Starting phenix.real_space_refine on Thu Feb 22 14:09:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of6_12871/02_2024/7of6_12871_updated.pdb" } resolution = 2.6 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= 0.004 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 88 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 "5 PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 100321 Number of models: 1 Model: "" Number of chains: 61 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 149 Unusual residues: {' MG': 85, 'GTP': 2} Classifications: {'undetermined': 87} Link IDs: {None: 86} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 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: "T" 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 0 110 134.247 40.314 126.528 1.00 73.37 S ATOM 286 SG CYS 0 113 137.571 41.581 124.997 1.00 76.43 S ATOM 366 SG CYS 0 123 134.502 43.414 124.437 1.00 69.81 S ATOM 389 SG CYS 0 126 134.872 39.901 122.802 1.00 73.25 S ATOM 2605 SG CYS 4 76 57.344 111.261 167.633 1.00 75.74 S ATOM 2628 SG CYS 4 79 61.046 110.405 167.368 1.00 72.54 S ATOM 2752 SG CYS 4 92 58.375 107.696 166.870 1.00 70.12 S ATOM 55608 SG CYS I 64 80.827 114.533 198.223 1.00 80.99 S ATOM 96084 SG CYS r 70 80.252 110.539 198.756 1.00 75.05 S ATOM 96105 SG CYS r 73 83.422 112.205 198.452 1.00 75.67 S ATOM 96399 SG CYS r 108 80.502 112.087 195.442 1.00 75.01 S Time building chain proxies: 38.50, per 1000 atoms: 0.38 Number of scatterers: 100321 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 88 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: 37.51 Conformation dependent library (CDL) restraints added in 9.6 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 r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " 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: 274 helices and 80 sheets defined 41.6% alpha, 14.0% beta 399 base pairs and 700 stacking pairs defined. Time for finding SS restraints: 60.29 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: 5.650A 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: 3.836A 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: 3.592A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.704A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.470A 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: 3.862A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.799A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 3.635A pdb=" N HIS 3 181 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 5.042A 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: 5.131A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 3.709A 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: 4.038A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 3.992A 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: 4.190A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.579A 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: 4.051A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 4.918A 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: 4.060A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.279A 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: 3.752A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 5.294A 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: 4.933A pdb=" N LEU 6 366 " --> pdb=" O PRO 6 362 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 3.910A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 4.019A 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: 3.910A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 3.863A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.480A 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: 4.121A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 4.855A 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: 4.975A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 removed outlier: 3.728A pdb=" N LEU 8 168 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) removed outlier: 3.908A 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 34 Processing helix chain '9' and resid 53 through 58 removed outlier: 3.533A 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 95 Processing helix chain '9' and resid 96 through 106 Processing helix chain '9' and resid 113 through 118 removed outlier: 4.668A pdb=" N TYR 9 117 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 removed outlier: 4.015A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) 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 211 Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 255 through 293 removed outlier: 6.147A pdb=" N GLN C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 261 " --> pdb=" O MET C 257 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.087A 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 363 removed outlier: 5.232A pdb=" N GLU C 363 " --> pdb=" O HIS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 375 removed outlier: 4.864A pdb=" N THR C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 404 removed outlier: 3.796A pdb=" N GLN C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 removed outlier: 4.440A pdb=" N SER C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.921A 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 514 Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.674A 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: 3.605A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 removed outlier: 4.664A pdb=" N HIS E 52 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU E 53 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 54' Processing helix chain 'E' and resid 55 through 83 Proline residue: E 59 - end of helix removed outlier: 3.639A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.822A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.620A 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: 4.337A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.117A 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: 4.614A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.211A 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 92 through 108 removed outlier: 4.747A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.155A 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: 3.597A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.769A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.011A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.817A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.598A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.228A 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: 3.976A 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 Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.985A 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: 3.819A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 139 Proline residue: I 133 - end of helix removed outlier: 4.173A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.669A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.912A 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: 3.688A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.339A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.792A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.018A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.061A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 4.150A 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: 4.906A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 4.966A 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: 5.497A 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: 4.550A pdb=" N ARG L 128 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.995A 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: 5.268A 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: 3.670A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.582A 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: 3.558A 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: 3.571A 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: 3.820A 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: 4.020A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.495A 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: 4.763A pdb=" N ILE N 72 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 4.977A 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: 3.914A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.831A 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: 4.597A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.392A 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: 4.346A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 4.966A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.304A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.995A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.216A 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: 4.713A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 6.018A 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: 4.085A 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: 3.918A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 194 removed outlier: 4.707A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.588A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.707A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.237A 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: 4.006A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.560A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 80 removed outlier: 4.372A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.954A 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 109 Processing helix chain 'R' and resid 110 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.669A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.853A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.596A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.136A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.630A 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: 4.721A 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: 3.809A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.613A 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: 5.638A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 3.959A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.775A 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: 3.656A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.599A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.141A 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: 5.668A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.709A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.572A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.731A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.440A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 4.955A 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: 4.664A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.394A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.765A 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: 4.061A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.643A 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: 4.629A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.821A 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: 4.542A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.418A 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: 3.683A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.195A 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: 5.421A 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: 3.806A 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: 5.308A 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: 3.708A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.895A 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: 4.269A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (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: 3.639A 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: 5.142A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.510A 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: 3.569A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 removed outlier: 4.698A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.686A 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: 4.062A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER e 196 " --> pdb=" O LEU e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.538A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.713A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.205A 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: 3.534A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU f 178 " --> pdb=" O ILE f 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.483A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.849A 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: 4.166A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.232A 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: 4.639A 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: 4.067A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.141A 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: 3.763A 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 Processing helix chain 'k' and resid 40 through 47 Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'l' and resid 114 through 135 removed outlier: 4.643A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 52 removed outlier: 4.065A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.838A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.119A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.846A 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: 4.910A 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: 4.062A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.064A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.657A 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 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.327A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.349A 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: 4.481A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.703A 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: 3.939A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 4.977A 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: 5.520A 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: 3.709A 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 167 through 193 removed outlier: 4.051A 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: 4.315A 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: 4.259A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.336A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.604A 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: 5.859A 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: 5.976A 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: 6.872A 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: 5.123A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR 5 290 " --> pdb=" O LEU 5 230 " (cutoff:3.500A) removed outlier: 8.819A 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: 4.720A 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: 6.600A 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: 4.590A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.701A 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: 6.618A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.993A 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: 8.262A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) removed outlier: 6.731A 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: 5.153A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 7.019A 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: 4.639A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 7.541A 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: 7.004A 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: 4.721A 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: 5.448A 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: 3.657A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 137 through 145 removed outlier: 3.553A pdb=" N GLN C 138 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 332 through 339 removed outlier: 3.925A pdb=" N MET C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 379 through 383 Processing sheet with id= 22, first strand: chain 'C' and resid 463 through 470 removed outlier: 3.928A pdb=" N ALA C 495 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 128 through 131 removed outlier: 3.794A pdb=" N GLN D 128 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.551A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 139 through 144 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: 3.773A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.529A 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: 6.526A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.974A 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: 4.378A 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: 7.088A 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: 4.097A 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: 3.550A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.993A 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: 5.254A 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: 7.352A 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 96 Processing sheet with id= 43, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.560A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.405A 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 45 removed outlier: 4.315A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.634A 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 removed outlier: 6.296A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 129 through 135 removed outlier: 4.473A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.643A 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: 3.851A 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: 3.917A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 154 through 157 Processing sheet with id= 51, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 52, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.086A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.923A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.351A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.588A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.990A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'V' and resid 132 through 135 removed outlier: 7.332A pdb=" N GLU V 132 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG V 152 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 81 through 84 removed outlier: 4.518A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'W' and resid 97 through 103 Processing sheet with id= 61, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.187A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.064A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 64, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.226A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'a' and resid 44 through 52 removed outlier: 5.610A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL a 65 " --> pdb=" O ASN a 44 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'b' and resid 61 through 68 removed outlier: 4.115A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 68, first strand: chain 'c' and resid 269 through 274 removed outlier: 3.838A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'd' and resid 212 through 218 removed outlier: 3.876A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 175 through 178 removed outlier: 3.856A pdb=" N TRP e 178 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.336A 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: 6.292A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.061A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.803A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR f 125 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.428A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'k' and resid 51 through 56 removed outlier: 4.115A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'm' and resid 53 through 56 Processing sheet with id= 76, first strand: chain 'p' and resid 78 through 82 Processing sheet with id= 77, first strand: chain 'r' and resid 35 through 42 removed outlier: 4.229A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 's' and resid 90 through 93 removed outlier: 4.151A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 's' and resid 112 through 116 removed outlier: 6.225A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.537A 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: 5.165A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 's' and resid 241 through 244 removed outlier: 6.622A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) 2656 hydrogen bonds defined for protein. 7878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 978 hydrogen bonds 1662 hydrogen bond angles 0 basepair planarities 399 basepair parallelities 700 stacking parallelities Total time for adding SS restraints: 81.70 Time building geometry restraints manager: 40.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 26747 1.34 - 1.46: 31840 1.46 - 1.58: 43626 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 1.329 0.160 2.00e-02 2.50e+03 6.38e+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 5.11e+01 bond pdb=" N3 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 1.492 1.353 0.139 2.00e-02 2.50e+03 4.81e+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 3.88e+01 bond pdb=" C5 OMU A3039 " pdb=" C6 OMU A3039 " ideal model delta sigma weight residual 1.496 1.377 0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 105688 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.23: 11151 106.23 - 113.73: 60629 113.73 - 121.23: 51373 121.23 - 128.74: 24790 128.74 - 136.24: 2247 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 108.29 125.14 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C8 OMG A2815 " ideal model delta sigma weight residual 142.82 126.38 16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 108.29 123.65 -15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C8 OMG A3040 " ideal model delta sigma weight residual 142.82 127.71 15.11 3.00e+00 1.11e-01 2.54e+01 angle pdb=" C3' U A3041 " pdb=" C2' U A3041 " pdb=" O2' U A3041 " ideal model delta sigma weight residual 110.70 117.81 -7.11 1.50e+00 4.44e-01 2.25e+01 ... (remaining 150185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 61158 35.63 - 71.25: 3529 71.25 - 106.88: 489 106.88 - 142.50: 23 142.50 - 178.13: 43 Dihedral angle restraints: 65242 sinusoidal: 41027 harmonic: 24215 Sorted by residual: 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 23.98 176.02 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A2898 " pdb=" C1' U A2898 " pdb=" N1 U A2898 " pdb=" C2 U A2898 " ideal model delta sinusoidal sigma weight residual -160.00 14.02 -174.02 1 1.50e+01 4.44e-03 8.51e+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 13.53 -173.53 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 65239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 15626 0.052 - 0.104: 1545 0.104 - 0.157: 451 0.157 - 0.209: 18 0.209 - 0.261: 3 Chirality restraints: 17643 Sorted by residual: chirality pdb=" C3' U A3041 " pdb=" C4' U A3041 " pdb=" O3' U A3041 " pdb=" C2' U A3041 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' A A1823 " pdb=" C4' A A1823 " pdb=" O3' A A1823 " pdb=" C2' A A1823 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' U A3067 " pdb=" O4' U A3067 " pdb=" C2' U A3067 " pdb=" N1 U A3067 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 17640 not shown) Planarity restraints: 13626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2815 " 0.054 2.00e-02 2.50e+03 5.59e-01 7.02e+03 pdb=" C4' OMG A2815 " 0.416 2.00e-02 2.50e+03 pdb=" O4' OMG A2815 " 0.536 2.00e-02 2.50e+03 pdb=" C3' OMG A2815 " -0.597 2.00e-02 2.50e+03 pdb=" O3' OMG A2815 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMG A2815 " -0.194 2.00e-02 2.50e+03 pdb=" O2' OMG A2815 " 0.943 2.00e-02 2.50e+03 pdb=" C1' OMG A2815 " 0.239 2.00e-02 2.50e+03 pdb=" N9 OMG A2815 " -0.821 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " -0.002 2.00e-02 2.50e+03 5.48e-01 6.77e+03 pdb=" C4' OMG A3040 " 0.433 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.598 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.582 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.516 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.214 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.868 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.247 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.834 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMU A3039 " -0.027 2.00e-02 2.50e+03 5.38e-01 6.51e+03 pdb=" C4' OMU A3039 " 0.433 2.00e-02 2.50e+03 pdb=" O4' OMU A3039 " 0.633 2.00e-02 2.50e+03 pdb=" C3' OMU A3039 " -0.564 2.00e-02 2.50e+03 pdb=" O3' OMU A3039 " -0.461 2.00e-02 2.50e+03 pdb=" C2' OMU A3039 " -0.217 2.00e-02 2.50e+03 pdb=" O2' OMU A3039 " 0.802 2.00e-02 2.50e+03 pdb=" C1' OMU A3039 " 0.255 2.00e-02 2.50e+03 pdb=" N1 OMU A3039 " -0.854 2.00e-02 2.50e+03 ... (remaining 13623 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 395 2.41 - 3.03: 59834 3.03 - 3.65: 171329 3.65 - 4.28: 270839 4.28 - 4.90: 405193 Nonbonded interactions: 907590 Sorted by model distance: nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3313 " model vdw 1.785 2.170 nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3313 " model vdw 1.812 2.170 nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3337 " model vdw 1.856 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3337 " model vdw 1.867 2.170 nonbonded pdb=" OP2 U A2660 " pdb="MG MG A3348 " model vdw 1.883 2.170 ... (remaining 907585 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 12.530 Check model and map are aligned: 1.140 Set scattering table: 0.680 Process input model: 315.400 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 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 : 0.003 0.160 105693 Z= 0.181 Angle : 0.530 16.846 150190 Z= 0.268 Chirality : 0.037 0.261 17643 Planarity : 0.009 0.559 13626 Dihedral : 19.403 178.127 49562 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.01 % Allowed : 0.01 % Favored : 99.97 % 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: 1.49 (0.10), residues: 8170 helix: 2.23 (0.10), residues: 2810 sheet: -0.16 (0.16), residues: 1053 loop : 0.58 (0.10), residues: 4307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP h 156 HIS 0.015 0.001 HIS S 76 PHE 0.015 0.001 PHE c 140 TYR 0.022 0.001 TYR F 280 ARG 0.012 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 1591 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1590 time to evaluate : 7.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 125 TYR cc_start: 0.8905 (t80) cc_final: 0.8685 (t80) REVERT: 0 174 ILE cc_start: 0.9577 (mm) cc_final: 0.9007 (mp) REVERT: 0 178 ASP cc_start: 0.8020 (t0) cc_final: 0.7771 (OUTLIER) REVERT: 1 26 THR cc_start: 0.8957 (m) cc_final: 0.8556 (p) REVERT: 5 366 CYS cc_start: 0.7694 (t) cc_final: 0.5159 (t) REVERT: 6 274 LYS cc_start: 0.8718 (tttm) cc_final: 0.8492 (tttp) REVERT: 7 93 MET cc_start: 0.8600 (mtm) cc_final: 0.8197 (mtp) REVERT: 7 232 HIS cc_start: 0.8728 (m-70) cc_final: 0.8495 (m-70) REVERT: 9 66 THR cc_start: 0.9069 (p) cc_final: 0.8683 (p) REVERT: 9 90 GLN cc_start: 0.8610 (tt0) cc_final: 0.8402 (tt0) REVERT: 9 117 TYR cc_start: 0.8151 (m-80) cc_final: 0.7148 (m-80) REVERT: H 104 ASN cc_start: 0.8582 (m-40) cc_final: 0.8166 (m-40) REVERT: H 137 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8880 (mtpp) REVERT: I 79 ILE cc_start: 0.8807 (pt) cc_final: 0.8465 (mp) REVERT: I 86 ILE cc_start: 0.9606 (mm) cc_final: 0.9060 (mm) REVERT: I 95 MET cc_start: 0.8896 (ppp) cc_final: 0.8525 (ppp) REVERT: I 105 SER cc_start: 0.8782 (m) cc_final: 0.8320 (p) REVERT: I 108 ASP cc_start: 0.8828 (m-30) cc_final: 0.8260 (m-30) REVERT: I 119 HIS cc_start: 0.7938 (t70) cc_final: 0.7570 (t70) REVERT: I 123 MET cc_start: 0.9004 (tmm) cc_final: 0.8668 (tmt) REVERT: I 128 ASN cc_start: 0.8190 (m-40) cc_final: 0.7940 (m110) REVERT: J 92 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7392 (pttt) REVERT: K 52 ASP cc_start: 0.8083 (t0) cc_final: 0.7795 (t0) REVERT: K 99 ASP cc_start: 0.8504 (t0) cc_final: 0.8302 (t0) REVERT: K 122 MET cc_start: 0.8911 (mmm) cc_final: 0.8699 (mmm) REVERT: K 160 GLN cc_start: 0.8664 (tp40) cc_final: 0.8251 (tp-100) REVERT: K 164 ASP cc_start: 0.8516 (m-30) cc_final: 0.8062 (m-30) REVERT: L 133 GLU cc_start: 0.7488 (tt0) cc_final: 0.7191 (tt0) REVERT: N 96 TYR cc_start: 0.9209 (m-80) cc_final: 0.8989 (m-80) REVERT: N 114 ASP cc_start: 0.8729 (t0) cc_final: 0.8462 (t0) REVERT: N 148 ASP cc_start: 0.8117 (t0) cc_final: 0.7339 (t0) REVERT: N 149 HIS cc_start: 0.5428 (m-70) cc_final: 0.4843 (m-70) REVERT: P 114 LYS cc_start: 0.9448 (ptmt) cc_final: 0.9154 (ptmm) REVERT: P 115 HIS cc_start: 0.8636 (m-70) cc_final: 0.8198 (m90) REVERT: P 134 GLN cc_start: 0.8914 (tt0) cc_final: 0.8328 (tm-30) REVERT: Q 184 ASP cc_start: 0.8375 (m-30) cc_final: 0.8144 (m-30) REVERT: Q 274 ASP cc_start: 0.8311 (t0) cc_final: 0.8043 (t0) REVERT: U 52 ASP cc_start: 0.8472 (m-30) cc_final: 0.8212 (m-30) REVERT: V 111 SER cc_start: 0.8746 (t) cc_final: 0.8364 (p) REVERT: V 119 GLN cc_start: 0.9305 (mt0) cc_final: 0.9093 (mt0) REVERT: W 60 TYR cc_start: 0.9055 (t80) cc_final: 0.8843 (t80) REVERT: W 94 GLU cc_start: 0.8043 (tt0) cc_final: 0.7751 (tt0) REVERT: W 147 MET cc_start: 0.9005 (tpt) cc_final: 0.8555 (tpt) REVERT: X 159 MET cc_start: 0.9272 (mmm) cc_final: 0.8932 (mmm) REVERT: Y 70 ASP cc_start: 0.8051 (t70) cc_final: 0.7541 (t0) REVERT: c 231 MET cc_start: 0.8977 (mtm) cc_final: 0.8699 (mtm) REVERT: c 238 MET cc_start: 0.9088 (tpp) cc_final: 0.8880 (tpp) REVERT: d 88 TYR cc_start: 0.8638 (t80) cc_final: 0.8340 (t80) REVERT: d 184 SER cc_start: 0.9170 (t) cc_final: 0.8888 (p) REVERT: d 209 TYR cc_start: 0.8648 (m-80) cc_final: 0.8344 (m-80) REVERT: d 211 GLN cc_start: 0.7749 (mt0) cc_final: 0.7548 (mt0) REVERT: d 258 SER cc_start: 0.9168 (t) cc_final: 0.8915 (p) REVERT: e 154 ASP cc_start: 0.7858 (p0) cc_final: 0.7530 (m-30) REVERT: h 67 GLN cc_start: 0.8826 (mt0) cc_final: 0.8435 (tp40) REVERT: h 106 ASP cc_start: 0.8395 (m-30) cc_final: 0.8146 (m-30) REVERT: h 107 ASP cc_start: 0.8394 (t0) cc_final: 0.7934 (t0) REVERT: h 124 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7882 (ttp80) REVERT: h 125 ASP cc_start: 0.8927 (m-30) cc_final: 0.8521 (m-30) REVERT: i 84 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8792 (ttpp) REVERT: j 45 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8272 (mt-10) REVERT: k 41 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8147 (tmtt) REVERT: k 85 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8388 (mt-10) REVERT: l 117 TYR cc_start: 0.8825 (t80) cc_final: 0.7151 (m-10) REVERT: l 123 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8434 (tptt) REVERT: l 128 ARG cc_start: 0.8728 (tmm-80) cc_final: 0.8369 (mtt180) REVERT: m 77 MET cc_start: 0.4327 (tpt) cc_final: 0.3924 (ttm) REVERT: p 47 LYS cc_start: 0.9238 (mttp) cc_final: 0.9032 (mttp) REVERT: p 132 GLU cc_start: 0.8332 (pt0) cc_final: 0.7694 (pt0) REVERT: p 149 ASP cc_start: 0.8382 (t0) cc_final: 0.8045 (t0) REVERT: p 152 GLN cc_start: 0.9000 (tp40) cc_final: 0.8444 (tp40) REVERT: p 156 ASP cc_start: 0.8451 (m-30) cc_final: 0.8208 (m-30) REVERT: p 157 MET cc_start: 0.8273 (mtm) cc_final: 0.8050 (mtp) REVERT: q 44 ASP cc_start: 0.8676 (t0) cc_final: 0.8476 (t0) REVERT: s 382 GLN cc_start: 0.8331 (tt0) cc_final: 0.8071 (tt0) outliers start: 1 outliers final: 3 residues processed: 1591 average time/residue: 1.8349 time to fit residues: 3983.1023 Evaluate side-chains 1150 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1148 time to evaluate : 6.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain d residue 146 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 809 optimal weight: 5.9990 chunk 726 optimal weight: 8.9990 chunk 403 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 490 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 751 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 457 optimal weight: 10.0000 chunk 559 optimal weight: 0.9990 chunk 870 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 154 GLN 5 165 GLN ** 5 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 243 ASN 6 354 GLN C 102 HIS C 177 ASN F 63 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN H 126 GLN I 93 ASN J 48 GLN ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 80 GLN N 98 HIS N 149 HIS N 202 GLN O 150 GLN O 154 GLN O 160 GLN P 97 GLN Q 158 GLN Q 239 ASN S 84 ASN S 118 ASN T 101 GLN T 133 ASN T 202 GLN U 23 ASN V 35 ASN V 78 GLN X 239 GLN Y 73 ASN Z 148 GLN b 58 ASN c 172 ASN d 154 ASN d 167 HIS ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 ASN f 61 HIS h 135 GLN k 15 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 ASN r 146 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 105693 Z= 0.395 Angle : 0.649 16.525 150190 Z= 0.334 Chirality : 0.043 0.311 17643 Planarity : 0.005 0.127 13626 Dihedral : 21.168 179.802 32014 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.92 % Allowed : 10.33 % Favored : 87.75 % 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: 1.37 (0.10), residues: 8170 helix: 2.02 (0.10), residues: 2822 sheet: -0.16 (0.16), residues: 1056 loop : 0.57 (0.10), residues: 4292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Z 81 HIS 0.009 0.001 HIS S 76 PHE 0.030 0.002 PHE 8 108 TYR 0.028 0.002 TYR Y 103 ARG 0.014 0.001 ARG 6 121 *********************** 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 1308 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1167 time to evaluate : 7.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 178 ASP cc_start: 0.7994 (t0) cc_final: 0.7783 (t0) REVERT: 1 26 THR cc_start: 0.9006 (m) cc_final: 0.8718 (p) REVERT: 6 50 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8550 (mmtm) REVERT: 6 214 TRP cc_start: 0.8635 (m100) cc_final: 0.8111 (m100) REVERT: 6 274 LYS cc_start: 0.8688 (tttm) cc_final: 0.8480 (tttp) REVERT: 7 93 MET cc_start: 0.8697 (mtm) cc_final: 0.8453 (mtp) REVERT: 7 143 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.6338 (m-90) REVERT: 7 149 MET cc_start: 0.9154 (mtp) cc_final: 0.8943 (mtm) REVERT: 7 163 MET cc_start: 0.7837 (ppp) cc_final: 0.6958 (ppp) REVERT: 9 71 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9208 (mmtm) REVERT: E 63 GLN cc_start: 0.8321 (tm-30) cc_final: 0.8065 (tm-30) REVERT: E 142 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7726 (mtm) REVERT: F 201 GLN cc_start: 0.8378 (tp40) cc_final: 0.8051 (tp-100) REVERT: H 84 GLU cc_start: 0.7904 (tt0) cc_final: 0.7112 (tt0) REVERT: H 122 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7246 (mpt-90) REVERT: H 142 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8010 (mm-30) REVERT: I 79 ILE cc_start: 0.8968 (pt) cc_final: 0.8628 (mp) REVERT: I 95 MET cc_start: 0.8819 (ppp) cc_final: 0.8419 (ppp) REVERT: I 105 SER cc_start: 0.8972 (m) cc_final: 0.8204 (p) REVERT: I 108 ASP cc_start: 0.8706 (m-30) cc_final: 0.8233 (m-30) REVERT: I 115 GLN cc_start: 0.9259 (mm110) cc_final: 0.9038 (mm-40) REVERT: I 123 MET cc_start: 0.8897 (tmm) cc_final: 0.8412 (tmm) REVERT: I 156 SER cc_start: 0.7856 (t) cc_final: 0.7281 (m) REVERT: J 92 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7451 (ptmt) REVERT: J 142 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8012 (mtm180) REVERT: K 52 ASP cc_start: 0.8150 (t0) cc_final: 0.7852 (t0) REVERT: K 153 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8858 (mtpp) REVERT: K 160 GLN cc_start: 0.8877 (tp40) cc_final: 0.8270 (tp-100) REVERT: K 164 ASP cc_start: 0.8561 (m-30) cc_final: 0.8140 (m-30) REVERT: K 175 ASP cc_start: 0.8824 (p0) cc_final: 0.8617 (p0) REVERT: N 114 ASP cc_start: 0.8719 (t0) cc_final: 0.8463 (t0) REVERT: N 148 ASP cc_start: 0.8106 (t0) cc_final: 0.7456 (t0) REVERT: N 149 HIS cc_start: 0.5643 (m90) cc_final: 0.5174 (m90) REVERT: P 114 LYS cc_start: 0.9401 (ptmt) cc_final: 0.9035 (ptmm) REVERT: P 115 HIS cc_start: 0.8704 (m-70) cc_final: 0.8278 (m-70) REVERT: P 134 GLN cc_start: 0.8951 (tt0) cc_final: 0.8370 (tm-30) REVERT: P 142 ASN cc_start: 0.9179 (m-40) cc_final: 0.8948 (m110) REVERT: Q 184 ASP cc_start: 0.8372 (m-30) cc_final: 0.8170 (m-30) REVERT: Q 274 ASP cc_start: 0.8280 (t0) cc_final: 0.8078 (t0) REVERT: S 133 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9063 (t) REVERT: U 12 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9329 (tm) REVERT: U 52 ASP cc_start: 0.8540 (m-30) cc_final: 0.8262 (m-30) REVERT: U 131 GLU cc_start: 0.7973 (tp30) cc_final: 0.7749 (tp30) REVERT: U 136 GLN cc_start: 0.8329 (mt0) cc_final: 0.8127 (tp-100) REVERT: U 143 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7706 (mpt180) REVERT: V 108 MET cc_start: 0.8991 (ttm) cc_final: 0.8779 (ttm) REVERT: V 111 SER cc_start: 0.8836 (t) cc_final: 0.8494 (p) REVERT: W 60 TYR cc_start: 0.9126 (t80) cc_final: 0.8892 (t80) REVERT: W 94 GLU cc_start: 0.8121 (tt0) cc_final: 0.7782 (tt0) REVERT: W 147 MET cc_start: 0.9024 (tpt) cc_final: 0.8418 (tpt) REVERT: d 154 ASN cc_start: 0.8578 (t160) cc_final: 0.8216 (t160) REVERT: d 184 SER cc_start: 0.9171 (t) cc_final: 0.8713 (p) REVERT: d 209 TYR cc_start: 0.8821 (m-80) cc_final: 0.8483 (m-80) REVERT: d 211 GLN cc_start: 0.7963 (mt0) cc_final: 0.7750 (mt0) REVERT: d 258 SER cc_start: 0.9204 (t) cc_final: 0.8997 (p) REVERT: e 70 MET cc_start: 0.8583 (mtp) cc_final: 0.8220 (mtp) REVERT: e 154 ASP cc_start: 0.7893 (p0) cc_final: 0.7499 (m-30) REVERT: f 60 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8315 (mmmm) REVERT: f 150 LEU cc_start: 0.4385 (pp) cc_final: 0.4177 (mp) REVERT: g 81 ASN cc_start: 0.8151 (p0) cc_final: 0.7904 (p0) REVERT: h 58 ARG cc_start: 0.8866 (mtm110) cc_final: 0.8348 (mtm-85) REVERT: h 87 GLN cc_start: 0.8549 (mp10) cc_final: 0.8292 (mp10) REVERT: h 93 ASP cc_start: 0.8613 (t70) cc_final: 0.8371 (t0) REVERT: h 106 ASP cc_start: 0.8393 (m-30) cc_final: 0.8151 (m-30) REVERT: h 120 MET cc_start: 0.7792 (mmp) cc_final: 0.7571 (mmp) REVERT: h 125 ASP cc_start: 0.8871 (m-30) cc_final: 0.8574 (m-30) REVERT: k 41 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8175 (tmtt) REVERT: k 85 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8283 (mt-10) REVERT: l 117 TYR cc_start: 0.8571 (t80) cc_final: 0.7127 (m-10) REVERT: l 123 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8421 (tptt) REVERT: l 128 ARG cc_start: 0.8764 (tmm-80) cc_final: 0.8383 (mtt180) REVERT: m 77 MET cc_start: 0.4408 (tpt) cc_final: 0.4026 (ttm) REVERT: p 47 LYS cc_start: 0.9307 (mttp) cc_final: 0.9069 (mttp) REVERT: p 156 ASP cc_start: 0.8360 (m-30) cc_final: 0.8091 (m-30) REVERT: p 157 MET cc_start: 0.8377 (mtm) cc_final: 0.8123 (mtp) outliers start: 141 outliers final: 64 residues processed: 1228 average time/residue: 1.8810 time to fit residues: 3218.7129 Evaluate side-chains 1156 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1086 time to evaluate : 6.959 ------------------------------------------------------------------------------- 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 29 CYS Chi-restraints excluded: chain 1 residue 64 SER 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 8 residue 168 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 71 LYS Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 106 ASP Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain U residue 143 ARG Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain V residue 150 SER Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER 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: 0.9990 chunk 270 optimal weight: 7.9990 chunk 724 optimal weight: 1.9990 chunk 593 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 872 optimal weight: 2.9990 chunk 942 optimal weight: 5.9990 chunk 776 optimal weight: 1.9990 chunk 865 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 699 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 165 GLN ** 5 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN F 63 GLN F 228 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN I 128 ASN I 151 ASN L 33 GLN L 142 GLN M 99 ASN N 98 HIS O 150 GLN O 154 GLN P 97 GLN Q 239 ASN S 91 GLN S 118 ASN T 101 GLN T 133 ASN U 23 ASN V 78 GLN a 46 ASN b 58 ASN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 105693 Z= 0.224 Angle : 0.582 13.594 150190 Z= 0.301 Chirality : 0.039 0.268 17643 Planarity : 0.004 0.127 13626 Dihedral : 21.171 179.496 32010 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.98 % Allowed : 12.06 % Favored : 85.96 % 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: 1.36 (0.09), residues: 8170 helix: 1.98 (0.10), residues: 2815 sheet: -0.18 (0.16), residues: 1042 loop : 0.59 (0.10), residues: 4313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 81 HIS 0.017 0.001 HIS I 119 PHE 0.021 0.001 PHE 8 108 TYR 0.022 0.001 TYR 5 176 ARG 0.016 0.000 ARG 6 121 *********************** 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 1262 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1117 time to evaluate : 6.898 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: 0 128 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: 0 174 ILE cc_start: 0.9459 (mp) cc_final: 0.9082 (mp) REVERT: 0 178 ASP cc_start: 0.7960 (t0) cc_final: 0.7744 (t0) REVERT: 1 26 THR cc_start: 0.8992 (m) cc_final: 0.8771 (p) REVERT: 1 44 LEU cc_start: 0.9190 (tp) cc_final: 0.8975 (tp) REVERT: 6 47 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8407 (mmp80) REVERT: 6 214 TRP cc_start: 0.8665 (m100) cc_final: 0.8156 (m100) REVERT: 6 274 LYS cc_start: 0.8737 (tttm) cc_final: 0.8493 (tttp) REVERT: 6 305 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8736 (tmmt) REVERT: 7 93 MET cc_start: 0.8687 (mtm) cc_final: 0.8431 (mtp) REVERT: 7 143 TRP cc_start: 0.9287 (OUTLIER) cc_final: 0.6575 (m-90) REVERT: 9 103 ASP cc_start: 0.5612 (t0) cc_final: 0.5283 (t70) REVERT: D 197 GLU cc_start: 0.8707 (pt0) cc_final: 0.8482 (pt0) REVERT: E 63 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 142 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7625 (mtm) REVERT: H 89 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7664 (mtt-85) REVERT: H 100 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: H 122 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7278 (mpt-90) REVERT: I 79 ILE cc_start: 0.8989 (pt) cc_final: 0.8661 (mp) REVERT: I 95 MET cc_start: 0.8824 (ppp) cc_final: 0.8425 (ppp) REVERT: I 105 SER cc_start: 0.9036 (m) cc_final: 0.8458 (p) REVERT: I 108 ASP cc_start: 0.8692 (m-30) cc_final: 0.8045 (m-30) REVERT: I 115 GLN cc_start: 0.9252 (mm110) cc_final: 0.9001 (mm-40) REVERT: I 119 HIS cc_start: 0.7481 (t70) cc_final: 0.7057 (t70) REVERT: I 134 PHE cc_start: 0.8226 (t80) cc_final: 0.7934 (t80) REVERT: J 92 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7440 (pttt) REVERT: J 106 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4123 (mmpt) REVERT: J 142 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8246 (mtt90) REVERT: J 157 LYS cc_start: 0.4234 (OUTLIER) cc_final: 0.2725 (tptp) REVERT: K 52 ASP cc_start: 0.8110 (t0) cc_final: 0.7834 (t0) REVERT: K 99 ASP cc_start: 0.8376 (t0) cc_final: 0.8166 (t0) REVERT: K 153 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8834 (mtpp) REVERT: K 160 GLN cc_start: 0.8802 (tp40) cc_final: 0.8284 (tp-100) REVERT: K 164 ASP cc_start: 0.8524 (m-30) cc_final: 0.8140 (m-30) REVERT: K 175 ASP cc_start: 0.8808 (p0) cc_final: 0.8541 (p0) REVERT: L 113 ASN cc_start: 0.8887 (m-40) cc_final: 0.8557 (m-40) REVERT: L 142 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7903 (mm-40) REVERT: N 114 ASP cc_start: 0.8684 (t0) cc_final: 0.8406 (t0) REVERT: N 149 HIS cc_start: 0.5733 (m90) cc_final: 0.5166 (m90) REVERT: P 114 LYS cc_start: 0.9430 (ptmt) cc_final: 0.9072 (ptmm) REVERT: P 115 HIS cc_start: 0.8614 (m-70) cc_final: 0.8238 (m-70) REVERT: P 117 TYR cc_start: 0.8364 (t80) cc_final: 0.7858 (t80) REVERT: P 134 GLN cc_start: 0.8942 (tt0) cc_final: 0.8366 (tm-30) REVERT: Q 274 ASP cc_start: 0.8230 (t0) cc_final: 0.8030 (t0) REVERT: U 12 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9283 (tm) REVERT: U 52 ASP cc_start: 0.8504 (m-30) cc_final: 0.8269 (m-30) REVERT: U 131 GLU cc_start: 0.7832 (tp30) cc_final: 0.7590 (tp30) REVERT: U 136 GLN cc_start: 0.8326 (mt0) cc_final: 0.8115 (tp-100) REVERT: V 108 MET cc_start: 0.8931 (ttm) cc_final: 0.8719 (ttm) REVERT: V 111 SER cc_start: 0.8824 (t) cc_final: 0.8490 (p) REVERT: W 60 TYR cc_start: 0.9092 (t80) cc_final: 0.8880 (t80) REVERT: W 94 GLU cc_start: 0.8121 (tt0) cc_final: 0.7774 (tt0) REVERT: W 147 MET cc_start: 0.9044 (tpt) cc_final: 0.8611 (tpt) REVERT: Y 92 ASN cc_start: 0.8880 (m-40) cc_final: 0.8504 (t0) REVERT: b 103 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8648 (ttpp) REVERT: d 154 ASN cc_start: 0.8511 (t160) cc_final: 0.8271 (t0) REVERT: d 184 SER cc_start: 0.9195 (t) cc_final: 0.8748 (p) REVERT: d 209 TYR cc_start: 0.8838 (m-80) cc_final: 0.8545 (m-80) REVERT: d 258 SER cc_start: 0.9161 (t) cc_final: 0.8941 (p) REVERT: e 70 MET cc_start: 0.8640 (mtp) cc_final: 0.8426 (mtp) REVERT: e 122 ASP cc_start: 0.8703 (m-30) cc_final: 0.8162 (p0) REVERT: e 154 ASP cc_start: 0.7923 (p0) cc_final: 0.7604 (m-30) REVERT: e 169 ASP cc_start: 0.5754 (t0) cc_final: 0.4854 (m-30) REVERT: f 178 LEU cc_start: 0.7641 (mm) cc_final: 0.7335 (mm) REVERT: g 81 ASN cc_start: 0.8182 (p0) cc_final: 0.7966 (p0) REVERT: h 58 ARG cc_start: 0.8851 (mtm110) cc_final: 0.8247 (mtm-85) REVERT: h 67 GLN cc_start: 0.8814 (tp40) cc_final: 0.8492 (tp40) REVERT: h 93 ASP cc_start: 0.8638 (t70) cc_final: 0.8387 (t0) REVERT: h 106 ASP cc_start: 0.8345 (m-30) cc_final: 0.8115 (m-30) REVERT: j 97 LYS cc_start: 0.9103 (tppp) cc_final: 0.8709 (ttmm) REVERT: k 41 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8090 (tmtt) REVERT: l 117 TYR cc_start: 0.8575 (t80) cc_final: 0.7017 (m-10) REVERT: l 123 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8396 (tptt) REVERT: l 128 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8396 (mtt180) REVERT: m 77 MET cc_start: 0.4460 (tpt) cc_final: 0.4092 (ttm) REVERT: o 51 MET cc_start: 0.8566 (mtp) cc_final: 0.8320 (mtp) REVERT: p 47 LYS cc_start: 0.9306 (mttp) cc_final: 0.9070 (mttm) outliers start: 145 outliers final: 64 residues processed: 1188 average time/residue: 1.7915 time to fit residues: 2926.6964 Evaluate side-chains 1159 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1086 time to evaluate : 6.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 305 LYS 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 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 176 GLN 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 R residue 76 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER 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 U residue 12 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 74 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER 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: 3.9990 chunk 655 optimal weight: 9.9990 chunk 452 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 416 optimal weight: 1.9990 chunk 585 optimal weight: 4.9990 chunk 875 optimal weight: 0.8980 chunk 926 optimal weight: 0.8980 chunk 457 optimal weight: 9.9990 chunk 829 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 165 GLN 6 243 ASN 7 111 GLN ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 144 GLN 9 90 GLN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN L 33 GLN M 99 ASN M 170 ASN N 98 HIS O 150 GLN P 97 GLN P 142 ASN Q 239 ASN S 84 ASN S 91 GLN S 118 ASN T 101 GLN U 23 ASN V 78 GLN V 119 GLN ** a 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN d 154 ASN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 119 GLN k 15 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN r 146 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 105693 Z= 0.222 Angle : 0.576 13.832 150190 Z= 0.297 Chirality : 0.039 0.262 17643 Planarity : 0.004 0.126 13626 Dihedral : 21.100 179.520 32010 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.13 % Allowed : 13.41 % Favored : 84.46 % 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: 1.32 (0.09), residues: 8170 helix: 1.93 (0.10), residues: 2830 sheet: -0.19 (0.15), residues: 1050 loop : 0.58 (0.10), residues: 4290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 81 HIS 0.012 0.001 HIS I 119 PHE 0.023 0.001 PHE 6 273 TYR 0.024 0.001 TYR 9 117 ARG 0.008 0.000 ARG 1 38 *********************** 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 1277 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1121 time to evaluate : 7.387 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: 0.7904 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: 1 44 LEU cc_start: 0.9228 (tp) cc_final: 0.9025 (tp) REVERT: 6 47 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8425 (mmp80) REVERT: 6 50 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8610 (mmtm) REVERT: 6 305 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8753 (tmmt) REVERT: 7 93 MET cc_start: 0.8697 (mtm) cc_final: 0.8326 (mtp) REVERT: 7 143 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.6755 (m-90) REVERT: 8 144 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7573 (tp40) REVERT: D 197 GLU cc_start: 0.8712 (pt0) cc_final: 0.8427 (pt0) REVERT: E 63 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 142 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7579 (mtm) REVERT: H 89 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: H 122 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7266 (mpt-90) REVERT: H 138 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8300 (ttmm) REVERT: H 142 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8258 (mm-30) REVERT: I 79 ILE cc_start: 0.8997 (pt) cc_final: 0.8678 (mp) REVERT: I 95 MET cc_start: 0.8781 (ppp) cc_final: 0.8434 (ppp) REVERT: I 108 ASP cc_start: 0.8659 (m-30) cc_final: 0.8299 (m-30) REVERT: I 119 HIS cc_start: 0.7715 (t70) cc_final: 0.7270 (t70) REVERT: I 123 MET cc_start: 0.8212 (tmm) cc_final: 0.7889 (tmm) REVERT: I 128 ASN cc_start: 0.8899 (m-40) cc_final: 0.8688 (m110) REVERT: I 134 PHE cc_start: 0.8152 (t80) cc_final: 0.7915 (t80) REVERT: J 142 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8172 (mtt90) REVERT: J 157 LYS cc_start: 0.4056 (OUTLIER) cc_final: 0.2747 (tptp) REVERT: K 52 ASP cc_start: 0.8093 (t0) cc_final: 0.7878 (t0) REVERT: K 99 ASP cc_start: 0.8401 (t0) cc_final: 0.8133 (t0) REVERT: K 153 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8864 (mtpp) REVERT: K 160 GLN cc_start: 0.8745 (tp40) cc_final: 0.8317 (tp-100) REVERT: K 164 ASP cc_start: 0.8494 (m-30) cc_final: 0.8114 (m-30) REVERT: K 175 ASP cc_start: 0.8792 (p0) cc_final: 0.8500 (p0) REVERT: N 114 ASP cc_start: 0.8665 (t0) cc_final: 0.8382 (t0) REVERT: N 148 ASP cc_start: 0.7982 (t0) cc_final: 0.7441 (t0) REVERT: O 23 GLU cc_start: 0.8294 (tt0) cc_final: 0.8076 (tt0) REVERT: P 114 LYS cc_start: 0.9403 (ptmt) cc_final: 0.9080 (ptmm) REVERT: P 115 HIS cc_start: 0.8586 (m-70) cc_final: 0.8216 (m-70) REVERT: P 134 GLN cc_start: 0.8943 (tt0) cc_final: 0.8575 (tm-30) REVERT: P 142 ASN cc_start: 0.9223 (m-40) cc_final: 0.8800 (m-40) REVERT: T 167 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8063 (ttm) REVERT: U 12 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9267 (tm) REVERT: U 52 ASP cc_start: 0.8503 (m-30) cc_final: 0.8270 (m-30) REVERT: U 136 GLN cc_start: 0.8397 (mt0) cc_final: 0.8144 (tp-100) REVERT: V 111 SER cc_start: 0.8802 (t) cc_final: 0.8484 (p) REVERT: W 94 GLU cc_start: 0.8128 (tt0) cc_final: 0.7790 (tt0) REVERT: W 147 MET cc_start: 0.9044 (tpt) cc_final: 0.8605 (tpt) REVERT: Y 92 ASN cc_start: 0.8860 (m-40) cc_final: 0.8472 (t0) REVERT: b 103 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8665 (ttpp) REVERT: d 184 SER cc_start: 0.9211 (t) cc_final: 0.8778 (p) REVERT: d 209 TYR cc_start: 0.8792 (m-80) cc_final: 0.8507 (m-80) REVERT: d 258 SER cc_start: 0.9175 (t) cc_final: 0.8940 (p) REVERT: e 122 ASP cc_start: 0.8699 (m-30) cc_final: 0.8121 (p0) REVERT: e 154 ASP cc_start: 0.7947 (p0) cc_final: 0.7595 (m-30) REVERT: e 169 ASP cc_start: 0.5744 (t0) cc_final: 0.4853 (m-30) REVERT: e 237 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8298 (tm) REVERT: f 178 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7336 (mm) REVERT: h 93 ASP cc_start: 0.8672 (t70) cc_final: 0.8435 (t0) REVERT: i 84 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8721 (ttpp) REVERT: k 15 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5927 (tm-30) REVERT: k 41 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8142 (tmtt) REVERT: k 65 ASP cc_start: 0.7534 (t0) cc_final: 0.5988 (t0) REVERT: l 117 TYR cc_start: 0.8561 (t80) cc_final: 0.7009 (m-10) REVERT: l 123 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8384 (tptt) REVERT: l 128 ARG cc_start: 0.8750 (tmm-80) cc_final: 0.8409 (mtt180) REVERT: m 77 MET cc_start: 0.4438 (tpt) cc_final: 0.4009 (ttm) REVERT: o 51 MET cc_start: 0.8522 (mtp) cc_final: 0.8264 (mtp) REVERT: o 91 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: p 47 LYS cc_start: 0.9334 (mttp) cc_final: 0.9070 (mttm) REVERT: p 149 ASP cc_start: 0.8237 (t0) cc_final: 0.7912 (t70) REVERT: r 70 CYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7799 (p) outliers start: 156 outliers final: 74 residues processed: 1205 average time/residue: 1.7416 time to fit residues: 2904.7898 Evaluate side-chains 1161 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1073 time to evaluate : 6.835 ------------------------------------------------------------------------------- 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 1 residue 29 CYS Chi-restraints excluded: chain 5 residue 64 MET Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 305 LYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 246 GLN Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 144 GLN Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 176 GLN 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 R residue 76 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 161 ILE 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 U residue 12 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain h residue 74 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 15 GLN Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 279 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 772 optimal weight: 1.9990 chunk 526 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 690 optimal weight: 0.9980 chunk 382 optimal weight: 10.0000 chunk 791 optimal weight: 10.0000 chunk 640 optimal weight: 6.9990 chunk 1 optimal weight: 0.0570 chunk 473 optimal weight: 8.9990 chunk 832 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 165 GLN 6 243 ASN ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN H 136 ASN L 33 GLN L 43 ASN L 48 ASN M 170 ASN N 98 HIS O 150 GLN O 154 GLN P 97 GLN Q 239 ASN S 118 ASN T 101 GLN U 23 ASN V 78 GLN V 119 GLN X 236 GLN Y 89 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 87 GLN h 119 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 105693 Z= 0.201 Angle : 0.570 13.912 150190 Z= 0.294 Chirality : 0.038 0.270 17643 Planarity : 0.004 0.124 13626 Dihedral : 21.057 179.682 32010 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.09 % Allowed : 14.47 % Favored : 83.44 % 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: 1.33 (0.09), residues: 8170 helix: 1.91 (0.10), residues: 2835 sheet: -0.19 (0.15), residues: 1040 loop : 0.59 (0.10), residues: 4295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 81 HIS 0.011 0.001 HIS I 119 PHE 0.016 0.001 PHE I 173 TYR 0.021 0.001 TYR d 88 ARG 0.008 0.000 ARG 1 38 *********************** 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 1269 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1116 time to evaluate : 6.918 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: 0 128 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7587 (tm-30) REVERT: 1 44 LEU cc_start: 0.9199 (tp) cc_final: 0.8995 (tp) REVERT: 6 47 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8442 (mmp80) REVERT: 6 50 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8684 (mmtm) REVERT: 6 305 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8750 (tmmt) REVERT: 7 93 MET cc_start: 0.8699 (mtm) cc_final: 0.8392 (mtp) REVERT: D 197 GLU cc_start: 0.8698 (pt0) cc_final: 0.8389 (pt0) REVERT: D 235 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: E 63 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8124 (tm-30) REVERT: E 142 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7545 (mtm) REVERT: H 84 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: H 89 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.7833 (mtt-85) REVERT: H 122 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7273 (mpt-90) REVERT: H 138 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8320 (ttmm) REVERT: H 142 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8260 (mm-30) REVERT: I 79 ILE cc_start: 0.9002 (pt) cc_final: 0.8689 (mp) REVERT: I 95 MET cc_start: 0.8736 (ppp) cc_final: 0.8328 (ppp) REVERT: I 108 ASP cc_start: 0.8769 (m-30) cc_final: 0.8244 (m-30) REVERT: I 115 GLN cc_start: 0.9281 (mm110) cc_final: 0.9048 (mm-40) REVERT: I 119 HIS cc_start: 0.7749 (t70) cc_final: 0.7421 (t70) REVERT: I 128 ASN cc_start: 0.8882 (m-40) cc_final: 0.8657 (m110) REVERT: I 134 PHE cc_start: 0.8105 (t80) cc_final: 0.7899 (t80) REVERT: I 152 MET cc_start: 0.8568 (ppp) cc_final: 0.8124 (ppp) REVERT: J 92 LYS cc_start: 0.7281 (ptmt) cc_final: 0.6879 (pptt) REVERT: J 157 LYS cc_start: 0.4121 (OUTLIER) cc_final: 0.2932 (tmtm) REVERT: K 52 ASP cc_start: 0.8084 (t0) cc_final: 0.7874 (t0) REVERT: K 99 ASP cc_start: 0.8371 (t0) cc_final: 0.8097 (t0) REVERT: K 164 ASP cc_start: 0.8460 (m-30) cc_final: 0.8257 (m-30) REVERT: K 175 ASP cc_start: 0.8780 (p0) cc_final: 0.8475 (p0) REVERT: N 114 ASP cc_start: 0.8624 (t0) cc_final: 0.8367 (t0) REVERT: N 148 ASP cc_start: 0.7928 (t0) cc_final: 0.7679 (t0) REVERT: O 23 GLU cc_start: 0.8292 (tt0) cc_final: 0.8088 (tt0) REVERT: P 114 LYS cc_start: 0.9392 (ptmt) cc_final: 0.9059 (ptmm) REVERT: P 115 HIS cc_start: 0.8600 (m-70) cc_final: 0.8246 (m-70) REVERT: P 134 GLN cc_start: 0.8960 (tt0) cc_final: 0.8633 (tm-30) REVERT: P 142 ASN cc_start: 0.9189 (m-40) cc_final: 0.8748 (m-40) REVERT: U 12 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9250 (tm) REVERT: U 52 ASP cc_start: 0.8496 (m-30) cc_final: 0.8265 (m-30) REVERT: U 132 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7734 (tm-30) REVERT: U 136 GLN cc_start: 0.8374 (mt0) cc_final: 0.8148 (tp-100) REVERT: V 111 SER cc_start: 0.8832 (t) cc_final: 0.8509 (p) REVERT: V 119 GLN cc_start: 0.9239 (mt0) cc_final: 0.8966 (mt0) REVERT: V 122 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8551 (mt) REVERT: W 147 MET cc_start: 0.9056 (tpt) cc_final: 0.8614 (tpt) REVERT: Y 92 ASN cc_start: 0.8845 (m-40) cc_final: 0.8447 (t0) REVERT: Z 61 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7542 (mm110) REVERT: b 103 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8661 (ttpp) REVERT: d 184 SER cc_start: 0.9228 (t) cc_final: 0.8803 (p) REVERT: d 209 TYR cc_start: 0.8785 (m-80) cc_final: 0.8531 (m-80) REVERT: d 258 SER cc_start: 0.9161 (t) cc_final: 0.8945 (p) REVERT: e 122 ASP cc_start: 0.8810 (m-30) cc_final: 0.8289 (p0) REVERT: e 139 GLU cc_start: 0.3330 (OUTLIER) cc_final: 0.2509 (tp30) REVERT: e 154 ASP cc_start: 0.7969 (p0) cc_final: 0.7526 (m-30) REVERT: e 169 ASP cc_start: 0.5706 (t0) cc_final: 0.4808 (m-30) REVERT: e 205 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6039 (pt) REVERT: e 237 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8327 (tm) REVERT: f 178 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7453 (mm) REVERT: g 81 ASN cc_start: 0.7983 (p0) cc_final: 0.7766 (p0) REVERT: h 93 ASP cc_start: 0.8676 (t70) cc_final: 0.8437 (t0) REVERT: h 107 ASP cc_start: 0.8036 (t0) cc_final: 0.7783 (t0) REVERT: k 41 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8145 (tmtt) REVERT: k 65 ASP cc_start: 0.7558 (t0) cc_final: 0.7080 (t0) REVERT: k 67 LEU cc_start: 0.7608 (mm) cc_final: 0.7297 (mm) REVERT: k 84 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9193 (tm) REVERT: k 88 THR cc_start: 0.9431 (m) cc_final: 0.9113 (p) REVERT: l 117 TYR cc_start: 0.8629 (t80) cc_final: 0.6993 (m-10) REVERT: l 123 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8387 (tptt) REVERT: l 128 ARG cc_start: 0.8768 (tmm-80) cc_final: 0.8401 (mtt180) REVERT: m 77 MET cc_start: 0.4401 (tpt) cc_final: 0.3972 (ttm) REVERT: o 91 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: p 47 LYS cc_start: 0.9382 (mttp) cc_final: 0.9104 (mttm) REVERT: p 149 ASP cc_start: 0.8247 (t0) cc_final: 0.7918 (t70) REVERT: r 70 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7750 (p) outliers start: 153 outliers final: 70 residues processed: 1195 average time/residue: 1.8058 time to fit residues: 2994.3202 Evaluate side-chains 1159 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1074 time to evaluate : 6.903 ------------------------------------------------------------------------------- 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 29 CYS Chi-restraints excluded: chain 5 residue 64 MET Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 305 LYS Chi-restraints excluded: chain 7 residue 246 GLN Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 114 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 176 GLN 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 R residue 76 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 T residue 191 THR Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain h residue 74 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 279 GLU Chi-restraints excluded: chain s residue 360 VAL 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: 4.9990 chunk 183 optimal weight: 10.0000 chunk 544 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 927 optimal weight: 7.9990 chunk 770 optimal weight: 10.0000 chunk 429 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 306 optimal weight: 0.9990 chunk 487 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 165 GLN 7 111 GLN 7 165 ASN ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 126 GLN 9 90 GLN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN H 136 ASN K 94 GLN L 33 GLN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 276 ASN N 98 HIS O 27 HIS O 150 GLN P 97 GLN Q 239 ASN S 84 ASN S 118 ASN T 101 GLN U 23 ASN V 78 GLN X 236 GLN Y 89 GLN ** a 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 146 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 105693 Z= 0.237 Angle : 0.576 13.924 150190 Z= 0.298 Chirality : 0.039 0.324 17643 Planarity : 0.004 0.125 13626 Dihedral : 21.013 179.786 32010 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.24 % Allowed : 15.12 % Favored : 82.65 % 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: 1.32 (0.09), residues: 8170 helix: 1.93 (0.10), residues: 2823 sheet: -0.21 (0.15), residues: 1053 loop : 0.59 (0.10), residues: 4294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 81 HIS 0.010 0.001 HIS I 119 PHE 0.014 0.001 PHE T 108 TYR 0.023 0.001 TYR 9 117 ARG 0.009 0.000 ARG 1 38 *********************** 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 1265 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1101 time to evaluate : 6.948 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: 0.7953 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: 1 44 LEU cc_start: 0.9173 (tp) cc_final: 0.8963 (tp) REVERT: 6 47 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8456 (mmp80) REVERT: 6 50 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8723 (mmtm) REVERT: 6 274 LYS cc_start: 0.8651 (tttp) cc_final: 0.8248 (tttp) REVERT: 6 305 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8753 (tmmt) REVERT: 7 93 MET cc_start: 0.8714 (mtm) cc_final: 0.8395 (mtp) REVERT: 7 143 TRP cc_start: 0.9321 (OUTLIER) cc_final: 0.7385 (m-90) REVERT: 7 150 MET cc_start: 0.8929 (ttp) cc_final: 0.8720 (ptt) REVERT: D 187 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9451 (mm) REVERT: D 197 GLU cc_start: 0.8717 (pt0) cc_final: 0.8481 (pt0) REVERT: E 63 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 142 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7621 (mtm) REVERT: F 201 GLN cc_start: 0.8381 (tp40) cc_final: 0.8131 (tp-100) REVERT: H 84 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6693 (tt0) REVERT: H 89 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.7845 (mtt-85) REVERT: H 122 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7244 (mpt-90) REVERT: H 138 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8385 (ttmm) REVERT: H 142 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8334 (mm-30) REVERT: I 79 ILE cc_start: 0.9005 (pt) cc_final: 0.8701 (mp) REVERT: I 95 MET cc_start: 0.8716 (ppp) cc_final: 0.8392 (ppp) REVERT: I 108 ASP cc_start: 0.8823 (m-30) cc_final: 0.8301 (m-30) REVERT: I 115 GLN cc_start: 0.9322 (mm110) cc_final: 0.9050 (mm-40) REVERT: I 119 HIS cc_start: 0.7791 (t70) cc_final: 0.7444 (t70) REVERT: I 152 MET cc_start: 0.8557 (ppp) cc_final: 0.7995 (ppp) REVERT: J 92 LYS cc_start: 0.7413 (ptmt) cc_final: 0.7131 (pttp) REVERT: J 139 SER cc_start: 0.8393 (m) cc_final: 0.7811 (p) REVERT: J 157 LYS cc_start: 0.4336 (OUTLIER) cc_final: 0.3092 (tmtm) REVERT: K 52 ASP cc_start: 0.8096 (t0) cc_final: 0.7885 (t0) REVERT: K 99 ASP cc_start: 0.8366 (t0) cc_final: 0.8096 (t0) REVERT: K 153 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8811 (mtpp) REVERT: N 114 ASP cc_start: 0.8631 (t0) cc_final: 0.8383 (t0) REVERT: N 148 ASP cc_start: 0.8004 (t0) cc_final: 0.7726 (t0) REVERT: O 23 GLU cc_start: 0.8340 (tt0) cc_final: 0.8112 (tt0) REVERT: P 114 LYS cc_start: 0.9389 (ptmt) cc_final: 0.9061 (ptmm) REVERT: P 115 HIS cc_start: 0.8604 (m-70) cc_final: 0.8265 (m-70) REVERT: P 134 GLN cc_start: 0.8960 (tt0) cc_final: 0.8523 (tm-30) REVERT: P 142 ASN cc_start: 0.9154 (m-40) cc_final: 0.8760 (m-40) REVERT: U 12 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9238 (tm) REVERT: U 52 ASP cc_start: 0.8521 (m-30) cc_final: 0.8266 (m-30) REVERT: V 111 SER cc_start: 0.8823 (t) cc_final: 0.8508 (p) REVERT: V 119 GLN cc_start: 0.9270 (mt0) cc_final: 0.8968 (mt0) REVERT: W 147 MET cc_start: 0.9070 (tpt) cc_final: 0.8712 (tpt) REVERT: Y 92 ASN cc_start: 0.8814 (m-40) cc_final: 0.8419 (t0) REVERT: Z 62 ASN cc_start: 0.8668 (p0) cc_final: 0.8414 (p0) REVERT: d 184 SER cc_start: 0.9253 (t) cc_final: 0.8823 (p) REVERT: d 209 TYR cc_start: 0.8793 (m-80) cc_final: 0.8561 (m-80) REVERT: e 122 ASP cc_start: 0.8768 (m-30) cc_final: 0.8226 (p0) REVERT: e 139 GLU cc_start: 0.3259 (OUTLIER) cc_final: 0.2391 (tp30) REVERT: e 154 ASP cc_start: 0.7960 (p0) cc_final: 0.7561 (m-30) REVERT: e 169 ASP cc_start: 0.5683 (t0) cc_final: 0.4780 (m-30) REVERT: e 237 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (tm) REVERT: e 262 ASP cc_start: 0.8594 (t0) cc_final: 0.8377 (m-30) REVERT: g 81 ASN cc_start: 0.8105 (p0) cc_final: 0.7868 (p0) REVERT: h 93 ASP cc_start: 0.8660 (t70) cc_final: 0.8419 (t0) REVERT: h 106 ASP cc_start: 0.8293 (m-30) cc_final: 0.8037 (m-30) REVERT: h 156 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7607 (m100) REVERT: k 41 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8155 (tmtt) REVERT: k 65 ASP cc_start: 0.7790 (t0) cc_final: 0.6548 (t0) REVERT: k 88 THR cc_start: 0.9419 (m) cc_final: 0.9106 (p) REVERT: l 117 TYR cc_start: 0.8601 (t80) cc_final: 0.7000 (m-10) REVERT: l 123 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8392 (tptt) REVERT: l 128 ARG cc_start: 0.8780 (tmm-80) cc_final: 0.8406 (mtt180) REVERT: m 77 MET cc_start: 0.4370 (tpt) cc_final: 0.4002 (ttm) REVERT: o 91 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: p 47 LYS cc_start: 0.9383 (mttp) cc_final: 0.9118 (mttm) REVERT: p 149 ASP cc_start: 0.8249 (t0) cc_final: 0.7918 (t70) REVERT: p 181 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: q 128 MET cc_start: 0.8802 (tpt) cc_final: 0.8534 (tpt) REVERT: r 39 VAL cc_start: 0.9169 (t) cc_final: 0.8743 (m) REVERT: r 70 CYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7742 (p) REVERT: s 356 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8935 (p) outliers start: 164 outliers final: 83 residues processed: 1191 average time/residue: 1.7623 time to fit residues: 2906.0490 Evaluate side-chains 1174 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1076 time to evaluate : 6.948 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 305 LYS 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 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 114 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 176 GLN 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 R residue 76 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 188 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 U residue 12 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 72 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 279 GLU Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 360 VAL 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: 3.9990 chunk 528 optimal weight: 6.9990 chunk 677 optimal weight: 2.9990 chunk 524 optimal weight: 5.9990 chunk 781 optimal weight: 9.9990 chunk 518 optimal weight: 0.9990 chunk 924 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 563 optimal weight: 0.5980 chunk 426 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 146 HIS 5 165 GLN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 43 ASN N 98 HIS O 150 GLN O 154 GLN P 97 GLN Q 139 GLN Q 239 ASN S 118 ASN T 101 GLN U 23 ASN U 136 GLN V 78 GLN X 236 GLN Y 89 GLN Z 61 GLN ** a 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN q 134 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 105693 Z= 0.255 Angle : 0.589 13.938 150190 Z= 0.304 Chirality : 0.039 0.271 17643 Planarity : 0.004 0.125 13626 Dihedral : 21.003 179.918 32010 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.10 % Allowed : 15.73 % Favored : 82.17 % 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: 1.31 (0.09), residues: 8170 helix: 1.93 (0.10), residues: 2825 sheet: -0.23 (0.15), residues: 1064 loop : 0.57 (0.10), residues: 4281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP q 143 HIS 0.009 0.001 HIS I 119 PHE 0.013 0.001 PHE T 108 TYR 0.027 0.001 TYR d 88 ARG 0.009 0.000 ARG g 50 *********************** 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 1255 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1101 time to evaluate : 7.271 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: 0 128 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: 0 160 TYR cc_start: 0.8901 (m-80) cc_final: 0.8595 (m-80) REVERT: 6 47 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8444 (mmp80) REVERT: 6 50 LYS cc_start: 0.9011 (mmtp) cc_final: 0.8744 (mmtm) REVERT: 6 214 TRP cc_start: 0.8773 (m100) cc_final: 0.8444 (m100) REVERT: 6 274 LYS cc_start: 0.8538 (tttp) cc_final: 0.8220 (tttp) REVERT: 6 305 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8753 (tmmt) REVERT: 7 93 MET cc_start: 0.8724 (mtm) cc_final: 0.8396 (mtp) REVERT: 7 143 TRP cc_start: 0.9361 (OUTLIER) cc_final: 0.7622 (m-90) REVERT: D 197 GLU cc_start: 0.8725 (pt0) cc_final: 0.8500 (pt0) REVERT: E 63 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 142 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7638 (mtm) REVERT: H 84 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6670 (tt0) REVERT: H 89 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.7836 (mtt-85) REVERT: H 122 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7247 (mpt-90) REVERT: H 138 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8388 (ttmm) REVERT: H 142 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8313 (mm-30) REVERT: I 79 ILE cc_start: 0.8683 (pt) cc_final: 0.8410 (mp) REVERT: I 95 MET cc_start: 0.8690 (ppp) cc_final: 0.8316 (ppp) REVERT: I 108 ASP cc_start: 0.8902 (m-30) cc_final: 0.8245 (m-30) REVERT: I 119 HIS cc_start: 0.7815 (t70) cc_final: 0.7462 (t70) REVERT: I 152 MET cc_start: 0.8549 (ppp) cc_final: 0.7969 (ppp) REVERT: J 92 LYS cc_start: 0.7568 (ptmt) cc_final: 0.7074 (pptt) REVERT: J 157 LYS cc_start: 0.4394 (OUTLIER) cc_final: 0.3154 (tmtm) REVERT: K 52 ASP cc_start: 0.8100 (t0) cc_final: 0.7897 (t0) REVERT: K 99 ASP cc_start: 0.8358 (t0) cc_final: 0.8102 (t0) REVERT: K 160 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8001 (tp-100) REVERT: K 164 ASP cc_start: 0.8344 (m-30) cc_final: 0.8055 (m-30) REVERT: N 114 ASP cc_start: 0.8583 (t0) cc_final: 0.8340 (t0) REVERT: N 148 ASP cc_start: 0.7996 (t0) cc_final: 0.7678 (t0) REVERT: O 23 GLU cc_start: 0.8373 (tt0) cc_final: 0.8148 (tt0) REVERT: P 114 LYS cc_start: 0.9352 (ptmt) cc_final: 0.9013 (ptmm) REVERT: P 115 HIS cc_start: 0.8575 (m-70) cc_final: 0.8222 (m-70) REVERT: P 134 GLN cc_start: 0.8957 (tt0) cc_final: 0.8502 (tm-30) REVERT: P 142 ASN cc_start: 0.9137 (m-40) cc_final: 0.8752 (m-40) REVERT: U 12 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9236 (tm) REVERT: U 52 ASP cc_start: 0.8533 (m-30) cc_final: 0.8283 (m-30) REVERT: V 111 SER cc_start: 0.8840 (t) cc_final: 0.8534 (p) REVERT: V 119 GLN cc_start: 0.9274 (mt0) cc_final: 0.8952 (mt0) REVERT: W 147 MET cc_start: 0.9047 (tpt) cc_final: 0.8655 (tpt) REVERT: Y 92 ASN cc_start: 0.8852 (m-40) cc_final: 0.8468 (t0) REVERT: d 184 SER cc_start: 0.9258 (t) cc_final: 0.8829 (p) REVERT: d 209 TYR cc_start: 0.8790 (m-80) cc_final: 0.8493 (m-80) REVERT: e 122 ASP cc_start: 0.8767 (m-30) cc_final: 0.8248 (p0) REVERT: e 139 GLU cc_start: 0.3409 (OUTLIER) cc_final: 0.2468 (tp30) REVERT: e 154 ASP cc_start: 0.7977 (p0) cc_final: 0.7576 (m-30) REVERT: e 169 ASP cc_start: 0.5677 (t0) cc_final: 0.4767 (m-30) REVERT: e 205 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.5881 (pt) REVERT: e 237 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8319 (tm) REVERT: g 81 ASN cc_start: 0.8108 (p0) cc_final: 0.7865 (p0) REVERT: h 93 ASP cc_start: 0.8657 (t70) cc_final: 0.8419 (t0) REVERT: h 156 TRP cc_start: 0.8286 (OUTLIER) cc_final: 0.7691 (m100) REVERT: k 41 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8161 (tmtt) REVERT: k 65 ASP cc_start: 0.7639 (t0) cc_final: 0.6794 (t0) REVERT: k 84 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9172 (tm) REVERT: k 88 THR cc_start: 0.9419 (m) cc_final: 0.9108 (p) REVERT: l 117 TYR cc_start: 0.8596 (t80) cc_final: 0.6955 (m-10) REVERT: l 123 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8411 (tptt) REVERT: l 128 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8371 (mtt180) REVERT: m 51 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8419 (tm) REVERT: m 77 MET cc_start: 0.4371 (tpt) cc_final: 0.4002 (ttm) REVERT: p 47 LYS cc_start: 0.9396 (mttp) cc_final: 0.9130 (mttm) REVERT: p 149 ASP cc_start: 0.8252 (t0) cc_final: 0.7899 (t70) REVERT: p 181 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: r 70 CYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7703 (p) REVERT: s 356 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8954 (p) outliers start: 154 outliers final: 81 residues processed: 1186 average time/residue: 1.7830 time to fit residues: 2922.9981 Evaluate side-chains 1168 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1071 time to evaluate : 7.276 ------------------------------------------------------------------------------- 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 1 residue 29 CYS Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 305 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 78 VAL 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 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 76 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 T residue 191 THR Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 279 GLU Chi-restraints excluded: chain s residue 356 VAL 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: 3.9990 chunk 369 optimal weight: 0.0470 chunk 552 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 587 optimal weight: 8.9990 chunk 629 optimal weight: 9.9990 chunk 456 optimal weight: 30.0000 chunk 86 optimal weight: 6.9990 chunk 726 optimal weight: 0.0000 overall best weight: 4.0088 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 146 HIS 5 150 GLN 5 165 GLN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 304 ASN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN I 36 HIS ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 43 ASN M 219 ASN N 98 HIS O 69 ASN O 150 GLN P 97 GLN Q 239 ASN S 84 ASN S 118 ASN T 101 GLN U 23 ASN V 78 GLN X 236 GLN Y 89 GLN Z 148 GLN ** a 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN ** r 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 105693 Z= 0.329 Angle : 0.624 13.910 150190 Z= 0.322 Chirality : 0.041 0.292 17643 Planarity : 0.005 0.127 13626 Dihedral : 21.002 179.944 32010 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.99 % Allowed : 16.42 % Favored : 81.59 % 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: 1.87 (0.10), residues: 2826 sheet: -0.31 (0.15), residues: 1079 loop : 0.57 (0.10), residues: 4265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP q 143 HIS 0.009 0.001 HIS I 119 PHE 0.015 0.001 PHE 5 60 TYR 0.021 0.001 TYR d 88 ARG 0.016 0.000 ARG h 58 *********************** 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 1236 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1090 time to evaluate : 7.042 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: 0.8032 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: 6 47 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8468 (mmp80) REVERT: 6 50 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8778 (mmtm) REVERT: 6 305 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8803 (tmmt) REVERT: 7 93 MET cc_start: 0.8751 (mtm) cc_final: 0.8396 (mtp) REVERT: 7 143 TRP cc_start: 0.9426 (OUTLIER) cc_final: 0.7995 (m-90) REVERT: D 197 GLU cc_start: 0.8741 (pt0) cc_final: 0.8456 (pt0) REVERT: E 63 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8197 (tm-30) REVERT: E 142 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (mtm) REVERT: H 89 ARG cc_start: 0.8356 (mtt-85) cc_final: 0.8108 (mtt-85) REVERT: H 122 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7292 (mpt-90) REVERT: H 138 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8395 (ttmm) REVERT: I 79 ILE cc_start: 0.8668 (pt) cc_final: 0.8415 (mp) REVERT: I 95 MET cc_start: 0.8669 (ppp) cc_final: 0.8355 (ppp) REVERT: I 108 ASP cc_start: 0.8899 (m-30) cc_final: 0.8381 (m-30) REVERT: I 115 GLN cc_start: 0.9226 (mm110) cc_final: 0.8997 (mm-40) REVERT: I 119 HIS cc_start: 0.7873 (t70) cc_final: 0.7508 (t70) REVERT: I 152 MET cc_start: 0.8559 (ppp) cc_final: 0.8070 (ppp) REVERT: J 92 LYS cc_start: 0.7579 (ptmt) cc_final: 0.7093 (pptt) REVERT: J 157 LYS cc_start: 0.4385 (OUTLIER) cc_final: 0.3188 (tmtm) REVERT: K 52 ASP cc_start: 0.8138 (t0) cc_final: 0.7923 (t0) REVERT: K 99 ASP cc_start: 0.8449 (t0) cc_final: 0.8186 (t0) REVERT: K 160 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7914 (tp-100) REVERT: K 164 ASP cc_start: 0.8378 (m-30) cc_final: 0.7999 (m-30) REVERT: N 114 ASP cc_start: 0.8557 (t0) cc_final: 0.8338 (t0) REVERT: O 23 GLU cc_start: 0.8403 (tt0) cc_final: 0.8127 (tt0) REVERT: P 114 LYS cc_start: 0.9355 (ptmt) cc_final: 0.9010 (ptmm) REVERT: P 115 HIS cc_start: 0.8603 (m-70) cc_final: 0.8230 (m-70) REVERT: P 134 GLN cc_start: 0.8957 (tt0) cc_final: 0.8511 (tm-30) REVERT: U 12 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9253 (tm) REVERT: U 52 ASP cc_start: 0.8544 (m-30) cc_final: 0.8289 (m-30) REVERT: U 131 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7819 (mp0) REVERT: V 111 SER cc_start: 0.8814 (t) cc_final: 0.8514 (p) REVERT: V 119 GLN cc_start: 0.9305 (mt0) cc_final: 0.8989 (mt0) REVERT: W 57 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: W 112 GLU cc_start: 0.8012 (mp0) cc_final: 0.7689 (mp0) REVERT: W 147 MET cc_start: 0.9082 (tpt) cc_final: 0.8684 (tpt) REVERT: Y 92 ASN cc_start: 0.8875 (m-40) cc_final: 0.8469 (t0) REVERT: a 110 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7400 (pp20) REVERT: d 184 SER cc_start: 0.9274 (t) cc_final: 0.8774 (p) REVERT: d 209 TYR cc_start: 0.8711 (m-80) cc_final: 0.8466 (m-80) REVERT: e 122 ASP cc_start: 0.8779 (m-30) cc_final: 0.8531 (m-30) REVERT: e 139 GLU cc_start: 0.3321 (OUTLIER) cc_final: 0.2276 (tp30) REVERT: e 154 ASP cc_start: 0.7973 (p0) cc_final: 0.7618 (m-30) REVERT: e 169 ASP cc_start: 0.5654 (t0) cc_final: 0.4723 (m-30) REVERT: e 205 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.5826 (pt) REVERT: e 237 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8291 (tm) REVERT: e 262 ASP cc_start: 0.8718 (t0) cc_final: 0.8479 (m-30) REVERT: f 178 LEU cc_start: 0.7705 (mm) cc_final: 0.7492 (mm) REVERT: g 81 ASN cc_start: 0.8145 (p0) cc_final: 0.7904 (p0) REVERT: h 86 TRP cc_start: 0.8807 (p-90) cc_final: 0.8509 (p-90) REVERT: h 93 ASP cc_start: 0.8628 (t70) cc_final: 0.8384 (t0) REVERT: h 106 ASP cc_start: 0.8367 (m-30) cc_final: 0.8117 (m-30) REVERT: k 41 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8179 (tmtt) REVERT: k 84 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9164 (tm) REVERT: k 88 THR cc_start: 0.9403 (m) cc_final: 0.9084 (p) REVERT: l 117 TYR cc_start: 0.8433 (t80) cc_final: 0.6875 (m-10) REVERT: l 123 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8342 (tptt) REVERT: l 128 ARG cc_start: 0.8775 (tmm-80) cc_final: 0.8315 (mtt180) REVERT: m 51 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8439 (tm) REVERT: m 77 MET cc_start: 0.4372 (tpt) cc_final: 0.3941 (ttm) REVERT: o 91 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: p 47 LYS cc_start: 0.9366 (mttp) cc_final: 0.9115 (mttm) REVERT: p 149 ASP cc_start: 0.8247 (t0) cc_final: 0.7887 (t70) REVERT: p 181 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: r 70 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7795 (p) REVERT: s 356 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9027 (p) outliers start: 146 outliers final: 86 residues processed: 1178 average time/residue: 1.9013 time to fit residues: 3149.6701 Evaluate side-chains 1170 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1068 time to evaluate : 6.940 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 29 CYS 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 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 305 LYS Chi-restraints excluded: chain 7 residue 38 THR 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 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 176 GLN Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 76 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 U residue 12 LEU Chi-restraints excluded: chain U residue 127 TYR 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 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 72 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 279 GLU Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 840 optimal weight: 1.9990 chunk 885 optimal weight: 0.9980 chunk 807 optimal weight: 20.0000 chunk 861 optimal weight: 7.9990 chunk 518 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 chunk 676 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 778 optimal weight: 9.9990 chunk 814 optimal weight: 30.0000 chunk 858 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 146 HIS 5 150 GLN 5 165 GLN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN I 43 GLN I 101 ASN I 128 ASN L 33 GLN L 43 ASN N 98 HIS O 150 GLN P 97 GLN P 142 ASN Q 239 ASN S 118 ASN T 101 GLN U 23 ASN V 78 GLN X 236 GLN Y 89 GLN Z 148 GLN ** a 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN q 134 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 105693 Z= 0.277 Angle : 0.615 13.928 150190 Z= 0.317 Chirality : 0.040 0.278 17643 Planarity : 0.004 0.126 13626 Dihedral : 21.021 179.906 32010 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.70 % Allowed : 17.00 % Favored : 81.30 % 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: 1.86 (0.10), residues: 2825 sheet: -0.31 (0.15), residues: 1070 loop : 0.56 (0.10), residues: 4275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP q 143 HIS 0.028 0.001 HIS N 149 PHE 0.016 0.001 PHE I 134 TYR 0.026 0.001 TYR U 127 ARG 0.016 0.000 ARG h 58 *********************** 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 1216 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1091 time to evaluate : 6.955 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: 0.8024 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: 6 47 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8471 (mmp80) REVERT: 6 50 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8784 (mmtm) REVERT: 6 305 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8816 (tmmt) REVERT: 7 93 MET cc_start: 0.8742 (mtm) cc_final: 0.8383 (mtp) REVERT: 7 143 TRP cc_start: 0.9416 (OUTLIER) cc_final: 0.8160 (m-90) REVERT: D 197 GLU cc_start: 0.8738 (pt0) cc_final: 0.8488 (pt0) REVERT: E 63 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8184 (tm-30) REVERT: E 142 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: H 89 ARG cc_start: 0.8350 (mtt-85) cc_final: 0.8118 (mtt-85) REVERT: H 122 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7262 (mpt-90) REVERT: H 138 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8389 (ttmm) REVERT: I 79 ILE cc_start: 0.8670 (pt) cc_final: 0.8440 (mp) REVERT: I 108 ASP cc_start: 0.8897 (m-30) cc_final: 0.8426 (m-30) REVERT: I 115 GLN cc_start: 0.9227 (mm110) cc_final: 0.8986 (mm-40) REVERT: I 119 HIS cc_start: 0.7829 (t70) cc_final: 0.7526 (t70) REVERT: I 152 MET cc_start: 0.8545 (ppp) cc_final: 0.8090 (ppp) REVERT: I 156 SER cc_start: 0.7971 (t) cc_final: 0.7485 (m) REVERT: J 92 LYS cc_start: 0.7510 (ptmt) cc_final: 0.7052 (pptt) REVERT: J 157 LYS cc_start: 0.4608 (OUTLIER) cc_final: 0.3358 (tmtm) REVERT: K 52 ASP cc_start: 0.8126 (t0) cc_final: 0.7913 (t0) REVERT: K 99 ASP cc_start: 0.8429 (t0) cc_final: 0.8187 (t0) REVERT: K 162 GLU cc_start: 0.8285 (mp0) cc_final: 0.8018 (pm20) REVERT: O 23 GLU cc_start: 0.8390 (tt0) cc_final: 0.8110 (tt0) REVERT: P 114 LYS cc_start: 0.9353 (ptmt) cc_final: 0.9012 (ptmm) REVERT: P 115 HIS cc_start: 0.8592 (m-70) cc_final: 0.8222 (m-70) REVERT: P 134 GLN cc_start: 0.8952 (tt0) cc_final: 0.8510 (tm-30) REVERT: P 142 ASN cc_start: 0.9229 (m-40) cc_final: 0.8996 (m110) REVERT: U 12 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9242 (tm) REVERT: U 52 ASP cc_start: 0.8536 (m-30) cc_final: 0.8277 (m-30) REVERT: V 111 SER cc_start: 0.8798 (t) cc_final: 0.8499 (p) REVERT: V 119 GLN cc_start: 0.9297 (mt0) cc_final: 0.8955 (mt0) REVERT: W 57 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: W 147 MET cc_start: 0.9082 (tpt) cc_final: 0.8699 (tpt) REVERT: Y 92 ASN cc_start: 0.8857 (m-40) cc_final: 0.8459 (t0) REVERT: d 184 SER cc_start: 0.9265 (t) cc_final: 0.8818 (p) REVERT: d 209 TYR cc_start: 0.8696 (m-80) cc_final: 0.8453 (m-80) REVERT: e 122 ASP cc_start: 0.8769 (m-30) cc_final: 0.8518 (m-30) REVERT: e 139 GLU cc_start: 0.3204 (OUTLIER) cc_final: 0.2143 (tp30) REVERT: e 154 ASP cc_start: 0.7991 (p0) cc_final: 0.7749 (m-30) REVERT: e 169 ASP cc_start: 0.5653 (t0) cc_final: 0.4691 (m-30) REVERT: e 205 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.5964 (pt) REVERT: e 237 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8296 (tm) REVERT: e 262 ASP cc_start: 0.8732 (t0) cc_final: 0.8497 (m-30) REVERT: f 90 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8468 (p) REVERT: g 81 ASN cc_start: 0.8149 (p0) cc_final: 0.7914 (p0) REVERT: h 106 ASP cc_start: 0.8308 (m-30) cc_final: 0.8055 (m-30) REVERT: k 41 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8196 (tmtt) REVERT: k 84 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9119 (tm) REVERT: k 88 THR cc_start: 0.9389 (m) cc_final: 0.9065 (p) REVERT: l 117 TYR cc_start: 0.8394 (t80) cc_final: 0.6846 (m-10) REVERT: l 123 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8350 (tptt) REVERT: l 128 ARG cc_start: 0.8770 (tmm-80) cc_final: 0.8288 (mtt180) REVERT: m 51 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8453 (tm) REVERT: m 77 MET cc_start: 0.4369 (tpt) cc_final: 0.3941 (ttm) REVERT: o 91 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: p 47 LYS cc_start: 0.9375 (mttp) cc_final: 0.9112 (mttm) REVERT: p 149 ASP cc_start: 0.8229 (t0) cc_final: 0.7853 (t70) REVERT: p 181 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: r 70 CYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7697 (p) REVERT: s 356 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9004 (p) outliers start: 125 outliers final: 84 residues processed: 1167 average time/residue: 1.7890 time to fit residues: 2884.2280 Evaluate side-chains 1170 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1069 time to evaluate : 6.886 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 1 residue 60 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 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 305 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 110 GLU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 176 GLN 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 76 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 127 TYR 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 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 279 GLU Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 565 optimal weight: 2.9990 chunk 910 optimal weight: 7.9990 chunk 555 optimal weight: 5.9990 chunk 432 optimal weight: 1.9990 chunk 633 optimal weight: 0.9990 chunk 955 optimal weight: 6.9990 chunk 879 optimal weight: 10.0000 chunk 760 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 587 optimal weight: 8.9990 chunk 466 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 146 HIS 5 165 GLN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 201 GLN F 257 GLN I 43 GLN I 128 ASN L 33 GLN L 43 ASN N 98 HIS ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN P 97 GLN Q 239 ASN S 118 ASN T 101 GLN U 23 ASN V 78 GLN Y 89 GLN Z 148 GLN ** d 235 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 73 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN ** r 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 105693 Z= 0.242 Angle : 0.614 14.028 150190 Z= 0.316 Chirality : 0.039 0.295 17643 Planarity : 0.004 0.124 13626 Dihedral : 21.014 179.959 32010 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.99 % Favored : 97.00 % Rotamer: Outliers : 1.58 % Allowed : 17.31 % Favored : 81.11 % 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: 1.84 (0.10), residues: 2819 sheet: -0.29 (0.15), residues: 1072 loop : 0.56 (0.10), residues: 4279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP h 86 HIS 0.022 0.001 HIS N 149 PHE 0.017 0.001 PHE J 90 TYR 0.021 0.001 TYR 5 176 ARG 0.017 0.000 ARG h 58 ********************** 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 1217 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1101 time to evaluate : 6.863 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: 0.8019 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: 6 47 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8465 (mmp80) REVERT: 6 50 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8732 (mmtm) REVERT: 6 107 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9140 (mmtm) REVERT: 6 305 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8776 (tmmt) REVERT: 7 93 MET cc_start: 0.8738 (mtm) cc_final: 0.8396 (mtp) REVERT: 7 143 TRP cc_start: 0.9415 (OUTLIER) cc_final: 0.8165 (m-90) REVERT: D 197 GLU cc_start: 0.8736 (pt0) cc_final: 0.8488 (pt0) REVERT: E 63 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8186 (tm-30) REVERT: E 142 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7681 (mtm) REVERT: F 74 GLN cc_start: 0.8688 (mt0) cc_final: 0.8450 (mp10) REVERT: H 84 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: H 89 ARG cc_start: 0.8354 (mtt-85) cc_final: 0.7856 (mtt-85) REVERT: H 122 ARG cc_start: 0.7457 (ttm110) cc_final: 0.7216 (mpt-90) REVERT: I 79 ILE cc_start: 0.8651 (pt) cc_final: 0.8427 (mp) REVERT: I 93 ASN cc_start: 0.9004 (m-40) cc_final: 0.8756 (t0) REVERT: I 95 MET cc_start: 0.8739 (ppp) cc_final: 0.8364 (ppp) REVERT: I 108 ASP cc_start: 0.8905 (m-30) cc_final: 0.8235 (m-30) REVERT: I 119 HIS cc_start: 0.7861 (t70) cc_final: 0.7521 (t70) REVERT: I 152 MET cc_start: 0.8540 (ppp) cc_final: 0.8062 (ppp) REVERT: J 58 LYS cc_start: 0.7771 (mmpt) cc_final: 0.7457 (mppt) REVERT: J 92 LYS cc_start: 0.7204 (ptmt) cc_final: 0.6830 (pptt) REVERT: J 157 LYS cc_start: 0.4578 (OUTLIER) cc_final: 0.3432 (tmtm) REVERT: K 52 ASP cc_start: 0.8120 (t0) cc_final: 0.7905 (t0) REVERT: K 99 ASP cc_start: 0.8410 (t0) cc_final: 0.8146 (t0) REVERT: K 135 GLU cc_start: 0.6881 (tp30) cc_final: 0.6618 (tp30) REVERT: K 160 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7994 (tp-100) REVERT: O 23 GLU cc_start: 0.8373 (tt0) cc_final: 0.8101 (tt0) REVERT: O 98 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8472 (ptpp) REVERT: P 114 LYS cc_start: 0.9357 (ptmt) cc_final: 0.9017 (ptmm) REVERT: P 115 HIS cc_start: 0.8576 (m-70) cc_final: 0.8211 (m-70) REVERT: P 134 GLN cc_start: 0.8956 (tt0) cc_final: 0.8671 (tm-30) REVERT: P 142 ASN cc_start: 0.9106 (m-40) cc_final: 0.8887 (m110) REVERT: U 12 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9226 (tm) REVERT: U 52 ASP cc_start: 0.8549 (m-30) cc_final: 0.8297 (m-30) REVERT: V 111 SER cc_start: 0.8786 (t) cc_final: 0.8498 (p) REVERT: V 119 GLN cc_start: 0.9289 (mt0) cc_final: 0.8932 (mt0) REVERT: W 147 MET cc_start: 0.9083 (tpt) cc_final: 0.8698 (tpt) REVERT: X 36 ARG cc_start: 0.7093 (ptm-80) cc_final: 0.6853 (ptm-80) REVERT: Y 92 ASN cc_start: 0.8842 (m-40) cc_final: 0.8446 (t0) REVERT: d 184 SER cc_start: 0.9245 (t) cc_final: 0.8827 (p) REVERT: d 209 TYR cc_start: 0.8649 (m-80) cc_final: 0.8407 (m-80) REVERT: e 122 ASP cc_start: 0.8771 (m-30) cc_final: 0.8519 (m-30) REVERT: e 139 GLU cc_start: 0.3219 (OUTLIER) cc_final: 0.2136 (tp30) REVERT: e 154 ASP cc_start: 0.7966 (p0) cc_final: 0.7722 (m-30) REVERT: e 169 ASP cc_start: 0.5664 (t0) cc_final: 0.4729 (m-30) REVERT: e 205 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.5934 (pt) REVERT: e 237 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8299 (tm) REVERT: f 90 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8455 (p) REVERT: g 81 ASN cc_start: 0.8108 (p0) cc_final: 0.7891 (p0) REVERT: h 106 ASP cc_start: 0.8275 (m-30) cc_final: 0.8016 (m-30) REVERT: k 41 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8195 (tmtt) REVERT: k 65 ASP cc_start: 0.7437 (t0) cc_final: 0.7108 (t0) REVERT: k 84 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9089 (tm) REVERT: k 88 THR cc_start: 0.9380 (m) cc_final: 0.9043 (p) REVERT: l 117 TYR cc_start: 0.8432 (t80) cc_final: 0.6891 (m-10) REVERT: l 123 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8384 (tptt) REVERT: l 128 ARG cc_start: 0.8771 (tmm-80) cc_final: 0.8290 (mtt180) REVERT: m 51 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (tm) REVERT: m 77 MET cc_start: 0.4364 (tpt) cc_final: 0.3940 (ttm) REVERT: o 42 GLU cc_start: 0.7988 (tt0) cc_final: 0.7751 (tt0) REVERT: o 91 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: p 47 LYS cc_start: 0.9384 (mttp) cc_final: 0.9124 (mttm) REVERT: p 149 ASP cc_start: 0.8231 (t0) cc_final: 0.7857 (t70) REVERT: p 181 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: q 128 MET cc_start: 0.8662 (tpt) cc_final: 0.8310 (tpt) REVERT: r 70 CYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7680 (p) REVERT: s 356 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8967 (p) outliers start: 116 outliers final: 77 residues processed: 1166 average time/residue: 1.8108 time to fit residues: 2953.7561 Evaluate side-chains 1172 residues out of total 7338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1077 time to evaluate : 7.012 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 1 residue 60 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 6 residue 182 ASP Chi-restraints excluded: chain 6 residue 305 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 110 GLU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 176 GLN 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 76 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 147 SER Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 279 GLU Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 604 optimal weight: 7.9990 chunk 810 optimal weight: 0.0970 chunk 233 optimal weight: 10.0000 chunk 701 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 762 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 782 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 140 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: ** 0 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 5 146 HIS 5 165 GLN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 304 ASN ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 257 GLN I 128 ASN L 33 GLN L 43 ASN N 98 HIS ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN O 154 GLN P 97 GLN Q 239 ASN S 84 ASN S 118 ASN T 101 GLN U 23 ASN V 78 GLN X 236 GLN Y 89 GLN Y 225 ASN ** a 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS q 134 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.042724 restraints weight = 261332.246| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 1.90 r_work: 0.2461 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 105693 Z= 0.330 Angle : 0.639 14.733 150190 Z= 0.329 Chirality : 0.041 0.308 17643 Planarity : 0.005 0.127 13626 Dihedral : 20.996 179.834 32010 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.59 % Allowed : 17.36 % Favored : 81.04 % 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: 1.80 (0.10), residues: 2813 sheet: -0.34 (0.15), residues: 1076 loop : 0.55 (0.10), residues: 4281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP h 86 HIS 0.015 0.001 HIS N 149 PHE 0.015 0.001 PHE 5 60 TYR 0.021 0.001 TYR 5 176 ARG 0.017 0.000 ARG h 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42026.34 seconds wall clock time: 730 minutes 57.63 seconds (43857.63 seconds total)