805 (t0) REVERT: H 100 GLN cc_start: 0.8196 (mt0) cc_final: 0.7872 (pm20) REVERT: H 138 LYS cc_start: 0.8261 (tmmm) cc_final: 0.8021 (tmtp) REVERT: I 48 MET cc_start: 0.8786 (mmm) cc_final: 0.8449 (mmm) REVERT: I 95 MET cc_start: 0.8448 (ppp) cc_final: 0.8150 (ppp) REVERT: I 108 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: I 115 GLN cc_start: 0.9363 (mt0) cc_final: 0.8897 (tt0) REVERT: I 119 HIS cc_start: 0.7287 (t-90) cc_final: 0.7006 (t-90) REVERT: I 123 MET cc_start: 0.8692 (ttp) cc_final: 0.8213 (tmm) REVERT: I 144 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7313 (mm) REVERT: J 107 GLU cc_start: 0.8692 (pm20) cc_final: 0.8416 (pm20) REVERT: K 34 MET cc_start: 0.8665 (mtp) cc_final: 0.8345 (mtm) REVERT: K 52 ASP cc_start: 0.8023 (t0) cc_final: 0.7659 (t0) REVERT: K 99 ASP cc_start: 0.8555 (t0) cc_final: 0.8325 (t0) REVERT: K 157 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8125 (mp0) REVERT: N 148 ASP cc_start: 0.7870 (t70) cc_final: 0.7529 (t70) REVERT: N 149 HIS cc_start: 0.6028 (m90) cc_final: 0.5086 (m90) REVERT: P 58 LEU cc_start: 0.9321 (mt) cc_final: 0.9005 (mt) REVERT: P 114 LYS cc_start: 0.9374 (ptmm) cc_final: 0.9089 (ptpp) REVERT: P 134 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8446 (tm-30) REVERT: P 142 ASN cc_start: 0.8998 (m-40) cc_final: 0.8702 (m-40) REVERT: P 159 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8549 (mtmm) REVERT: P 161 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9283 (tp) REVERT: R 147 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8651 (mm-40) REVERT: T 126 ASP cc_start: 0.8019 (t0) cc_final: 0.7695 (t0) REVERT: U 103 GLN cc_start: 0.8093 (mp10) cc_final: 0.7779 (mp10) REVERT: V 23 MET cc_start: 0.8862 (mmm) cc_final: 0.8375 (mmp) REVERT: V 82 GLN cc_start: 0.8843 (mp10) cc_final: 0.8516 (mp10) REVERT: V 91 LEU cc_start: 0.9574 (mm) cc_final: 0.9295 (mm) REVERT: V 111 SER cc_start: 0.9254 (m) cc_final: 0.8718 (p) REVERT: V 119 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9011 (mt0) REVERT: W 57 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: W 117 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9194 (mp) REVERT: W 147 MET cc_start: 0.8935 (tpt) cc_final: 0.8430 (tpt) REVERT: Y 70 ASP cc_start: 0.7566 (t0) cc_final: 0.7318 (t0) REVERT: Y 157 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8611 (mm-40) REVERT: Z 131 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: c 67 ASP cc_start: 0.8876 (t0) cc_final: 0.8672 (t0) REVERT: d 121 SER cc_start: 0.8925 (m) cc_final: 0.8207 (t) REVERT: d 124 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7701 (ttp-170) REVERT: d 125 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8672 (mp) REVERT: d 154 ASN cc_start: 0.8389 (t0) cc_final: 0.7851 (t0) REVERT: d 184 SER cc_start: 0.9134 (t) cc_final: 0.8639 (p) REVERT: e 123 MET cc_start: 0.7535 (tmm) cc_final: 0.7162 (ptt) REVERT: e 133 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.3708 (mt) REVERT: e 169 ASP cc_start: 0.6938 (t70) cc_final: 0.6666 (t70) REVERT: e 205 LEU cc_start: 0.7330 (pt) cc_final: 0.6986 (mm) REVERT: e 278 ASP cc_start: 0.3922 (m-30) cc_final: 0.2240 (OUTLIER) REVERT: f 102 LEU cc_start: 0.8232 (tp) cc_final: 0.7829 (pt) REVERT: f 178 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7267 (tm) REVERT: g 81 ASN cc_start: 0.8021 (p0) cc_final: 0.7817 (p0) REVERT: g 116 ASP cc_start: 0.8585 (t0) cc_final: 0.8238 (t70) REVERT: h 116 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7990 (mtp85) REVERT: h 142 GLU cc_start: 0.7590 (tp30) cc_final: 0.7363 (tp30) REVERT: h 156 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.7801 (m100) REVERT: i 45 ASP cc_start: 0.8394 (t0) cc_final: 0.8119 (t0) REVERT: k 19 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7669 (tm-30) REVERT: k 76 MET cc_start: 0.7770 (mmm) cc_final: 0.7497 (mmm) REVERT: l 119 ARG cc_start: 0.8589 (ttm170) cc_final: 0.7685 (ttt180) REVERT: l 120 ARG cc_start: 0.6617 (ttp-170) cc_final: 0.6096 (tpp80) REVERT: o 35 MET cc_start: 0.8876 (ttm) cc_final: 0.8542 (ttt) REVERT: p 47 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9056 (mttt) REVERT: p 124 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8917 (ptpp) REVERT: p 149 ASP cc_start: 0.8484 (t0) cc_final: 0.8011 (t0) REVERT: q 41 ASP cc_start: 0.8398 (p0) cc_final: 0.7895 (p0) REVERT: q 44 ASP cc_start: 0.9014 (t0) cc_final: 0.8718 (t0) REVERT: s 51 MET cc_start: 0.8501 (tpp) cc_final: 0.8218 (tpt) REVERT: s 66 TRP cc_start: 0.8072 (OUTLIER) cc_final: 0.6855 (t60) REVERT: s 89 MET cc_start: 0.9257 (mmm) cc_final: 0.8948 (mmm) outliers start: 128 outliers final: 73 residues processed: 1072 average time/residue: 1.8421 time to fit residues: 2744.2011 Evaluate side-chains 1076 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 984 time to evaluate : 7.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 4 residue 69 LYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 119 GLN Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 85 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 72 HIS Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 118 LYS Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 840 optimal weight: 2.9990 chunk 885 optimal weight: 3.9990 chunk 807 optimal weight: 50.0000 chunk 861 optimal weight: 10.0000 chunk 518 optimal weight: 0.8980 chunk 375 optimal weight: 6.9990 chunk 676 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 778 optimal weight: 10.0000 chunk 814 optimal weight: 10.0000 chunk 858 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN 9 90 GLN C 232 ASN C 304 ASN D 156 ASN F 257 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS N 138 HIS N 202 GLN O 150 GLN P 176 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 109 ASN T 133 ASN T 151 GLN T 201 GLN V 82 GLN ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 131 ASN d 211 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN k 26 ASN k 46 ASN k 72 HIS r 146 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 105693 Z= 0.297 Angle : 0.623 14.488 150190 Z= 0.321 Chirality : 0.040 0.373 17643 Planarity : 0.005 0.125 13626 Dihedral : 20.987 179.997 32010 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.93 % Favored : 97.06 % Rotamer: Outliers : 1.72 % Allowed : 16.79 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.24 (0.09), residues: 8170 helix: 1.88 (0.10), residues: 2829 sheet: -0.28 (0.15), residues: 1105 loop : 0.54 (0.10), residues: 4236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP q 143 HIS 0.010 0.001 HIS 6 307 PHE 0.021 0.001 PHE k 68 TYR 0.025 0.001 TYR C 426 ARG 0.016 0.000 ARG h 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1004 time to evaluate : 7.206 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: 0 128 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: 0 178 ASP cc_start: 0.8130 (t0) cc_final: 0.7908 (t0) REVERT: 1 26 THR cc_start: 0.8991 (m) cc_final: 0.8771 (p) REVERT: 2 88 LYS cc_start: 0.8904 (ttpp) cc_final: 0.8394 (ttpp) REVERT: 4 69 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8125 (mtpt) REVERT: 6 107 LYS cc_start: 0.9389 (mttp) cc_final: 0.9153 (mttp) REVERT: 6 116 ASN cc_start: 0.9079 (t0) cc_final: 0.8618 (t0) REVERT: 6 148 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8790 (mmmm) REVERT: 6 305 LYS cc_start: 0.9227 (tppp) cc_final: 0.9005 (tmmt) REVERT: 7 45 ASN cc_start: 0.9335 (m-40) cc_final: 0.8990 (m110) REVERT: 7 49 ASN cc_start: 0.9226 (m-40) cc_final: 0.9025 (m110) REVERT: 7 162 TYR cc_start: 0.9015 (m-80) cc_final: 0.8517 (m-80) REVERT: 7 231 GLN cc_start: 0.8861 (pm20) cc_final: 0.7948 (pp30) REVERT: 7 232 HIS cc_start: 0.8837 (m-70) cc_final: 0.8071 (m90) REVERT: 9 64 ASP cc_start: 0.8115 (t0) cc_final: 0.7891 (t0) REVERT: 9 120 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: C 410 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8921 (mm) REVERT: H 93 ASN cc_start: 0.9221 (m-40) cc_final: 0.8857 (t0) REVERT: H 100 GLN cc_start: 0.8229 (mt0) cc_final: 0.7900 (pm20) REVERT: H 138 LYS cc_start: 0.8186 (tmmm) cc_final: 0.7906 (tmtp) REVERT: I 48 MET cc_start: 0.8789 (mmm) cc_final: 0.8455 (mmm) REVERT: I 95 MET cc_start: 0.8476 (ppp) cc_final: 0.8159 (ppp) REVERT: I 108 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: I 115 GLN cc_start: 0.9388 (mt0) cc_final: 0.8939 (tt0) REVERT: I 119 HIS cc_start: 0.7523 (t-90) cc_final: 0.7257 (t-90) REVERT: I 123 MET cc_start: 0.8721 (ttp) cc_final: 0.8252 (tmm) REVERT: I 144 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7312 (mm) REVERT: K 34 MET cc_start: 0.8664 (mtp) cc_final: 0.8341 (mtm) REVERT: K 52 ASP cc_start: 0.8025 (t0) cc_final: 0.7666 (t0) REVERT: K 99 ASP cc_start: 0.8552 (t0) cc_final: 0.8331 (t0) REVERT: K 157 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8168 (mp0) REVERT: N 148 ASP cc_start: 0.7876 (t70) cc_final: 0.7530 (t70) REVERT: N 149 HIS cc_start: 0.6031 (m90) cc_final: 0.5075 (m90) REVERT: P 58 LEU cc_start: 0.9323 (mt) cc_final: 0.8999 (mt) REVERT: P 114 LYS cc_start: 0.9362 (ptmm) cc_final: 0.9116 (ptpp) REVERT: P 134 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8405 (tm-30) REVERT: P 142 ASN cc_start: 0.8999 (m-40) cc_final: 0.8682 (m-40) REVERT: P 159 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8610 (mtmm) REVERT: R 147 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8663 (mm-40) REVERT: T 126 ASP cc_start: 0.8038 (t0) cc_final: 0.7690 (t0) REVERT: U 103 GLN cc_start: 0.8098 (mp10) cc_final: 0.7858 (mp10) REVERT: V 23 MET cc_start: 0.8856 (mmm) cc_final: 0.8413 (mmp) REVERT: V 91 LEU cc_start: 0.9573 (mm) cc_final: 0.9296 (mm) REVERT: W 57 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: W 117 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9212 (mp) REVERT: W 147 MET cc_start: 0.8925 (tpt) cc_final: 0.8437 (tpt) REVERT: Y 157 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8595 (mm-40) REVERT: Z 131 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: c 67 ASP cc_start: 0.8866 (t0) cc_final: 0.8645 (t0) REVERT: d 121 SER cc_start: 0.8950 (m) cc_final: 0.8524 (t) REVERT: d 124 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7502 (ttp80) REVERT: d 154 ASN cc_start: 0.8392 (t0) cc_final: 0.7853 (t0) REVERT: d 184 SER cc_start: 0.9131 (t) cc_final: 0.8630 (p) REVERT: e 123 MET cc_start: 0.7509 (tmm) cc_final: 0.7168 (ptt) REVERT: e 169 ASP cc_start: 0.6960 (t70) cc_final: 0.6670 (t70) REVERT: e 205 LEU cc_start: 0.7311 (pt) cc_final: 0.6939 (mm) REVERT: f 102 LEU cc_start: 0.8228 (tp) cc_final: 0.7821 (pt) REVERT: f 178 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7318 (tm) REVERT: g 43 ASP cc_start: 0.8029 (m-30) cc_final: 0.7436 (m-30) REVERT: g 116 ASP cc_start: 0.8581 (t0) cc_final: 0.8268 (t0) REVERT: h 116 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7936 (mtp85) REVERT: h 142 GLU cc_start: 0.7596 (tp30) cc_final: 0.7341 (tp30) REVERT: h 156 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.7842 (m100) REVERT: i 45 ASP cc_start: 0.8392 (t0) cc_final: 0.8119 (t0) REVERT: k 19 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7677 (tm-30) REVERT: l 119 ARG cc_start: 0.8621 (ttm170) cc_final: 0.7698 (ttt180) REVERT: l 120 ARG cc_start: 0.6629 (ttp-170) cc_final: 0.6098 (tpp80) REVERT: o 35 MET cc_start: 0.8861 (ttm) cc_final: 0.8376 (ttt) REVERT: o 51 MET cc_start: 0.8477 (mtp) cc_final: 0.8270 (mtp) REVERT: p 47 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9161 (mttt) REVERT: p 124 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8909 (ptpp) REVERT: p 149 ASP cc_start: 0.8473 (t0) cc_final: 0.8008 (t0) REVERT: q 41 ASP cc_start: 0.8410 (p0) cc_final: 0.7907 (p0) REVERT: q 44 ASP cc_start: 0.9026 (t0) cc_final: 0.8740 (t0) REVERT: q 128 MET cc_start: 0.9252 (mmt) cc_final: 0.8734 (tpt) REVERT: s 51 MET cc_start: 0.8507 (tpp) cc_final: 0.8213 (tpt) REVERT: s 66 TRP cc_start: 0.8110 (OUTLIER) cc_final: 0.6912 (t60) REVERT: s 89 MET cc_start: 0.9258 (mmm) cc_final: 0.8943 (mmm) outliers start: 126 outliers final: 71 residues processed: 1066 average time/residue: 1.8297 time to fit residues: 2695.1617 Evaluate side-chains 1070 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 983 time to evaluate : 8.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 4 residue 69 LYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 565 optimal weight: 8.9990 chunk 910 optimal weight: 5.9990 chunk 555 optimal weight: 5.9990 chunk 432 optimal weight: 20.0000 chunk 633 optimal weight: 2.9990 chunk 955 optimal weight: 4.9990 chunk 879 optimal weight: 10.0000 chunk 760 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 587 optimal weight: 10.0000 chunk 466 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 144 GLN 3 154 GLN 9 90 GLN C 232 ASN C 261 GLN C 304 ASN D 156 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS N 138 HIS N 202 GLN O 150 GLN P 176 GLN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 109 ASN T 151 GLN T 201 GLN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN V 119 GLN ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 ASN d 131 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 105693 Z= 0.335 Angle : 0.642 14.506 150190 Z= 0.331 Chirality : 0.041 0.375 17643 Planarity : 0.005 0.126 13626 Dihedral : 20.982 179.795 32010 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.00 % Favored : 96.99 % Rotamer: Outliers : 1.51 % Allowed : 17.20 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 1.19 (0.09), residues: 8170 helix: 1.82 (0.10), residues: 2832 sheet: -0.29 (0.15), residues: 1109 loop : 0.52 (0.10), residues: 4229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP q 143 HIS 0.006 0.001 HIS S 76 PHE 0.024 0.001 PHE J 90 TYR 0.023 0.001 TYR f 59 ARG 0.015 0.001 ARG M 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16340 Ramachandran restraints generated. 8170 Oldfield, 0 Emsley, 8170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 990 time to evaluate : 7.722 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: 0 128 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: 0 178 ASP cc_start: 0.8141 (t0) cc_final: 0.7910 (t0) REVERT: 1 26 THR cc_start: 0.8994 (m) cc_final: 0.8768 (p) REVERT: 2 88 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8399 (ttpp) REVERT: 4 69 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8127 (mtpt) REVERT: 6 107 LYS cc_start: 0.9389 (mttp) cc_final: 0.9154 (mttp) REVERT: 6 116 ASN cc_start: 0.9084 (t0) cc_final: 0.8623 (t0) REVERT: 6 148 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8791 (mmmm) REVERT: 6 305 LYS cc_start: 0.9243 (tppp) cc_final: 0.9014 (tmmt) REVERT: 7 45 ASN cc_start: 0.9341 (m-40) cc_final: 0.8976 (m110) REVERT: 7 49 ASN cc_start: 0.9217 (m-40) cc_final: 0.9016 (m110) REVERT: 7 162 TYR cc_start: 0.9109 (m-80) cc_final: 0.8705 (m-80) REVERT: 7 231 GLN cc_start: 0.8854 (pm20) cc_final: 0.8010 (pp30) REVERT: 7 232 HIS cc_start: 0.8841 (m-70) cc_final: 0.8046 (m90) REVERT: 9 64 ASP cc_start: 0.8142 (t0) cc_final: 0.7921 (t0) REVERT: 9 83 GLU cc_start: 0.7717 (tp30) cc_final: 0.7188 (tp30) REVERT: 9 120 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: C 410 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8939 (mm) REVERT: H 93 ASN cc_start: 0.9227 (m-40) cc_final: 0.8866 (t0) REVERT: H 100 GLN cc_start: 0.8183 (mt0) cc_final: 0.7855 (pm20) REVERT: I 48 MET cc_start: 0.8801 (mmm) cc_final: 0.8466 (mmm) REVERT: I 95 MET cc_start: 0.8499 (ppp) cc_final: 0.8191 (ppp) REVERT: I 108 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: I 115 GLN cc_start: 0.9389 (mt0) cc_final: 0.8889 (tt0) REVERT: I 119 HIS cc_start: 0.7674 (t-90) cc_final: 0.7392 (t-90) REVERT: I 123 MET cc_start: 0.8735 (ttp) cc_final: 0.8260 (tmm) REVERT: I 144 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7275 (mm) REVERT: J 21 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7263 (mmm160) REVERT: J 104 THR cc_start: 0.7757 (t) cc_final: 0.7449 (t) REVERT: K 34 MET cc_start: 0.8646 (mtp) cc_final: 0.8292 (mtm) REVERT: K 52 ASP cc_start: 0.8035 (t0) cc_final: 0.7677 (t0) REVERT: K 99 ASP cc_start: 0.8566 (t0) cc_final: 0.8352 (t0) REVERT: K 157 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8176 (mp0) REVERT: N 148 ASP cc_start: 0.7892 (t70) cc_final: 0.7547 (t70) REVERT: N 149 HIS cc_start: 0.6058 (m90) cc_final: 0.5091 (m90) REVERT: P 58 LEU cc_start: 0.9327 (mt) cc_final: 0.9014 (mt) REVERT: P 114 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9121 (ptpp) REVERT: P 134 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8424 (tm-30) REVERT: P 142 ASN cc_start: 0.9002 (m-40) cc_final: 0.8694 (m-40) REVERT: P 159 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8547 (mtmm) REVERT: R 147 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8655 (mm-40) REVERT: T 126 ASP cc_start: 0.8057 (t0) cc_final: 0.7711 (t0) REVERT: U 103 GLN cc_start: 0.8120 (mp10) cc_final: 0.7878 (mp10) REVERT: V 23 MET cc_start: 0.8873 (mmm) cc_final: 0.8392 (mmp) REVERT: V 82 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: V 91 LEU cc_start: 0.9575 (mm) cc_final: 0.9295 (mm) REVERT: V 119 GLN cc_start: 0.9240 (mt0) cc_final: 0.8909 (mt0) REVERT: W 57 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: W 117 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9242 (mp) REVERT: W 147 MET cc_start: 0.8908 (tpt) cc_final: 0.8424 (tpt) REVERT: Y 70 ASP cc_start: 0.7591 (t0) cc_final: 0.7373 (t0) REVERT: Y 157 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8598 (mm-40) REVERT: Z 131 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: d 121 SER cc_start: 0.8968 (m) cc_final: 0.8197 (t) REVERT: d 124 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7379 (ttp80) REVERT: d 125 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8699 (mp) REVERT: d 154 ASN cc_start: 0.8404 (t0) cc_final: 0.7883 (t0) REVERT: d 184 SER cc_start: 0.9115 (t) cc_final: 0.8595 (p) REVERT: e 123 MET cc_start: 0.7515 (tmm) cc_final: 0.7159 (ptt) REVERT: e 169 ASP cc_start: 0.6864 (t70) cc_final: 0.6597 (t70) REVERT: e 205 LEU cc_start: 0.7358 (pt) cc_final: 0.7014 (mm) REVERT: f 102 LEU cc_start: 0.8224 (tp) cc_final: 0.7819 (pt) REVERT: f 178 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7307 (tm) REVERT: g 116 ASP cc_start: 0.8592 (t0) cc_final: 0.8280 (t0) REVERT: h 116 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7875 (mtp85) REVERT: h 156 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7846 (m100) REVERT: i 45 ASP cc_start: 0.8386 (t0) cc_final: 0.8109 (t0) REVERT: k 19 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7704 (tm-30) REVERT: k 86 MET cc_start: 0.9042 (mmm) cc_final: 0.8654 (mtt) REVERT: l 119 ARG cc_start: 0.8674 (ttm170) cc_final: 0.7762 (ttt180) REVERT: l 120 ARG cc_start: 0.6644 (ttp-170) cc_final: 0.6098 (tpp80) REVERT: o 35 MET cc_start: 0.8873 (ttm) cc_final: 0.8381 (ttt) REVERT: o 51 MET cc_start: 0.8505 (mtp) cc_final: 0.8292 (mtp) REVERT: p 47 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9135 (mttt) REVERT: p 124 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8910 (ptpp) REVERT: p 149 ASP cc_start: 0.8489 (t0) cc_final: 0.8022 (t0) REVERT: q 41 ASP cc_start: 0.8422 (p0) cc_final: 0.7919 (p0) REVERT: q 44 ASP cc_start: 0.9030 (t0) cc_final: 0.8754 (t0) REVERT: q 128 MET cc_start: 0.9237 (mmt) cc_final: 0.8752 (tpt) REVERT: s 51 MET cc_start: 0.8519 (tpp) cc_final: 0.8184 (tpt) REVERT: s 66 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.6974 (t60) REVERT: s 89 MET cc_start: 0.9256 (mmm) cc_final: 0.8938 (mmm) outliers start: 111 outliers final: 78 residues processed: 1048 average time/residue: 1.8329 time to fit residues: 2667.7048 Evaluate side-chains 1074 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 978 time to evaluate : 7.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 153 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 4 residue 69 LYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 247 ASN Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 82 GLN Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain a residue 142 ARG Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 124 ARG Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 122 LYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain p residue 47 LYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 41 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 604 optimal weight: 0.6980 chunk 810 optimal weight: 30.0000 chunk 233 optimal weight: 10.0000 chunk 701 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 762 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 chunk 782 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN ** 5 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 232 ASN C 304 ASN D 156 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 72 GLN N 98 HIS N 138 HIS O 150 GLN P 176 GLN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 109 ASN T 151 GLN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 131 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN k 26 ASN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS r 146 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.041836 restraints weight = 297083.000| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.00 r_work: 0.2537 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.340 105693 Z= 0.360 Angle : 0.678 65.897 150190 Z= 0.358 Chirality : 0.041 1.148 17643 Planarity : 0.006 0.298 13626 Dihedral : 20.982 179.790 32010 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.00 % Favored : 96.99 % Rotamer: Outliers : 1.73 % Allowed : 17.17 % Favored : 81.10 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.26 % 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: 1.19 (0.09), residues: 8170 helix: 1.82 (0.10), residues: 2832 sheet: -0.29 (0.15), residues: 1109 loop : 0.51 (0.10), residues: 4229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP q 143 HIS 0.007 0.001 HIS I 61 PHE 0.022 0.001 PHE J 90 TYR 0.022 0.001 TYR 5 176 ARG 0.011 0.000 ARG Z 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40391.02 seconds wall clock time: 704 minutes 36.48 seconds (42276.48 seconds total)