Starting phenix.real_space_refine on Fri Mar 15 13:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/03_2024/4v19_2787_neut_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.025 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 2 6.06 5 P 1583 5.49 5 Mg 169 5.21 5 S 136 5.16 5 C 37703 2.51 5 N 12701 2.21 5 O 17115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69409 Number of models: 1 Model: "" Number of chains: 42 Chain: "0" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 878 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "1" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2036 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "2" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1544 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "3" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "4" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 381 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "5" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "6" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 391 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "7" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 833 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "9" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 335 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 32233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32233 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 171, 'rna2p_pyr': 115, 'rna3p_pur': 667, 'rna3p_pyr': 562} Link IDs: {'rna2p': 285, 'rna3p': 1229} Chain breaks: 6 Chain: "B" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1225 Classifications: {'RNA': 62} Modifications used: {'rna2p': 3, 'rna3p': 59} Link IDs: {'rna2p': 3, 'rna3p': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 183 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1860 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain: "E" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 25, 'TRANS': 281} Chain: "F" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2011 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "J" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1361 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 16, 'TRANS': 151} Chain: "K" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1081 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 132} Chain: "N" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1444 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "O" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 9, 'TRANS': 105} Chain: "P" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2312 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 27, 'TRANS': 260} Chain: "Q" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1792 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 17, 'TRANS': 203} Chain: "R" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "S" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1168 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 136} Chain: "T" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1860 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 208} Chain: "U" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "V" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 144} Chain: "W" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1374 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain: "X" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1120 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 12, 'TRANS': 121} Chain breaks: 1 Chain: "Y" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1663 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 17, 'TRANS': 186} Chain: "Z" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" 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: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Unusual residues: {' MG': 163} Classifications: {'undetermined': 163} Link IDs: {None: 162} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6070 SG CYS 5 110 185.523 66.249 137.964 1.00 86.49 S ATOM 6092 SG CYS 5 113 187.069 68.182 135.126 1.00 71.52 S ATOM 6173 SG CYS 5 123 183.401 67.259 135.007 1.00 49.14 S ATOM 6195 SG CYS 5 126 186.062 64.585 134.633 1.00 72.93 S ATOM 8410 SG CYS 9 73 76.739 85.544 172.210 1.00 66.86 S ATOM 8435 SG CYS 9 76 79.999 87.224 171.334 1.00 75.55 S ATOM 8559 SG CYS 9 89 79.975 83.634 172.423 1.00 64.30 S Time building chain proxies: 26.98, per 1000 atoms: 0.39 Number of scatterers: 69409 At special positions: 0 Unit cell: (226.8, 221.2, 233.8, 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 2 29.99 S 136 16.00 P 1583 15.00 Mg 169 11.99 O 17115 8.00 N 12701 7.00 C 37703 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: 24.49 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 500 " pdb="ZN ZN 5 500 " - pdb=" SG CYS 5 110 " pdb="ZN ZN 5 500 " - pdb=" SG CYS 5 113 " pdb="ZN ZN 5 500 " - pdb=" SG CYS 5 126 " pdb="ZN ZN 5 500 " - pdb=" SG CYS 5 123 " pdb=" ZN 9 500 " pdb="ZN ZN 9 500 " - pdb=" SG CYS 9 89 " pdb="ZN ZN 9 500 " - pdb=" SG CYS 9 73 " pdb="ZN ZN 9 500 " - pdb=" ND1 HIS 9 95 " pdb="ZN ZN 9 500 " - pdb=" SG CYS 9 76 " Number of angles added : 9 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 51 sheets defined 29.1% alpha, 14.0% beta 379 base pairs and 799 stacking pairs defined. Time for finding SS restraints: 25.30 Creating SS restraints... Processing helix chain '0' and resid 111 through 119 Processing helix chain '1' and resid 11 through 14 No H-bonds generated for 'chain '1' and resid 11 through 14' Processing helix chain '1' and resid 19 through 23 Processing helix chain '1' and resid 26 through 33 Processing helix chain '1' and resid 92 through 94 No H-bonds generated for 'chain '1' and resid 92 through 94' Processing helix chain '1' and resid 129 through 137 Processing helix chain '1' and resid 141 through 146 Processing helix chain '1' and resid 150 through 153 No H-bonds generated for 'chain '1' and resid 150 through 153' Processing helix chain '1' and resid 156 through 171 Processing helix chain '1' and resid 181 through 190 removed outlier: 3.560A pdb=" N ARG 1 190 " --> pdb=" O ALA 1 186 " (cutoff:3.500A) Processing helix chain '1' and resid 192 through 194 No H-bonds generated for 'chain '1' and resid 192 through 194' Processing helix chain '1' and resid 198 through 203 removed outlier: 3.743A pdb=" N GLU 1 202 " --> pdb=" O GLU 1 198 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP 1 203 " --> pdb=" O ALA 1 199 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 198 through 203' Processing helix chain '1' and resid 208 through 218 Processing helix chain '1' and resid 226 through 244 Processing helix chain '2' and resid 67 through 69 No H-bonds generated for 'chain '2' and resid 67 through 69' Processing helix chain '2' and resid 73 through 75 No H-bonds generated for 'chain '2' and resid 73 through 75' Processing helix chain '2' and resid 89 through 93 Processing helix chain '2' and resid 97 through 123 removed outlier: 4.043A pdb=" N TYR 2 105 " --> pdb=" O HIS 2 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 159 removed outlier: 3.812A pdb=" N VAL 2 137 " --> pdb=" O LEU 2 134 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER 2 140 " --> pdb=" O VAL 2 137 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP 2 145 " --> pdb=" O ASP 2 142 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN 2 149 " --> pdb=" O LYS 2 146 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU 2 150 " --> pdb=" O VAL 2 147 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA 2 154 " --> pdb=" O ARG 2 151 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG 2 156 " --> pdb=" O ASP 2 153 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN 2 159 " --> pdb=" O ARG 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 192 No H-bonds generated for 'chain '2' and resid 190 through 192' Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 206 through 239 removed outlier: 3.601A pdb=" N VAL 2 211 " --> pdb=" O GLU 2 208 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG 2 214 " --> pdb=" O VAL 2 211 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN 2 218 " --> pdb=" O ILE 2 215 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 2 222 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG 2 224 " --> pdb=" O ILE 2 221 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG 2 226 " --> pdb=" O ALA 2 223 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER 2 227 " --> pdb=" O ARG 2 224 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG 2 230 " --> pdb=" O SER 2 227 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS 2 232 " --> pdb=" O GLU 2 229 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE 2 235 " --> pdb=" O LYS 2 232 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU 2 236 " --> pdb=" O GLU 2 233 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 46 Processing helix chain '3' and resid 50 through 56 removed outlier: 4.076A pdb=" N GLU 3 54 " --> pdb=" O PRO 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 89 Processing helix chain '3' and resid 104 through 113 removed outlier: 3.958A pdb=" N LYS 3 109 " --> pdb=" O SER 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 136 removed outlier: 4.542A pdb=" N ALA 3 135 " --> pdb=" O GLU 3 132 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 94 Processing helix chain '5' and resid 124 through 143 removed outlier: 3.580A pdb=" N LYS 5 129 " --> pdb=" O TYR 5 125 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 67 Processing helix chain '7' and resid 69 through 74 Processing helix chain '7' and resid 76 through 87 Processing helix chain '8' and resid 108 through 113 removed outlier: 3.882A pdb=" N ARG 8 113 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) Processing helix chain '8' and resid 138 through 145 Processing helix chain '8' and resid 152 through 160 Processing helix chain '8' and resid 164 through 166 No H-bonds generated for 'chain '8' and resid 164 through 166' Processing helix chain '8' and resid 176 through 180 removed outlier: 3.836A pdb=" N LYS 8 179 " --> pdb=" O PRO 8 176 " (cutoff:3.500A) Processing helix chain '9' and resid 93 through 95 No H-bonds generated for 'chain '9' and resid 93 through 95' Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 251 through 254 removed outlier: 4.314A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'E' and resid 55 through 77 Proline residue: E 59 - end of helix removed outlier: 3.540A pdb=" N LYS E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 310 through 313 removed outlier: 3.843A pdb=" N ASN E 313 " --> pdb=" O PHE E 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 321 through 324 No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.526A pdb=" N LYS F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 228 through 235 Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.788A pdb=" N GLU F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 116 through 121 removed outlier: 3.580A pdb=" N ASN I 121 " --> pdb=" O SER I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 126 No H-bonds generated for 'chain 'I' and resid 123 through 126' Processing helix chain 'I' and resid 134 through 147 removed outlier: 3.990A pdb=" N LEU I 139 " --> pdb=" O GLU I 135 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE I 140 " --> pdb=" O ASN I 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 50 Processing helix chain 'J' and resid 77 through 92 removed outlier: 3.719A pdb=" N ARG J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 118 Processing helix chain 'J' and resid 128 through 135 Proline residue: J 133 - end of helix Processing helix chain 'J' and resid 141 through 146 Proline residue: J 145 - end of helix Processing helix chain 'J' and resid 161 through 170 removed outlier: 3.842A pdb=" N ILE J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU J 168 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY J 170 " --> pdb=" O ARG J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 195 Processing helix chain 'K' and resid 35 through 39 Processing helix chain 'K' and resid 46 through 57 Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 114 through 126 removed outlier: 5.202A pdb=" N GLN K 126 " --> pdb=" O ARG K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 149 Processing helix chain 'N' and resid 6 through 14 Processing helix chain 'N' and resid 28 through 40 removed outlier: 3.765A pdb=" N MET N 34 " --> pdb=" O LYS N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 71 through 74 No H-bonds generated for 'chain 'N' and resid 71 through 74' Processing helix chain 'N' and resid 92 through 98 Processing helix chain 'N' and resid 102 through 110 Processing helix chain 'N' and resid 116 through 124 removed outlier: 3.526A pdb=" N MET N 122 " --> pdb=" O ARG N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 140 Processing helix chain 'N' and resid 160 through 165 Processing helix chain 'O' and resid 45 through 48 No H-bonds generated for 'chain 'O' and resid 45 through 48' Processing helix chain 'O' and resid 125 through 129 Processing helix chain 'O' and resid 131 through 139 removed outlier: 6.327A pdb=" N LYS O 136 " --> pdb=" O GLY O 132 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL O 137 " --> pdb=" O GLU O 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 18 removed outlier: 3.544A pdb=" N ARG P 17 " --> pdb=" O ASP P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 45 No H-bonds generated for 'chain 'P' and resid 42 through 45' Processing helix chain 'P' and resid 74 through 77 No H-bonds generated for 'chain 'P' and resid 74 through 77' Processing helix chain 'P' and resid 98 through 106 Processing helix chain 'P' and resid 118 through 123 Processing helix chain 'P' and resid 131 through 133 No H-bonds generated for 'chain 'P' and resid 131 through 133' Processing helix chain 'P' and resid 161 through 169 Processing helix chain 'P' and resid 181 through 188 Processing helix chain 'P' and resid 190 through 194 Processing helix chain 'P' and resid 208 through 214 Proline residue: P 212 - end of helix No H-bonds generated for 'chain 'P' and resid 208 through 214' Processing helix chain 'P' and resid 226 through 239 Proline residue: P 230 - end of helix removed outlier: 4.756A pdb=" N ARG P 233 " --> pdb=" O PRO P 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS P 239 " --> pdb=" O LEU P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 256 No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 288 through 295 Processing helix chain 'Q' and resid 69 through 71 No H-bonds generated for 'chain 'Q' and resid 69 through 71' Processing helix chain 'Q' and resid 99 through 111 Processing helix chain 'Q' and resid 169 through 181 removed outlier: 4.550A pdb=" N LEU Q 178 " --> pdb=" O GLY Q 174 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL Q 179 " --> pdb=" O PHE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 207 removed outlier: 3.946A pdb=" N GLU Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 221 Processing helix chain 'Q' and resid 223 through 228 removed outlier: 5.574A pdb=" N ARG Q 227 " --> pdb=" O LEU Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 237 removed outlier: 3.816A pdb=" N LEU Q 235 " --> pdb=" O PRO Q 232 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS Q 237 " --> pdb=" O ASP Q 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 39 Processing helix chain 'R' and resid 46 through 65 removed outlier: 4.504A pdb=" N GLY R 54 " --> pdb=" O ASP R 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE R 60 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU R 65 " --> pdb=" O ASP R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 79 removed outlier: 3.515A pdb=" N MET R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 91 Proline residue: R 87 - end of helix removed outlier: 4.125A pdb=" N GLN R 91 " --> pdb=" O LYS R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 160 removed outlier: 3.964A pdb=" N GLY R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 59 Processing helix chain 'S' and resid 110 through 115 removed outlier: 3.615A pdb=" N HIS S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 139 Processing helix chain 'S' and resid 152 through 154 No H-bonds generated for 'chain 'S' and resid 152 through 154' Processing helix chain 'S' and resid 156 through 168 Processing helix chain 'T' and resid 78 through 80 No H-bonds generated for 'chain 'T' and resid 78 through 80' Processing helix chain 'T' and resid 89 through 103 removed outlier: 3.539A pdb=" N GLN T 93 " --> pdb=" O LEU T 90 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU T 95 " --> pdb=" O PHE T 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG T 96 " --> pdb=" O GLN T 93 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU T 100 " --> pdb=" O LYS T 97 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG T 103 " --> pdb=" O LEU T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 146 No H-bonds generated for 'chain 'T' and resid 144 through 146' Processing helix chain 'T' and resid 189 through 191 No H-bonds generated for 'chain 'T' and resid 189 through 191' Processing helix chain 'T' and resid 195 through 198 Processing helix chain 'T' and resid 236 through 238 No H-bonds generated for 'chain 'T' and resid 236 through 238' Processing helix chain 'T' and resid 245 through 248 No H-bonds generated for 'chain 'T' and resid 245 through 248' Processing helix chain 'T' and resid 251 through 259 removed outlier: 3.732A pdb=" N GLN T 258 " --> pdb=" O MET T 254 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS T 259 " --> pdb=" O ARG T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 263 through 267 removed outlier: 3.822A pdb=" N GLU T 266 " --> pdb=" O PRO T 263 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 271 No H-bonds generated for 'chain 'T' and resid 269 through 271' Processing helix chain 'T' and resid 276 through 291 Processing helix chain 'U' and resid 17 through 28 removed outlier: 3.698A pdb=" N VAL U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA U 28 " --> pdb=" O VAL U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 78 removed outlier: 3.585A pdb=" N ARG U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG U 62 " --> pdb=" O ARG U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 92 Processing helix chain 'U' and resid 99 through 108 Processing helix chain 'U' and resid 110 through 133 Processing helix chain 'V' and resid 73 through 93 Processing helix chain 'W' and resid 49 through 53 Processing helix chain 'W' and resid 82 through 91 removed outlier: 3.936A pdb=" N TYR W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU W 88 " --> pdb=" O LYS W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 106 removed outlier: 3.505A pdb=" N PHE W 106 " --> pdb=" O ALA W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 128 Processing helix chain 'W' and resid 135 through 137 No H-bonds generated for 'chain 'W' and resid 135 through 137' Processing helix chain 'W' and resid 190 through 203 removed outlier: 3.634A pdb=" N ARG W 195 " --> pdb=" O VAL W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 61 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 179 through 183 Processing helix chain 'Y' and resid 194 through 201 Processing sheet with id= A, first strand: chain '0' and resid 75 through 77 removed outlier: 9.208A pdb=" N HIS 0 76 " --> pdb=" O TYR 0 127 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR 0 129 " --> pdb=" O HIS 0 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 81 through 83 removed outlier: 6.208A pdb=" N ALA 0 91 " --> pdb=" O ILE 0 66 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE 0 66 " --> pdb=" O ALA 0 91 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 50 through 52 Processing sheet with id= D, first strand: chain '1' and resid 86 through 91 Processing sheet with id= E, first strand: chain '1' and resid 109 through 116 Processing sheet with id= F, first strand: chain '2' and resid 168 through 172 Processing sheet with id= G, first strand: chain '3' and resid 97 through 101 Processing sheet with id= H, first strand: chain '3' and resid 138 through 140 Processing sheet with id= I, first strand: chain '4' and resid 64 through 69 Processing sheet with id= J, first strand: chain '5' and resid 107 through 109 Processing sheet with id= K, first strand: chain '5' and resid 156 through 159 removed outlier: 6.214A pdb=" N ARG 5 173 " --> pdb=" O VAL 5 157 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU 5 159 " --> pdb=" O ARG 5 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE 5 175 " --> pdb=" O LEU 5 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '6' and resid 28 through 34 Processing sheet with id= M, first strand: chain '8' and resid 114 through 116 Processing sheet with id= N, first strand: chain '9' and resid 76 through 81 Processing sheet with id= O, first strand: chain 'D' and resid 162 through 166 removed outlier: 3.556A pdb=" N ASP D 162 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 142 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL D 130 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE D 140 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 182 through 184 Processing sheet with id= Q, first strand: chain 'D' and resid 234 through 238 removed outlier: 3.675A pdb=" N ARG D 219 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN D 228 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU D 217 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 265 through 268 removed outlier: 5.302A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL E 273 " --> pdb=" O ASN E 286 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= T, first strand: chain 'F' and resid 47 through 49 Processing sheet with id= U, first strand: chain 'F' and resid 109 through 111 Processing sheet with id= V, first strand: chain 'F' and resid 187 through 190 removed outlier: 6.650A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU F 261 " --> pdb=" O VAL F 190 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 110 through 114 removed outlier: 3.759A pdb=" N ASP I 110 " --> pdb=" O LEU I 98 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 54 through 58 removed outlier: 6.661A pdb=" N GLU I 57 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU I 82 " --> pdb=" O GLU I 57 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 95 through 100 Processing sheet with id= Z, first strand: chain 'J' and resid 179 through 181 Processing sheet with id= AA, first strand: chain 'K' and resid 18 through 24 removed outlier: 3.611A pdb=" N GLY K 18 " --> pdb=" O VAL K 72 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 110 through 113 Processing sheet with id= AC, first strand: chain 'N' and resid 19 through 22 Processing sheet with id= AD, first strand: chain 'N' and resid 76 through 80 Processing sheet with id= AE, first strand: chain 'O' and resid 56 through 60 removed outlier: 6.585A pdb=" N LEU O 74 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL O 60 " --> pdb=" O ARG O 72 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG O 72 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN O 104 " --> pdb=" O VAL O 87 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'P' and resid 153 through 156 removed outlier: 6.434A pdb=" N VAL P 173 " --> pdb=" O ILE P 154 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL P 156 " --> pdb=" O VAL P 173 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR P 175 " --> pdb=" O VAL P 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'P' and resid 274 through 276 Processing sheet with id= AH, first strand: chain 'P' and resid 92 through 97 removed outlier: 7.234A pdb=" N GLN P 94 " --> pdb=" O TYR P 136 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL P 138 " --> pdb=" O GLN P 94 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU P 96 " --> pdb=" O VAL P 138 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU P 140 " --> pdb=" O LEU P 96 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Q' and resid 87 through 91 Processing sheet with id= AJ, first strand: chain 'Q' and resid 95 through 98 removed outlier: 6.729A pdb=" N ILE Q 131 " --> pdb=" O ASP Q 148 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR Q 150 " --> pdb=" O LYS Q 129 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS Q 129 " --> pdb=" O TYR Q 150 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Q' and resid 118 through 122 Processing sheet with id= AL, first strand: chain 'R' and resid 41 through 45 Processing sheet with id= AM, first strand: chain 'S' and resid 79 through 85 removed outlier: 3.773A pdb=" N VAL S 103 " --> pdb=" O VAL S 94 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N HIS S 96 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL S 101 " --> pdb=" O HIS S 96 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 173 through 178 removed outlier: 3.705A pdb=" N GLU T 173 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE T 116 " --> pdb=" O VAL T 177 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N LEU T 134 " --> pdb=" O THR T 154 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR T 154 " --> pdb=" O LEU T 134 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE T 150 " --> pdb=" O ILE T 138 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG T 140 " --> pdb=" O THR T 148 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR T 148 " --> pdb=" O ARG T 140 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'V' and resid 108 through 113 removed outlier: 6.673A pdb=" N HIS V 104 " --> pdb=" O VAL V 137 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL V 137 " --> pdb=" O HIS V 104 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 117 through 120 Processing sheet with id= AQ, first strand: chain 'V' and resid 131 through 134 removed outlier: 4.381A pdb=" N VAL V 160 " --> pdb=" O LEU V 134 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR V 163 " --> pdb=" O ILE V 199 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE V 199 " --> pdb=" O THR V 163 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'V' and resid 173 through 179 removed outlier: 4.340A pdb=" N TYR V 184 " --> pdb=" O GLN V 179 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'W' and resid 70 through 75 removed outlier: 6.328A pdb=" N VAL W 177 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL W 140 " --> pdb=" O VAL W 177 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'W' and resid 151 through 156 Processing sheet with id= AU, first strand: chain 'X' and resid 39 through 44 removed outlier: 4.131A pdb=" N LYS X 93 " --> pdb=" O ILE X 44 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Y' and resid 73 through 75 removed outlier: 5.370A pdb=" N LYS Y 61 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Y 122 " --> pdb=" O THR Y 131 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS Y 129 " --> pdb=" O ASP Y 124 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Y' and resid 93 through 97 Processing sheet with id= AX, first strand: chain 'Y' and resid 99 through 101 Processing sheet with id= AY, first strand: chain 'Y' and resid 133 through 137 995 hydrogen bonds defined for protein. 2637 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 917 hydrogen bonds 1604 hydrogen bond angles 0 basepair planarities 379 basepair parallelities 799 stacking parallelities Total time for adding SS restraints: 51.19 Time building geometry restraints manager: 26.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13546 1.33 - 1.46: 27372 1.46 - 1.59: 29813 1.59 - 1.72: 2950 1.72 - 1.84: 223 Bond restraints: 73904 Sorted by residual: bond pdb=" C5 Y5P B 44 " pdb=" C6 Y5P B 44 " ideal model delta sigma weight residual 1.515 1.328 0.187 2.00e-02 2.50e+03 8.71e+01 bond pdb=" C5 Y5P B 13 " pdb=" C6 Y5P B 13 " ideal model delta sigma weight residual 1.515 1.328 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C5 Y5P B 8 " pdb=" C6 Y5P B 8 " ideal model delta sigma weight residual 1.515 1.332 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C5 Y5P B 26 " pdb=" C6 Y5P B 26 " ideal model delta sigma weight residual 1.515 1.333 0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C5 Y5P B 3 " pdb=" C6 Y5P B 3 " ideal model delta sigma weight residual 1.515 1.335 0.180 2.00e-02 2.50e+03 8.13e+01 ... (remaining 73899 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.35: 8499 105.35 - 112.96: 42350 112.96 - 120.57: 31258 120.57 - 128.17: 22644 128.17 - 135.78: 2712 Bond angle restraints: 107463 Sorted by residual: angle pdb=" C PHE X 111 " pdb=" N PRO X 112 " pdb=" CA PRO X 112 " ideal model delta sigma weight residual 119.87 130.65 -10.78 1.04e+00 9.25e-01 1.07e+02 angle pdb=" C LEU Y 15 " pdb=" N PRO Y 16 " pdb=" CA PRO Y 16 " ideal model delta sigma weight residual 120.38 129.89 -9.51 1.03e+00 9.43e-01 8.52e+01 angle pdb=" C GLY P 9 " pdb=" N PRO P 10 " pdb=" CA PRO P 10 " ideal model delta sigma weight residual 119.84 130.67 -10.83 1.25e+00 6.40e-01 7.51e+01 angle pdb=" C1' P5P B 29 " pdb=" N9 P5P B 29 " pdb=" C8 P5P B 29 " ideal model delta sigma weight residual 105.08 129.74 -24.66 3.00e+00 1.11e-01 6.76e+01 angle pdb=" C1' P5P B 45 " pdb=" N9 P5P B 45 " pdb=" C8 P5P B 45 " ideal model delta sigma weight residual 105.08 129.28 -24.20 3.00e+00 1.11e-01 6.51e+01 ... (remaining 107458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 40696 35.99 - 71.99: 4239 71.99 - 107.98: 502 107.98 - 143.98: 33 143.98 - 179.97: 44 Dihedral angle restraints: 45514 sinusoidal: 32913 harmonic: 12601 Sorted by residual: dihedral pdb=" CA PHE E 316 " pdb=" C PHE E 316 " pdb=" N PRO E 317 " pdb=" CA PRO E 317 " ideal model delta harmonic sigma weight residual 180.00 103.73 76.27 0 5.00e+00 4.00e-02 2.33e+02 dihedral pdb=" O4' U A1517 " pdb=" C1' U A1517 " pdb=" N1 U A1517 " pdb=" C2 U A1517 " ideal model delta sinusoidal sigma weight residual -160.00 19.97 -179.97 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1523 " pdb=" C1' C A1523 " pdb=" N1 C A1523 " pdb=" C2 C A1523 " ideal model delta sinusoidal sigma weight residual -160.00 18.78 -178.78 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 45511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 11031 0.065 - 0.131: 1828 0.131 - 0.196: 184 0.196 - 0.262: 20 0.262 - 0.327: 14 Chirality restraints: 13077 Sorted by residual: chirality pdb=" C3' A A 160 " pdb=" C4' A A 160 " pdb=" O3' A A 160 " pdb=" C2' A A 160 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C3' U A 48 " pdb=" C4' U A 48 " pdb=" O3' U A 48 " pdb=" C2' U A 48 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C3' U A1140 " pdb=" C4' U A1140 " pdb=" O3' U A1140 " pdb=" C2' U A1140 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 13074 not shown) Planarity restraints: 7900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 9 92 " 0.056 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO 9 93 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO 9 93 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO 9 93 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 432 " 0.039 2.00e-02 2.50e+03 1.75e-02 9.20e+00 pdb=" N9 G A 432 " -0.045 2.00e-02 2.50e+03 pdb=" C8 G A 432 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 432 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 432 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 432 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 432 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G A 432 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 432 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 432 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 432 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 432 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 342 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO E 343 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 343 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 343 " -0.039 5.00e-02 4.00e+02 ... (remaining 7897 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 484 2.47 - 3.08: 42352 3.08 - 3.68: 114468 3.68 - 4.29: 175200 4.29 - 4.90: 251802 Nonbonded interactions: 584306 Sorted by model distance: nonbonded pdb=" OP1 A A 830 " pdb="MG MG A2650 " model vdw 1.860 2.170 nonbonded pdb=" OP1 U A 371 " pdb="MG MG A2593 " model vdw 1.917 2.170 nonbonded pdb=" OP1 U A1371 " pdb="MG MG A2647 " model vdw 1.926 2.170 nonbonded pdb=" OP1 U A 183 " pdb="MG MG A2576 " model vdw 1.935 2.170 nonbonded pdb=" O2' A A 68 " pdb=" O4' C A 69 " model vdw 1.975 2.440 ... (remaining 584301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'Z' } 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: 0.380 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: 0.040 Extract box with map and model: 5.140 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 185.990 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.200 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.009 0.187 73904 Z= 0.551 Angle : 1.321 24.660 107463 Z= 0.744 Chirality : 0.049 0.327 13077 Planarity : 0.006 0.087 7900 Dihedral : 23.556 179.972 37382 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 6.97 % Allowed : 8.75 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.02 % 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: -2.85 (0.10), residues: 4303 helix: -3.04 (0.10), residues: 1248 sheet: -1.12 (0.17), residues: 641 loop : -1.40 (0.10), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 222 HIS 0.010 0.002 HIS U 27 PHE 0.025 0.003 PHE P 89 TYR 0.024 0.003 TYR 2 105 ARG 0.009 0.001 ARG W 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1584 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1318 time to evaluate : 4.941 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: 0 86 ASN cc_start: 0.9141 (p0) cc_final: 0.8822 (p0) REVERT: 0 88 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8329 (m) REVERT: 0 127 TYR cc_start: 0.9215 (m-80) cc_final: 0.8756 (m-80) REVERT: 1 20 ILE cc_start: 0.8047 (tt) cc_final: 0.7100 (tt) REVERT: 1 124 THR cc_start: 0.8744 (m) cc_final: 0.8541 (t) REVERT: 1 156 LYS cc_start: 0.8916 (tptt) cc_final: 0.8624 (tptp) REVERT: 2 81 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7276 (t) REVERT: 2 135 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8127 (mp0) REVERT: 2 139 ASP cc_start: 0.7908 (m-30) cc_final: 0.7608 (m-30) REVERT: 2 185 GLN cc_start: 0.9222 (pt0) cc_final: 0.8860 (pt0) REVERT: 2 215 ILE cc_start: 0.9502 (mt) cc_final: 0.9255 (mm) REVERT: 2 220 ARG cc_start: 0.8542 (mtt180) cc_final: 0.7702 (mmt180) REVERT: 3 62 TYR cc_start: 0.8193 (m-80) cc_final: 0.7622 (m-80) REVERT: 3 73 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8657 (mmmt) REVERT: 3 88 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8635 (mtt) REVERT: 3 134 MET cc_start: 0.7761 (mmp) cc_final: 0.7299 (mmt) REVERT: 4 60 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.5685 (tp-100) REVERT: 5 92 CYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8610 (m) REVERT: 5 108 ASP cc_start: 0.8279 (m-30) cc_final: 0.7977 (m-30) REVERT: 5 129 LYS cc_start: 0.8553 (pttt) cc_final: 0.7958 (mmtt) REVERT: 5 144 GLN cc_start: 0.7878 (mt0) cc_final: 0.7604 (tm-30) REVERT: 5 160 TYR cc_start: 0.7879 (m-80) cc_final: 0.7675 (m-10) REVERT: 5 163 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7284 (tt0) REVERT: 7 64 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8389 (mttt) REVERT: 7 91 LYS cc_start: 0.9058 (tttt) cc_final: 0.8685 (ttpt) REVERT: 8 124 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8833 (ptt90) REVERT: 8 152 LYS cc_start: 0.8519 (tttt) cc_final: 0.7632 (mmtt) REVERT: 9 100 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8116 (ptt) REVERT: D 126 LYS cc_start: 0.8774 (tttt) cc_final: 0.8429 (mttp) REVERT: D 250 ASN cc_start: 0.9007 (t0) cc_final: 0.8624 (t0) REVERT: E 72 GLN cc_start: 0.8454 (mt0) cc_final: 0.8249 (mt0) REVERT: E 102 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9039 (tt) REVERT: E 127 CYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8102 (t) REVERT: E 133 THR cc_start: 0.9135 (m) cc_final: 0.8806 (p) REVERT: E 163 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8094 (mt-10) REVERT: E 194 TYR cc_start: 0.8454 (m-80) cc_final: 0.8171 (m-80) REVERT: E 288 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8848 (p) REVERT: E 330 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7875 (mm-30) REVERT: E 344 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8398 (p) REVERT: F 76 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6753 (ptt180) REVERT: F 114 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9390 (t) REVERT: F 133 SER cc_start: 0.9305 (p) cc_final: 0.9069 (t) REVERT: F 226 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: F 238 LYS cc_start: 0.8695 (mttt) cc_final: 0.7923 (mmmt) REVERT: F 257 GLN cc_start: 0.9088 (mt0) cc_final: 0.8764 (mt0) REVERT: I 61 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8756 (ttpp) REVERT: I 139 LEU cc_start: 0.6935 (tp) cc_final: 0.6655 (mp) REVERT: J 35 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8033 (ptp90) REVERT: J 61 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8490 (t0) REVERT: J 63 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6714 (tmm160) REVERT: J 68 PRO cc_start: 0.5298 (Cg_exo) cc_final: 0.5058 (Cg_endo) REVERT: J 81 LEU cc_start: 0.6994 (mt) cc_final: 0.5900 (tt) REVERT: J 100 GLN cc_start: 0.5479 (tt0) cc_final: 0.5248 (tp-100) REVERT: J 121 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6804 (pt) REVERT: J 128 ASN cc_start: 0.6273 (t0) cc_final: 0.4624 (t0) REVERT: J 183 ASP cc_start: 0.4036 (OUTLIER) cc_final: 0.2467 (p0) REVERT: J 188 ARG cc_start: 0.6568 (tpt170) cc_final: 0.5753 (ptt90) REVERT: K 115 LYS cc_start: 0.6018 (mttt) cc_final: 0.5325 (mmtm) REVERT: K 116 HIS cc_start: 0.6076 (m90) cc_final: 0.5782 (m90) REVERT: N 78 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8665 (m) REVERT: N 154 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7744 (mmm160) REVERT: O 32 ILE cc_start: 0.9303 (tt) cc_final: 0.9033 (tt) REVERT: O 35 MET cc_start: 0.8899 (mmm) cc_final: 0.8540 (mmt) REVERT: O 72 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7541 (ttp-170) REVERT: O 74 LEU cc_start: 0.9447 (tp) cc_final: 0.9247 (tt) REVERT: O 101 ASP cc_start: 0.8523 (t0) cc_final: 0.8194 (t0) REVERT: O 102 SER cc_start: 0.9422 (m) cc_final: 0.9199 (p) REVERT: O 103 ASN cc_start: 0.9311 (m110) cc_final: 0.9086 (m-40) REVERT: O 104 ASN cc_start: 0.9116 (m-40) cc_final: 0.8796 (m-40) REVERT: O 134 PHE cc_start: 0.7837 (m-80) cc_final: 0.7415 (m-10) REVERT: O 140 ILE cc_start: 0.9141 (pt) cc_final: 0.8864 (pt) REVERT: P 23 SER cc_start: 0.9152 (p) cc_final: 0.8851 (t) REVERT: P 28 LYS cc_start: 0.7868 (tttt) cc_final: 0.7443 (mtmt) REVERT: P 61 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8884 (p) REVERT: P 62 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8699 (ptt180) REVERT: P 88 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8181 (t) REVERT: P 219 ASN cc_start: 0.8646 (m-40) cc_final: 0.8194 (m110) REVERT: P 258 THR cc_start: 0.8968 (m) cc_final: 0.8653 (p) REVERT: P 264 GLN cc_start: 0.8716 (mt0) cc_final: 0.8308 (tt0) REVERT: P 277 MET cc_start: 0.7915 (mmm) cc_final: 0.7494 (mtt) REVERT: Q 96 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8842 (m-10) REVERT: Q 104 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8118 (tmm) REVERT: Q 105 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8707 (mtp) REVERT: Q 117 ASN cc_start: 0.8842 (m-40) cc_final: 0.8320 (m-40) REVERT: Q 118 MET cc_start: 0.8516 (mtp) cc_final: 0.8192 (mmm) REVERT: Q 131 ILE cc_start: 0.9537 (mt) cc_final: 0.9315 (mt) REVERT: Q 140 MET cc_start: 0.9184 (tpp) cc_final: 0.8884 (mmt) REVERT: Q 162 GLU cc_start: 0.8527 (tt0) cc_final: 0.8313 (tt0) REVERT: Q 177 ASP cc_start: 0.8498 (m-30) cc_final: 0.8119 (p0) REVERT: Q 214 THR cc_start: 0.9519 (p) cc_final: 0.9243 (p) REVERT: R 9 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8164 (pt) REVERT: R 20 LEU cc_start: 0.9085 (mt) cc_final: 0.8797 (mt) REVERT: R 30 GLN cc_start: 0.8768 (mt0) cc_final: 0.8464 (tt0) REVERT: R 57 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8733 (mm-30) REVERT: R 75 MET cc_start: 0.9103 (tpp) cc_final: 0.8854 (tpp) REVERT: R 82 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6754 (mt-10) REVERT: R 125 GLU cc_start: 0.8095 (tt0) cc_final: 0.7836 (tt0) REVERT: S 90 ILE cc_start: 0.9111 (mm) cc_final: 0.8910 (mm) REVERT: S 110 TRP cc_start: 0.7270 (t-100) cc_final: 0.7056 (t60) REVERT: S 116 LEU cc_start: 0.7290 (tp) cc_final: 0.6880 (pp) REVERT: S 117 TYR cc_start: 0.6130 (t80) cc_final: 0.5740 (p90) REVERT: S 132 LEU cc_start: 0.8884 (tp) cc_final: 0.8293 (tp) REVERT: S 138 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7443 (tp30) REVERT: S 143 PHE cc_start: 0.8534 (m-80) cc_final: 0.8264 (m-80) REVERT: T 86 ARG cc_start: 0.7847 (ptt180) cc_final: 0.7647 (ptp-170) REVERT: T 98 ASP cc_start: 0.8992 (m-30) cc_final: 0.8396 (m-30) REVERT: T 99 MET cc_start: 0.9265 (ptm) cc_final: 0.8913 (ptm) REVERT: T 112 TYR cc_start: 0.8982 (m-80) cc_final: 0.8623 (m-80) REVERT: T 131 SER cc_start: 0.8696 (t) cc_final: 0.8370 (p) REVERT: T 192 ASP cc_start: 0.9157 (m-30) cc_final: 0.8734 (m-30) REVERT: T 268 ASP cc_start: 0.8948 (t0) cc_final: 0.8518 (t0) REVERT: U 10 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8984 (tp) REVERT: U 98 ASN cc_start: 0.8602 (m-40) cc_final: 0.8290 (m-40) REVERT: U 108 TYR cc_start: 0.8987 (m-80) cc_final: 0.8748 (m-80) REVERT: U 109 GLU cc_start: 0.8743 (mp0) cc_final: 0.8140 (tp30) REVERT: U 122 ARG cc_start: 0.9080 (tpt170) cc_final: 0.7775 (mmt180) REVERT: U 143 SER cc_start: 0.8378 (m) cc_final: 0.8078 (p) REVERT: V 86 GLN cc_start: 0.8632 (tt0) cc_final: 0.8395 (tt0) REVERT: V 116 ASP cc_start: 0.7224 (m-30) cc_final: 0.6990 (m-30) REVERT: V 121 GLU cc_start: 0.8648 (tp30) cc_final: 0.8391 (tp30) REVERT: V 150 LYS cc_start: 0.8410 (mttt) cc_final: 0.8191 (mttt) REVERT: V 174 ILE cc_start: 0.8654 (mt) cc_final: 0.8425 (mt) REVERT: W 67 ARG cc_start: 0.8142 (ptt180) cc_final: 0.7735 (ppt170) REVERT: W 75 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8705 (ttm170) REVERT: W 80 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8082 (t80) REVERT: W 85 MET cc_start: 0.9129 (tpp) cc_final: 0.8560 (tpt) REVERT: W 114 ILE cc_start: 0.9146 (mm) cc_final: 0.8824 (mt) REVERT: W 137 ASN cc_start: 0.8844 (t0) cc_final: 0.8366 (t0) REVERT: W 199 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8648 (tp40) REVERT: W 200 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8158 (mt-10) REVERT: X 39 THR cc_start: 0.9470 (m) cc_final: 0.9208 (m) REVERT: X 46 MET cc_start: 0.9239 (tpp) cc_final: 0.8776 (tpp) REVERT: X 84 ASN cc_start: 0.9304 (t0) cc_final: 0.8882 (t0) REVERT: X 97 VAL cc_start: 0.9537 (OUTLIER) cc_final: 0.9300 (t) REVERT: X 140 ARG cc_start: 0.7431 (mtt180) cc_final: 0.6911 (mmt180) REVERT: Y 23 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6872 (mmm) REVERT: Y 105 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.5911 (ptt180) REVERT: Y 111 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.7033 (p) REVERT: Y 193 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7469 (p) REVERT: Y 204 ILE cc_start: 0.8447 (mt) cc_final: 0.8173 (mt) outliers start: 266 outliers final: 60 residues processed: 1486 average time/residue: 0.8140 time to fit residues: 1941.7706 Evaluate side-chains 900 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 803 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 88 CYS Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 153 ASP Chi-restraints excluded: chain 2 residue 174 ILE Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 73 LYS Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 88 MET Chi-restraints excluded: chain 4 residue 60 GLN Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 92 CYS Chi-restraints excluded: chain 6 residue 42 THR Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 95 HIS Chi-restraints excluded: chain 8 residue 111 ILE Chi-restraints excluded: chain 8 residue 124 ARG Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 150 CYS Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 9 residue 100 MET Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 183 ASP Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 96 TYR Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 276 SER Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 128 CYS Chi-restraints excluded: chain V residue 170 SER Chi-restraints excluded: chain W residue 75 ARG Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 199 GLN Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 111 SER Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 193 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 489 optimal weight: 6.9990 chunk 439 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 150 optimal weight: 40.0000 chunk 296 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 454 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 276 optimal weight: 0.9990 chunk 338 optimal weight: 20.0000 chunk 526 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 ASN 0 59 HIS ** 0 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 27 HIS 1 42 HIS 1 111 GLN 2 101 HIS 2 112 ASN 2 124 GLN 2 149 GLN 2 197 ASN 3 67 HIS ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 65 HIS 8 118 HIS D 183 HIS D 272 ASN E 88 HIS E 280 HIS E 281 ASN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 153 HIS ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 93 ASN J 41 HIS ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 HIS K 126 GLN N 49 GLN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN O 113 ASN P 71 GLN P 84 ASN P 87 HIS P 91 HIS P 123 ASN ** P 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 HIS Q 209 ASN Q 210 GLN R 39 HIS R 112 ASN R 129 ASN ** R 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS ** S 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN T 262 GLN U 89 ASN U 94 GLN V 80 HIS V 104 HIS V 109 GLN V 122 ASN V 175 ASN ** V 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 GLN W 171 HIS X 73 GLN X 103 GLN Y 117 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 73904 Z= 0.277 Angle : 0.753 11.283 107463 Z= 0.387 Chirality : 0.042 0.288 13077 Planarity : 0.006 0.077 7900 Dihedral : 24.489 179.647 28292 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 5.40 % Allowed : 15.94 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 4303 helix: -1.12 (0.13), residues: 1236 sheet: -0.54 (0.18), residues: 654 loop : -0.67 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 85 HIS 0.007 0.001 HIS E 156 PHE 0.018 0.002 PHE U 31 TYR 0.030 0.002 TYR 4 69 ARG 0.023 0.001 ARG 1 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 844 time to evaluate : 3.987 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: 0 86 ASN cc_start: 0.9159 (p0) cc_final: 0.8817 (p0) REVERT: 0 88 CYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8268 (m) REVERT: 0 94 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: 0 127 TYR cc_start: 0.9221 (m-80) cc_final: 0.8907 (m-80) REVERT: 1 90 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8909 (ptm-80) REVERT: 2 139 ASP cc_start: 0.7882 (m-30) cc_final: 0.7669 (m-30) REVERT: 2 141 MET cc_start: 0.9186 (mtp) cc_final: 0.8976 (mtp) REVERT: 2 185 GLN cc_start: 0.8995 (pt0) cc_final: 0.8525 (pt0) REVERT: 2 220 ARG cc_start: 0.8454 (mtt180) cc_final: 0.7599 (mmt180) REVERT: 3 52 ASP cc_start: 0.8292 (m-30) cc_final: 0.8077 (m-30) REVERT: 3 56 TYR cc_start: 0.8841 (m-80) cc_final: 0.8416 (m-80) REVERT: 4 60 GLN cc_start: 0.7708 (pt0) cc_final: 0.6220 (tp-100) REVERT: 4 69 TYR cc_start: 0.6358 (t80) cc_final: 0.5906 (t80) REVERT: 5 108 ASP cc_start: 0.8200 (m-30) cc_final: 0.7994 (m-30) REVERT: 5 143 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8720 (mttt) REVERT: 5 163 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7112 (tt0) REVERT: 5 170 GLN cc_start: 0.6800 (pt0) cc_final: 0.6550 (pt0) REVERT: 7 64 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8194 (mttt) REVERT: 7 91 LYS cc_start: 0.9010 (tttt) cc_final: 0.8625 (ttpt) REVERT: 8 152 LYS cc_start: 0.8603 (tttt) cc_final: 0.7513 (mmmt) REVERT: D 90 GLN cc_start: 0.8981 (mt0) cc_final: 0.8719 (mm-40) REVERT: D 126 LYS cc_start: 0.8695 (tttt) cc_final: 0.8283 (mptt) REVERT: D 236 GLN cc_start: 0.8682 (tp40) cc_final: 0.7986 (tt0) REVERT: E 150 LYS cc_start: 0.9004 (tttt) cc_final: 0.8771 (tttp) REVERT: F 76 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7401 (ptt180) REVERT: F 114 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8965 (p) REVERT: F 226 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8659 (mtt) REVERT: F 238 LYS cc_start: 0.8990 (mttt) cc_final: 0.8173 (mmmt) REVERT: I 59 TRP cc_start: 0.8870 (m100) cc_final: 0.8541 (m100) REVERT: I 61 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8852 (ttpp) REVERT: I 100 GLN cc_start: 0.5984 (mp10) cc_final: 0.5480 (mp10) REVERT: I 139 LEU cc_start: 0.7237 (tp) cc_final: 0.6831 (mp) REVERT: J 61 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8620 (t0) REVERT: J 63 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7107 (tmm160) REVERT: J 91 ARG cc_start: 0.6155 (tmm-80) cc_final: 0.5900 (mtm110) REVERT: K 115 LYS cc_start: 0.6312 (mttt) cc_final: 0.5162 (mmtm) REVERT: N 78 SER cc_start: 0.9130 (p) cc_final: 0.8879 (m) REVERT: N 139 LYS cc_start: 0.6608 (pptt) cc_final: 0.6177 (pptt) REVERT: N 154 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7579 (mmm160) REVERT: O 32 ILE cc_start: 0.9278 (tt) cc_final: 0.9039 (tt) REVERT: O 73 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8750 (pt) REVERT: O 82 LYS cc_start: 0.8413 (tptp) cc_final: 0.8066 (mmmt) REVERT: O 142 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8963 (mt0) REVERT: P 23 SER cc_start: 0.9052 (p) cc_final: 0.8821 (t) REVERT: P 28 LYS cc_start: 0.7988 (tttt) cc_final: 0.7367 (mtmt) REVERT: P 61 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8858 (p) REVERT: P 219 ASN cc_start: 0.8387 (m-40) cc_final: 0.8006 (m110) REVERT: P 240 TYR cc_start: 0.8345 (m-80) cc_final: 0.7950 (m-80) REVERT: P 253 PHE cc_start: 0.8898 (t80) cc_final: 0.8625 (t80) REVERT: P 258 THR cc_start: 0.8850 (m) cc_final: 0.8441 (p) REVERT: Q 104 MET cc_start: 0.9184 (tmm) cc_final: 0.8831 (tmm) REVERT: Q 177 ASP cc_start: 0.8445 (m-30) cc_final: 0.8134 (p0) REVERT: R 30 GLN cc_start: 0.8719 (mt0) cc_final: 0.8416 (tt0) REVERT: R 50 ASP cc_start: 0.9081 (t0) cc_final: 0.8869 (t0) REVERT: R 57 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8750 (mm-30) REVERT: S 116 LEU cc_start: 0.7489 (tp) cc_final: 0.7149 (pp) REVERT: S 117 TYR cc_start: 0.6026 (t80) cc_final: 0.5782 (p90) REVERT: S 132 LEU cc_start: 0.8881 (tp) cc_final: 0.8483 (tp) REVERT: T 86 ARG cc_start: 0.7993 (ptt180) cc_final: 0.7602 (ptp-170) REVERT: T 98 ASP cc_start: 0.8943 (m-30) cc_final: 0.8461 (m-30) REVERT: T 268 ASP cc_start: 0.8904 (t0) cc_final: 0.8335 (t0) REVERT: U 109 GLU cc_start: 0.8619 (mp0) cc_final: 0.8093 (tp30) REVERT: U 122 ARG cc_start: 0.8887 (tpt170) cc_final: 0.7729 (mmt180) REVERT: U 126 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8748 (mm-30) REVERT: U 143 SER cc_start: 0.8397 (m) cc_final: 0.8144 (p) REVERT: V 116 ASP cc_start: 0.7441 (m-30) cc_final: 0.7147 (m-30) REVERT: W 67 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7743 (ppt170) REVERT: W 80 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8170 (t80) REVERT: W 98 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (p0) REVERT: W 108 ASP cc_start: 0.8807 (m-30) cc_final: 0.8583 (m-30) REVERT: W 137 ASN cc_start: 0.8776 (t0) cc_final: 0.8547 (t0) REVERT: X 37 GLU cc_start: 0.8856 (pm20) cc_final: 0.8449 (pt0) REVERT: X 40 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.9030 (t) REVERT: X 46 MET cc_start: 0.9082 (tpp) cc_final: 0.8842 (tpp) REVERT: X 81 ASP cc_start: 0.8793 (m-30) cc_final: 0.8564 (m-30) REVERT: X 84 ASN cc_start: 0.9310 (t0) cc_final: 0.8936 (t0) REVERT: X 140 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7029 (mmt180) REVERT: X 150 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6227 (mt) REVERT: Y 23 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6751 (mmm) REVERT: Y 25 ARG cc_start: 0.7826 (ttt180) cc_final: 0.6969 (tmt-80) REVERT: Y 104 TYR cc_start: 0.6031 (t80) cc_final: 0.5259 (t80) REVERT: Y 105 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5683 (ptt180) REVERT: Y 204 ILE cc_start: 0.8109 (mt) cc_final: 0.7768 (mt) outliers start: 206 outliers final: 112 residues processed: 977 average time/residue: 0.6933 time to fit residues: 1131.7537 Evaluate side-chains 869 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 740 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 88 CYS Chi-restraints excluded: chain 0 residue 94 GLU Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 90 ARG Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 116 SER Chi-restraints excluded: chain 1 residue 177 HIS Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 4 residue 56 LEU Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 141 MET Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 7 residue 74 ARG Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 150 CYS Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 183 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 115 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 275 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 128 CYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 168 THR Chi-restraints excluded: chain V residue 204 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 67 ARG Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 83 ASP Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 103 GLN Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 178 SER Chi-restraints excluded: chain Y residue 186 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 292 optimal weight: 0.0980 chunk 163 optimal weight: 10.0000 chunk 438 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 570 optimal weight: 20.0000 chunk 469 optimal weight: 4.9990 chunk 523 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 423 optimal weight: 5.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 83 ASN 5 140 GLN 7 80 GLN D 196 ASN D 236 GLN D 250 ASN E 88 HIS E 197 HIS E 233 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN N 80 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 HIS ** R 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS ** S 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN T 212 ASN V 86 GLN W 130 HIS X 103 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 73904 Z= 0.271 Angle : 0.696 9.568 107463 Z= 0.354 Chirality : 0.041 0.305 13077 Planarity : 0.006 0.098 7900 Dihedral : 24.054 179.852 28204 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 5.74 % Allowed : 16.88 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4303 helix: -0.18 (0.14), residues: 1220 sheet: -0.37 (0.18), residues: 658 loop : -0.44 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 283 HIS 0.009 0.001 HIS Q 149 PHE 0.021 0.002 PHE U 31 TYR 0.019 0.002 TYR Q 246 ARG 0.008 0.001 ARG P 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 755 time to evaluate : 4.054 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: 0 86 ASN cc_start: 0.9246 (p0) cc_final: 0.8934 (p0) REVERT: 0 88 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8340 (m) REVERT: 0 94 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: 0 127 TYR cc_start: 0.9208 (m-80) cc_final: 0.8963 (m-80) REVERT: 1 165 MET cc_start: 0.8350 (ptp) cc_final: 0.8138 (ptp) REVERT: 2 141 MET cc_start: 0.9132 (mtp) cc_final: 0.8816 (mtp) REVERT: 2 220 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7610 (mmt-90) REVERT: 3 56 TYR cc_start: 0.8905 (m-80) cc_final: 0.8661 (m-80) REVERT: 3 61 GLN cc_start: 0.8482 (tp40) cc_final: 0.8149 (tp40) REVERT: 4 60 GLN cc_start: 0.7769 (pt0) cc_final: 0.6309 (tp-100) REVERT: 5 143 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8634 (ttpp) REVERT: 5 144 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7671 (mt0) REVERT: 5 150 ARG cc_start: 0.7353 (mtp85) cc_final: 0.7086 (mtp85) REVERT: 7 64 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8284 (mttt) REVERT: 7 91 LYS cc_start: 0.9108 (tttt) cc_final: 0.8626 (ttpt) REVERT: 9 84 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8092 (mtt90) REVERT: D 126 LYS cc_start: 0.8497 (tttt) cc_final: 0.8089 (mptt) REVERT: D 236 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: E 150 LYS cc_start: 0.9069 (tttt) cc_final: 0.8744 (tttp) REVERT: F 76 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7462 (ptt180) REVERT: F 79 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8562 (tp) REVERT: F 199 ASP cc_start: 0.8330 (t0) cc_final: 0.8107 (t70) REVERT: F 238 LYS cc_start: 0.9087 (mttt) cc_final: 0.8178 (mmmt) REVERT: I 139 LEU cc_start: 0.7531 (tp) cc_final: 0.6943 (mp) REVERT: I 140 PHE cc_start: 0.6646 (m-10) cc_final: 0.6280 (m-10) REVERT: J 63 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7144 (tmm160) REVERT: J 91 ARG cc_start: 0.6114 (tmm-80) cc_final: 0.5868 (mtm110) REVERT: J 100 GLN cc_start: 0.5629 (tt0) cc_final: 0.5102 (tp-100) REVERT: N 154 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7047 (mmm160) REVERT: O 32 ILE cc_start: 0.9248 (tt) cc_final: 0.8994 (tt) REVERT: O 35 MET cc_start: 0.8869 (mmm) cc_final: 0.8250 (mtt) REVERT: O 72 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7979 (ttp-110) REVERT: O 80 GLN cc_start: 0.8810 (pt0) cc_final: 0.8601 (pt0) REVERT: O 82 LYS cc_start: 0.8466 (tptp) cc_final: 0.8064 (mmmt) REVERT: P 28 LYS cc_start: 0.8092 (tttt) cc_final: 0.7387 (mtmt) REVERT: P 219 ASN cc_start: 0.8219 (m-40) cc_final: 0.7975 (m110) REVERT: P 240 TYR cc_start: 0.8407 (m-80) cc_final: 0.8057 (m-80) REVERT: P 258 THR cc_start: 0.8849 (m) cc_final: 0.8473 (p) REVERT: Q 104 MET cc_start: 0.9159 (tmm) cc_final: 0.8778 (tmm) REVERT: Q 167 CYS cc_start: 0.7923 (m) cc_final: 0.7081 (m) REVERT: Q 177 ASP cc_start: 0.8448 (m-30) cc_final: 0.8195 (p0) REVERT: R 30 GLN cc_start: 0.8716 (mt0) cc_final: 0.8283 (tt0) REVERT: R 57 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8583 (mm-30) REVERT: R 105 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8286 (p) REVERT: S 116 LEU cc_start: 0.7624 (tp) cc_final: 0.7329 (pp) REVERT: S 117 TYR cc_start: 0.6324 (t80) cc_final: 0.6031 (p90) REVERT: S 132 LEU cc_start: 0.8884 (tp) cc_final: 0.8597 (tp) REVERT: S 141 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7729 (mt) REVERT: T 86 ARG cc_start: 0.8102 (ptt180) cc_final: 0.7725 (ptp-170) REVERT: T 98 ASP cc_start: 0.8938 (m-30) cc_final: 0.8478 (m-30) REVERT: T 239 ASN cc_start: 0.8318 (t0) cc_final: 0.8044 (t0) REVERT: T 252 GLU cc_start: 0.8459 (mp0) cc_final: 0.8137 (mm-30) REVERT: U 122 ARG cc_start: 0.8917 (tpt170) cc_final: 0.7681 (mmt180) REVERT: V 116 ASP cc_start: 0.7581 (m-30) cc_final: 0.7214 (m-30) REVERT: W 67 ARG cc_start: 0.8118 (ptt180) cc_final: 0.7679 (ppt170) REVERT: W 80 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8799 (t80) REVERT: W 137 ASN cc_start: 0.8873 (t0) cc_final: 0.8546 (t0) REVERT: W 189 THR cc_start: 0.8589 (m) cc_final: 0.8340 (p) REVERT: X 81 ASP cc_start: 0.8829 (m-30) cc_final: 0.8539 (m-30) REVERT: X 84 ASN cc_start: 0.9358 (t0) cc_final: 0.9000 (t0) REVERT: X 140 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7022 (mmt180) REVERT: X 150 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6313 (mt) REVERT: Y 25 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7209 (tmt-80) REVERT: Y 98 VAL cc_start: 0.7296 (t) cc_final: 0.6972 (m) REVERT: Y 105 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5817 (ptt180) outliers start: 219 outliers final: 142 residues processed: 896 average time/residue: 0.7015 time to fit residues: 1052.5316 Evaluate side-chains 845 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 691 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 88 CYS Chi-restraints excluded: chain 0 residue 94 GLU Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 102 GLU Chi-restraints excluded: chain 0 residue 120 LEU Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 129 THR Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 116 SER Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 4 residue 48 THR Chi-restraints excluded: chain 4 residue 56 LEU Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 141 MET Chi-restraints excluded: chain 5 residue 154 THR Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 5 residue 164 THR Chi-restraints excluded: chain 5 residue 175 ILE Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 7 residue 74 ARG Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 188 CYS Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 130 CYS Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 157 SER Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 115 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain T residue 175 GLN Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 128 CYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 168 THR Chi-restraints excluded: chain V residue 204 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 83 ASP Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 178 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 207 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 521 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 273 optimal weight: 0.0970 chunk 58 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 chunk 354 optimal weight: 9.9990 chunk 529 optimal weight: 0.9990 chunk 560 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 501 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 ASN 2 149 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 ASN D 206 GLN D 236 GLN D 250 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS F 83 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN J 101 HIS K 116 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 HIS ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS ** S 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN T 212 ASN V 86 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 73904 Z= 0.274 Angle : 0.672 9.873 107463 Z= 0.340 Chirality : 0.040 0.278 13077 Planarity : 0.005 0.093 7900 Dihedral : 23.817 179.989 28183 Min Nonbonded Distance : 0.965 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 5.50 % Allowed : 18.09 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 4303 helix: 0.17 (0.15), residues: 1207 sheet: -0.29 (0.19), residues: 661 loop : -0.33 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 69 HIS 0.006 0.001 HIS N 80 PHE 0.021 0.002 PHE U 31 TYR 0.018 0.002 TYR Y 216 ARG 0.018 0.001 ARG T 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 743 time to evaluate : 4.002 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: 0 94 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: 0 127 TYR cc_start: 0.9208 (m-80) cc_final: 0.8984 (m-80) REVERT: 1 165 MET cc_start: 0.8320 (ptp) cc_final: 0.7972 (ptp) REVERT: 2 75 ASN cc_start: 0.7522 (t0) cc_final: 0.7296 (t0) REVERT: 2 159 GLN cc_start: 0.8099 (tp40) cc_final: 0.7546 (mp10) REVERT: 2 220 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7584 (mmt180) REVERT: 3 56 TYR cc_start: 0.8968 (m-80) cc_final: 0.8703 (m-80) REVERT: 4 60 GLN cc_start: 0.7708 (pt0) cc_final: 0.6278 (tp-100) REVERT: 4 71 GLU cc_start: 0.5126 (tp30) cc_final: 0.4917 (mm-30) REVERT: 5 143 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8679 (ttpp) REVERT: 5 144 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7856 (mt0) REVERT: 7 64 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8385 (mttt) REVERT: 7 91 LYS cc_start: 0.9052 (tttt) cc_final: 0.8532 (ttpt) REVERT: 8 157 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9097 (tp) REVERT: 9 84 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8442 (mtp85) REVERT: D 126 LYS cc_start: 0.8542 (tttt) cc_final: 0.8126 (mptt) REVERT: D 173 MET cc_start: 0.7493 (mmt) cc_final: 0.7135 (pmm) REVERT: D 207 TYR cc_start: 0.9000 (m-80) cc_final: 0.8583 (m-80) REVERT: D 237 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8757 (m) REVERT: E 257 MET cc_start: 0.9116 (mtp) cc_final: 0.8732 (mtp) REVERT: F 76 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7324 (ptt180) REVERT: F 79 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8518 (tp) REVERT: F 238 LYS cc_start: 0.9090 (mttt) cc_final: 0.8168 (mmmt) REVERT: F 284 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (p90) REVERT: I 139 LEU cc_start: 0.7457 (tp) cc_final: 0.6886 (mp) REVERT: I 140 PHE cc_start: 0.6242 (m-10) cc_final: 0.5901 (m-10) REVERT: J 63 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7093 (tmm160) REVERT: J 91 ARG cc_start: 0.6146 (tmm-80) cc_final: 0.5777 (mtm110) REVERT: J 100 GLN cc_start: 0.5861 (tt0) cc_final: 0.5307 (tp-100) REVERT: J 123 MET cc_start: 0.4298 (ppp) cc_final: 0.3872 (ppp) REVERT: J 130 VAL cc_start: 0.6968 (m) cc_final: 0.6597 (t) REVERT: J 150 HIS cc_start: 0.2749 (OUTLIER) cc_final: 0.2487 (m90) REVERT: N 67 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8852 (m-10) REVERT: N 154 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7217 (mmm160) REVERT: N 157 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8012 (mt-10) REVERT: O 35 MET cc_start: 0.8866 (mmm) cc_final: 0.8284 (mtt) REVERT: O 72 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8067 (ttp-110) REVERT: O 80 GLN cc_start: 0.8817 (pt0) cc_final: 0.8559 (pt0) REVERT: O 82 LYS cc_start: 0.8555 (tptp) cc_final: 0.8103 (mmmt) REVERT: P 28 LYS cc_start: 0.8044 (tttt) cc_final: 0.7278 (mtmt) REVERT: P 186 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.8873 (mp) REVERT: P 219 ASN cc_start: 0.8216 (m-40) cc_final: 0.8016 (m110) REVERT: P 258 THR cc_start: 0.8792 (m) cc_final: 0.8465 (p) REVERT: P 265 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9034 (mt) REVERT: Q 104 MET cc_start: 0.9164 (tmm) cc_final: 0.8815 (tmm) REVERT: Q 118 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8398 (mpp) REVERT: R 30 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: R 57 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8541 (mm-30) REVERT: R 105 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8322 (p) REVERT: S 116 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7380 (pp) REVERT: S 132 LEU cc_start: 0.8849 (tp) cc_final: 0.8558 (tp) REVERT: S 141 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7750 (mt) REVERT: T 86 ARG cc_start: 0.8207 (ptt180) cc_final: 0.7851 (ptp-170) REVERT: T 98 ASP cc_start: 0.8977 (m-30) cc_final: 0.8524 (m-30) REVERT: T 115 SER cc_start: 0.9361 (OUTLIER) cc_final: 0.8969 (m) REVERT: T 239 ASN cc_start: 0.8411 (t0) cc_final: 0.8185 (t0) REVERT: T 252 GLU cc_start: 0.8394 (mp0) cc_final: 0.8063 (mm-30) REVERT: T 268 ASP cc_start: 0.8976 (t0) cc_final: 0.8480 (t0) REVERT: U 108 TYR cc_start: 0.8941 (m-80) cc_final: 0.8722 (m-80) REVERT: U 109 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: U 122 ARG cc_start: 0.8921 (tpt170) cc_final: 0.7706 (mmt180) REVERT: U 126 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8726 (mm-30) REVERT: V 77 THR cc_start: 0.8527 (m) cc_final: 0.8303 (p) REVERT: V 89 GLU cc_start: 0.8146 (mp0) cc_final: 0.7901 (mp0) REVERT: W 50 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8643 (mt-10) REVERT: W 67 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7633 (ppt170) REVERT: W 80 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8784 (t80) REVERT: W 189 THR cc_start: 0.8653 (m) cc_final: 0.8371 (p) REVERT: X 84 ASN cc_start: 0.9451 (t0) cc_final: 0.9137 (t0) REVERT: X 91 ASP cc_start: 0.8673 (m-30) cc_final: 0.8465 (m-30) REVERT: X 140 ARG cc_start: 0.7681 (mtt180) cc_final: 0.6624 (tpt170) REVERT: Y 25 ARG cc_start: 0.8101 (ttt180) cc_final: 0.7230 (tmt-80) REVERT: Y 98 VAL cc_start: 0.7324 (t) cc_final: 0.6981 (m) REVERT: Y 105 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6084 (ptt-90) REVERT: Y 204 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 210 outliers final: 147 residues processed: 871 average time/residue: 0.6824 time to fit residues: 1004.1874 Evaluate side-chains 864 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 694 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 GLU Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 102 GLU Chi-restraints excluded: chain 0 residue 120 LEU Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 129 THR Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 1 residue 231 VAL Chi-restraints excluded: chain 2 residue 88 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 164 LYS Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 213 MET Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 43 ASP Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 118 ARG Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 48 THR Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 154 THR Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 5 residue 164 THR Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 74 ARG Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 157 LEU Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 160 SER Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 188 CYS Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 265 ILE Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 43 GLU Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 130 CYS Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 115 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 175 GLN Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 282 ILE Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain V residue 128 CYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 168 THR Chi-restraints excluded: chain V residue 204 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 67 ARG Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 202 MET Chi-restraints excluded: chain Y residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 466 optimal weight: 0.0970 chunk 318 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 417 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 478 optimal weight: 7.9990 chunk 387 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 286 optimal weight: 8.9990 chunk 503 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 149 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 178 GLN 9 92 ASN D 253 HIS D 254 ASN E 88 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 HIS S 96 HIS ** S 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN T 212 ASN T 219 GLN U 77 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN W 60 GLN W 137 ASN X 73 GLN X 103 GLN Y 84 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 73904 Z= 0.374 Angle : 0.734 10.085 107463 Z= 0.370 Chirality : 0.043 0.290 13077 Planarity : 0.006 0.091 7900 Dihedral : 23.718 179.072 28177 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 5.98 % Allowed : 18.95 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 4303 helix: 0.12 (0.15), residues: 1203 sheet: -0.44 (0.19), residues: 672 loop : -0.39 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 283 HIS 0.009 0.001 HIS F 153 PHE 0.027 0.002 PHE U 31 TYR 0.026 0.002 TYR Y 216 ARG 0.007 0.001 ARG 5 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 714 time to evaluate : 4.029 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: 1 139 CYS cc_start: 0.8307 (m) cc_final: 0.7846 (p) REVERT: 1 148 THR cc_start: 0.9371 (m) cc_final: 0.8940 (p) REVERT: 1 165 MET cc_start: 0.8345 (ptp) cc_final: 0.7932 (ptp) REVERT: 1 221 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8233 (mttt) REVERT: 2 159 GLN cc_start: 0.8157 (tp40) cc_final: 0.7528 (mp10) REVERT: 2 164 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8637 (mtmm) REVERT: 2 220 ARG cc_start: 0.8527 (mtt180) cc_final: 0.7681 (mmt180) REVERT: 3 43 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7488 (t70) REVERT: 3 47 GLN cc_start: 0.8479 (mp10) cc_final: 0.8155 (mm-40) REVERT: 3 56 TYR cc_start: 0.8880 (m-80) cc_final: 0.8572 (m-80) REVERT: 3 61 GLN cc_start: 0.8672 (tp40) cc_final: 0.8337 (tp40) REVERT: 4 60 GLN cc_start: 0.7721 (pt0) cc_final: 0.6043 (tp-100) REVERT: 4 66 HIS cc_start: 0.7004 (m90) cc_final: 0.6782 (m-70) REVERT: 5 143 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8541 (ttpp) REVERT: 5 144 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7485 (mt0) REVERT: 6 21 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6042 (mtt) REVERT: 7 64 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8439 (mttt) REVERT: 7 91 LYS cc_start: 0.9065 (tttt) cc_final: 0.8545 (ttpt) REVERT: 9 84 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8497 (mtp85) REVERT: D 90 GLN cc_start: 0.9117 (mt0) cc_final: 0.8910 (mt0) REVERT: D 126 LYS cc_start: 0.8582 (tttt) cc_final: 0.8151 (mptt) REVERT: D 207 TYR cc_start: 0.9058 (m-80) cc_final: 0.8671 (m-80) REVERT: E 257 MET cc_start: 0.9280 (mtp) cc_final: 0.8910 (mtp) REVERT: F 76 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7364 (ptt180) REVERT: F 226 MET cc_start: 0.8469 (mtt) cc_final: 0.8197 (mtt) REVERT: F 238 LYS cc_start: 0.9092 (mttt) cc_final: 0.8120 (mmmt) REVERT: F 284 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8481 (p90) REVERT: I 139 LEU cc_start: 0.7697 (tp) cc_final: 0.6974 (mp) REVERT: I 140 PHE cc_start: 0.6660 (m-10) cc_final: 0.6413 (m-10) REVERT: J 35 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8257 (ptt180) REVERT: J 91 ARG cc_start: 0.6207 (tmm-80) cc_final: 0.5885 (mtm110) REVERT: J 100 GLN cc_start: 0.6277 (tt0) cc_final: 0.5541 (tp-100) REVERT: J 112 LEU cc_start: 0.7840 (mp) cc_final: 0.7596 (mp) REVERT: J 150 HIS cc_start: 0.3159 (OUTLIER) cc_final: 0.2860 (m90) REVERT: J 153 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7425 (tp) REVERT: N 67 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8950 (m-10) REVERT: N 154 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7173 (mmm160) REVERT: N 162 GLU cc_start: 0.8509 (tp30) cc_final: 0.8306 (tp30) REVERT: O 35 MET cc_start: 0.8906 (mmm) cc_final: 0.8437 (mtt) REVERT: O 72 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8144 (ttp-110) REVERT: O 104 ASN cc_start: 0.8828 (m-40) cc_final: 0.8508 (m-40) REVERT: O 111 ASN cc_start: 0.8455 (p0) cc_final: 0.8122 (p0) REVERT: P 28 LYS cc_start: 0.8217 (tttt) cc_final: 0.7281 (mtmt) REVERT: P 106 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: P 143 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: P 186 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.8825 (mp) REVERT: P 240 TYR cc_start: 0.8284 (m-80) cc_final: 0.7981 (m-80) REVERT: P 258 THR cc_start: 0.8827 (m) cc_final: 0.8551 (p) REVERT: Q 87 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: Q 104 MET cc_start: 0.9137 (tmm) cc_final: 0.8818 (tmm) REVERT: Q 118 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8518 (mpp) REVERT: R 30 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: R 57 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8595 (mm-30) REVERT: R 105 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8439 (p) REVERT: R 155 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7078 (mt0) REVERT: S 116 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7419 (pp) REVERT: S 132 LEU cc_start: 0.8895 (tp) cc_final: 0.8641 (tp) REVERT: S 141 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7820 (mt) REVERT: S 163 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8067 (t-90) REVERT: T 86 ARG cc_start: 0.8285 (ptt180) cc_final: 0.7827 (ptp-170) REVERT: T 98 ASP cc_start: 0.8974 (m-30) cc_final: 0.8712 (m-30) REVERT: T 115 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.9012 (m) REVERT: T 239 ASN cc_start: 0.8466 (t0) cc_final: 0.8176 (t0) REVERT: T 252 GLU cc_start: 0.8348 (mp0) cc_final: 0.8084 (mm-30) REVERT: T 268 ASP cc_start: 0.8876 (t0) cc_final: 0.8589 (t0) REVERT: U 122 ARG cc_start: 0.8951 (tpt170) cc_final: 0.7741 (mmt180) REVERT: V 150 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8448 (mtpt) REVERT: W 67 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7607 (ppt170) REVERT: W 80 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8756 (t80) REVERT: W 98 ASP cc_start: 0.8688 (p0) cc_final: 0.8457 (p0) REVERT: X 84 ASN cc_start: 0.9422 (t0) cc_final: 0.8979 (t0) REVERT: X 140 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7127 (mmt180) REVERT: Y 25 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7107 (tmt-80) REVERT: Y 98 VAL cc_start: 0.7399 (t) cc_final: 0.6961 (m) REVERT: Y 105 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.5942 (ptt-90) outliers start: 228 outliers final: 152 residues processed: 867 average time/residue: 0.6898 time to fit residues: 1004.4898 Evaluate side-chains 852 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 674 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 129 THR Chi-restraints excluded: chain 1 residue 46 HIS Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 164 LYS Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 213 MET Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 43 ASP Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 118 ARG Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 48 THR Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 141 MET Chi-restraints excluded: chain 5 residue 154 THR Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 7 residue 74 ARG Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain 9 residue 87 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain P residue 160 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 87 PHE Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 155 GLN Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 157 SER Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 115 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 175 GLN Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 282 ILE Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 111 LYS Chi-restraints excluded: chain V residue 132 ILE Chi-restraints excluded: chain V residue 150 LYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 204 ILE Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 67 ARG Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 83 ASP Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 108 MET Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 127 ASP Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 199 MET Chi-restraints excluded: chain Y residue 207 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 188 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 561 optimal weight: 1.9990 chunk 465 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 294 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 76 HIS 2 149 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 101 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 GLN P 219 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 115 HIS S 162 GLN T 212 ASN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 73904 Z= 0.222 Angle : 0.639 10.098 107463 Z= 0.322 Chirality : 0.038 0.274 13077 Planarity : 0.005 0.082 7900 Dihedral : 23.589 179.465 28169 Min Nonbonded Distance : 1.104 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 4.67 % Allowed : 20.66 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4303 helix: 0.34 (0.15), residues: 1204 sheet: -0.38 (0.19), residues: 649 loop : -0.26 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 86 HIS 0.005 0.001 HIS 1 89 PHE 0.017 0.001 PHE Q 175 TYR 0.022 0.001 TYR Y 216 ARG 0.009 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 728 time to evaluate : 4.020 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: 1 139 CYS cc_start: 0.8200 (m) cc_final: 0.7634 (p) REVERT: 1 148 THR cc_start: 0.9356 (m) cc_final: 0.8992 (p) REVERT: 1 165 MET cc_start: 0.8337 (ptp) cc_final: 0.8125 (ptp) REVERT: 1 221 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8161 (mttt) REVERT: 2 159 GLN cc_start: 0.8033 (tp40) cc_final: 0.7579 (mp10) REVERT: 2 220 ARG cc_start: 0.8479 (mtt180) cc_final: 0.7682 (mmt-90) REVERT: 3 43 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7638 (t70) REVERT: 3 56 TYR cc_start: 0.8901 (m-80) cc_final: 0.8608 (m-80) REVERT: 4 60 GLN cc_start: 0.7844 (pt0) cc_final: 0.6120 (tp-100) REVERT: 5 105 ASN cc_start: 0.8240 (p0) cc_final: 0.7955 (p0) REVERT: 5 143 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8540 (ttpp) REVERT: 5 144 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7485 (mt0) REVERT: 6 21 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6229 (mpp) REVERT: 7 64 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8395 (mttt) REVERT: 7 91 LYS cc_start: 0.9041 (tttt) cc_final: 0.8551 (ttpt) REVERT: 9 84 ARG cc_start: 0.8677 (mtp85) cc_final: 0.8426 (mtp85) REVERT: D 126 LYS cc_start: 0.8524 (tttt) cc_final: 0.8104 (mptt) REVERT: D 207 TYR cc_start: 0.9030 (m-80) cc_final: 0.8681 (m-80) REVERT: E 257 MET cc_start: 0.9193 (mtp) cc_final: 0.8805 (mtp) REVERT: F 76 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7299 (ptt180) REVERT: F 238 LYS cc_start: 0.8948 (mttt) cc_final: 0.8093 (mmmt) REVERT: F 284 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8383 (p90) REVERT: I 131 TYR cc_start: 0.8251 (m-80) cc_final: 0.8009 (m-10) REVERT: I 139 LEU cc_start: 0.7821 (tp) cc_final: 0.7140 (mp) REVERT: I 140 PHE cc_start: 0.6861 (m-10) cc_final: 0.6645 (m-10) REVERT: J 63 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7038 (tmm160) REVERT: J 74 GLU cc_start: 0.6226 (mp0) cc_final: 0.4865 (tp30) REVERT: J 91 ARG cc_start: 0.6257 (tmm-80) cc_final: 0.6035 (mtm110) REVERT: J 100 GLN cc_start: 0.6173 (tt0) cc_final: 0.5503 (tp-100) REVERT: J 107 GLU cc_start: 0.6954 (mp0) cc_final: 0.6371 (pp20) REVERT: J 123 MET cc_start: 0.4270 (ppp) cc_final: 0.3806 (ppp) REVERT: J 150 HIS cc_start: 0.3169 (OUTLIER) cc_final: 0.2826 (m90) REVERT: N 49 GLN cc_start: 0.8265 (mt0) cc_final: 0.8002 (mt0) REVERT: N 67 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8896 (m-10) REVERT: N 139 LYS cc_start: 0.5799 (pptt) cc_final: 0.5146 (pptt) REVERT: N 154 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7114 (mmm160) REVERT: N 157 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7939 (mt-10) REVERT: O 35 MET cc_start: 0.8877 (mmm) cc_final: 0.8380 (mtt) REVERT: O 37 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7072 (mtt90) REVERT: O 48 THR cc_start: 0.8115 (m) cc_final: 0.7338 (t) REVERT: O 72 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8124 (ttp-110) REVERT: O 104 ASN cc_start: 0.8806 (m-40) cc_final: 0.8513 (m-40) REVERT: O 111 ASN cc_start: 0.8461 (p0) cc_final: 0.8257 (p0) REVERT: P 28 LYS cc_start: 0.8177 (tttt) cc_final: 0.7281 (mtmt) REVERT: P 186 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.8781 (mp) REVERT: Q 104 MET cc_start: 0.9080 (tmm) cc_final: 0.8734 (tmm) REVERT: Q 118 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8570 (mpp) REVERT: R 30 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: R 57 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8520 (mm-30) REVERT: R 105 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8282 (p) REVERT: S 116 LEU cc_start: 0.7722 (tp) cc_final: 0.7397 (pp) REVERT: S 141 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7705 (mt) REVERT: S 163 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.8152 (t-90) REVERT: T 86 ARG cc_start: 0.8286 (ptt180) cc_final: 0.7898 (ptp-170) REVERT: T 98 ASP cc_start: 0.8979 (m-30) cc_final: 0.8716 (m-30) REVERT: T 239 ASN cc_start: 0.8443 (t0) cc_final: 0.8217 (t0) REVERT: T 255 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: T 268 ASP cc_start: 0.8863 (t0) cc_final: 0.8541 (t0) REVERT: U 122 ARG cc_start: 0.8911 (tpt170) cc_final: 0.7664 (mmt180) REVERT: U 126 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8568 (mm-30) REVERT: V 150 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8467 (mtpt) REVERT: W 80 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8743 (t80) REVERT: W 98 ASP cc_start: 0.8655 (p0) cc_final: 0.8370 (p0) REVERT: W 189 THR cc_start: 0.8611 (m) cc_final: 0.8406 (p) REVERT: X 84 ASN cc_start: 0.9401 (t0) cc_final: 0.8959 (t0) REVERT: X 140 ARG cc_start: 0.8073 (mtt180) cc_final: 0.6813 (tpt170) REVERT: X 150 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6238 (mt) REVERT: Y 25 ARG cc_start: 0.8058 (ttt180) cc_final: 0.6936 (tmt-80) REVERT: Y 98 VAL cc_start: 0.7245 (t) cc_final: 0.7023 (m) REVERT: Y 105 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5876 (ptt-90) REVERT: Y 131 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6886 (p) REVERT: Y 161 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.4616 (ptt180) REVERT: Y 204 ILE cc_start: 0.8388 (tp) cc_final: 0.8045 (tp) REVERT: Y 216 TYR cc_start: 0.5402 (m-10) cc_final: 0.5200 (m-10) outliers start: 178 outliers final: 124 residues processed: 840 average time/residue: 0.6904 time to fit residues: 976.3831 Evaluate side-chains 840 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 695 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 112 GLU Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 131 VAL Chi-restraints excluded: chain 1 residue 46 HIS Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 2 residue 88 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 43 ASP Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 104 LYS Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 160 SER Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 157 SER Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 282 ILE Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 150 LYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 204 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 60 ASP Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 161 ARG Chi-restraints excluded: chain Y residue 169 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 541 optimal weight: 10.0000 chunk 63 optimal weight: 0.0870 chunk 319 optimal weight: 0.0000 chunk 409 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 472 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 559 optimal weight: 6.9990 chunk 349 optimal weight: 30.0000 chunk 340 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 overall best weight: 3.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 13 GLN 2 112 ASN 2 149 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN T 212 ASN T 213 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN W 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 73904 Z= 0.232 Angle : 0.632 9.816 107463 Z= 0.318 Chirality : 0.038 0.273 13077 Planarity : 0.005 0.102 7900 Dihedral : 23.442 179.957 28166 Min Nonbonded Distance : 1.095 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.37 % Rotamer: Outliers : 4.95 % Allowed : 20.73 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4303 helix: 0.41 (0.15), residues: 1193 sheet: -0.30 (0.19), residues: 659 loop : -0.22 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 69 HIS 0.005 0.001 HIS F 153 PHE 0.017 0.001 PHE U 31 TYR 0.020 0.001 TYR Y 216 ARG 0.009 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 726 time to evaluate : 3.984 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: 1 139 CYS cc_start: 0.8316 (m) cc_final: 0.7679 (p) REVERT: 1 148 THR cc_start: 0.9360 (m) cc_final: 0.9003 (p) REVERT: 1 165 MET cc_start: 0.8331 (ptp) cc_final: 0.8124 (ptp) REVERT: 2 159 GLN cc_start: 0.8032 (tp40) cc_final: 0.7659 (mp10) REVERT: 2 220 ARG cc_start: 0.8514 (mtt180) cc_final: 0.7595 (mmt180) REVERT: 3 43 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7651 (t70) REVERT: 3 56 TYR cc_start: 0.8924 (m-80) cc_final: 0.8617 (m-80) REVERT: 5 91 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8872 (mtt90) REVERT: 5 105 ASN cc_start: 0.8186 (p0) cc_final: 0.7887 (p0) REVERT: 5 132 LYS cc_start: 0.7734 (ptpt) cc_final: 0.7483 (pttt) REVERT: 5 143 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8586 (ttpp) REVERT: 5 144 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8307 (tt0) REVERT: 6 58 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5995 (tt0) REVERT: 7 64 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8380 (mttt) REVERT: 7 74 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7895 (mmp-170) REVERT: 7 91 LYS cc_start: 0.9089 (tttt) cc_final: 0.8626 (ttpt) REVERT: D 126 LYS cc_start: 0.8508 (tttt) cc_final: 0.8113 (mptt) REVERT: D 207 TYR cc_start: 0.9042 (m-80) cc_final: 0.8687 (m-80) REVERT: D 209 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8804 (mtm-85) REVERT: E 257 MET cc_start: 0.9149 (mtp) cc_final: 0.8717 (mtp) REVERT: F 76 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7248 (ptt180) REVERT: F 202 TYR cc_start: 0.8909 (t80) cc_final: 0.8614 (t80) REVERT: F 238 LYS cc_start: 0.8935 (mttt) cc_final: 0.8083 (mmmt) REVERT: F 284 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8409 (p90) REVERT: I 100 GLN cc_start: 0.5141 (mp-120) cc_final: 0.4612 (mp-120) REVERT: I 139 LEU cc_start: 0.7655 (tp) cc_final: 0.6998 (mp) REVERT: I 143 GLU cc_start: 0.6974 (tt0) cc_final: 0.6143 (tm-30) REVERT: J 63 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7029 (tmm160) REVERT: J 74 GLU cc_start: 0.6228 (mp0) cc_final: 0.4867 (tp30) REVERT: J 100 GLN cc_start: 0.6046 (tt0) cc_final: 0.5419 (tp-100) REVERT: J 150 HIS cc_start: 0.3215 (OUTLIER) cc_final: 0.2922 (m90) REVERT: J 153 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7414 (tp) REVERT: J 169 LYS cc_start: 0.7406 (pttm) cc_final: 0.6933 (pttt) REVERT: N 67 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (m-10) REVERT: N 111 MET cc_start: 0.9431 (mmt) cc_final: 0.9040 (mmm) REVERT: N 139 LYS cc_start: 0.5838 (pptt) cc_final: 0.5182 (pptt) REVERT: N 154 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7096 (mmm160) REVERT: N 162 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: O 35 MET cc_start: 0.8885 (mmm) cc_final: 0.8370 (mtt) REVERT: O 37 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7059 (mtt90) REVERT: O 48 THR cc_start: 0.7986 (m) cc_final: 0.7165 (t) REVERT: O 72 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8160 (ttp-110) REVERT: O 104 ASN cc_start: 0.8834 (m-40) cc_final: 0.8521 (m-40) REVERT: P 28 LYS cc_start: 0.8120 (tttt) cc_final: 0.7284 (mtmt) REVERT: P 186 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.8750 (mp) REVERT: Q 104 MET cc_start: 0.9036 (tmm) cc_final: 0.8730 (tmm) REVERT: Q 118 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8576 (mpp) REVERT: Q 149 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7466 (t-170) REVERT: R 30 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: R 57 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8515 (mm-30) REVERT: R 105 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8190 (p) REVERT: R 115 GLU cc_start: 0.8462 (mp0) cc_final: 0.8074 (mt-10) REVERT: S 116 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7321 (pp) REVERT: S 141 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7701 (mt) REVERT: S 163 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8194 (t-90) REVERT: T 86 ARG cc_start: 0.8292 (ptt180) cc_final: 0.7915 (ptp-170) REVERT: T 98 ASP cc_start: 0.8973 (m-30) cc_final: 0.8713 (m-30) REVERT: T 224 MET cc_start: 0.8431 (mmp) cc_final: 0.8211 (mmt) REVERT: T 239 ASN cc_start: 0.8388 (t0) cc_final: 0.8151 (t0) REVERT: T 268 ASP cc_start: 0.8925 (t0) cc_final: 0.8657 (t0) REVERT: U 122 ARG cc_start: 0.8890 (tpt170) cc_final: 0.7629 (mmt180) REVERT: U 126 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8556 (mt-10) REVERT: V 150 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8318 (mtpt) REVERT: W 67 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7478 (ppt170) REVERT: W 80 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8806 (t80) REVERT: W 98 ASP cc_start: 0.8679 (p0) cc_final: 0.8407 (p0) REVERT: W 105 GLU cc_start: 0.8528 (tt0) cc_final: 0.8285 (tt0) REVERT: W 189 THR cc_start: 0.8600 (m) cc_final: 0.8380 (p) REVERT: X 84 ASN cc_start: 0.9387 (t0) cc_final: 0.8941 (t0) REVERT: X 140 ARG cc_start: 0.8099 (mtt180) cc_final: 0.6817 (tpt170) REVERT: X 150 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6332 (mt) REVERT: Y 25 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7087 (tmt-80) REVERT: Y 98 VAL cc_start: 0.7243 (t) cc_final: 0.6986 (m) REVERT: Y 105 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5633 (ptt-90) REVERT: Y 161 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.4530 (ptt180) REVERT: Y 204 ILE cc_start: 0.8300 (tp) cc_final: 0.7954 (tp) outliers start: 189 outliers final: 138 residues processed: 844 average time/residue: 0.7508 time to fit residues: 1077.0295 Evaluate side-chains 857 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 692 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 131 VAL Chi-restraints excluded: chain 1 residue 46 HIS Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 2 residue 88 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 213 MET Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 43 ASP Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 5 residue 91 ARG Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 154 THR Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain 9 residue 87 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 234 LEU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 197 LYS Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 157 SER Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 282 ILE Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 132 ILE Chi-restraints excluded: chain V residue 150 LYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 67 ARG Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 127 ASP Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 161 ARG Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 345 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 333 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 355 optimal weight: 40.0000 chunk 380 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 439 optimal weight: 9.9990 overall best weight: 6.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 97 ASN 2 112 ASN 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN J 101 HIS N 64 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN ** T 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 ASN ** U 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN X 62 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 73904 Z= 0.378 Angle : 0.728 9.691 107463 Z= 0.366 Chirality : 0.043 0.278 13077 Planarity : 0.006 0.108 7900 Dihedral : 23.447 179.709 28166 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 5.35 % Allowed : 20.50 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4303 helix: 0.20 (0.15), residues: 1189 sheet: -0.55 (0.20), residues: 658 loop : -0.39 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 7 69 HIS 0.009 0.001 HIS F 153 PHE 0.028 0.002 PHE U 31 TYR 0.044 0.002 TYR Y 216 ARG 0.012 0.001 ARG J 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 690 time to evaluate : 3.973 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: 1 139 CYS cc_start: 0.8642 (m) cc_final: 0.7530 (p) REVERT: 1 148 THR cc_start: 0.9241 (m) cc_final: 0.9018 (p) REVERT: 1 165 MET cc_start: 0.8418 (ptp) cc_final: 0.8169 (ptp) REVERT: 2 159 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: 2 220 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7562 (mmt180) REVERT: 3 56 TYR cc_start: 0.8942 (m-80) cc_final: 0.8615 (m-80) REVERT: 5 91 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8919 (mtt90) REVERT: 5 105 ASN cc_start: 0.8305 (p0) cc_final: 0.8031 (p0) REVERT: 5 143 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8617 (ttpp) REVERT: 5 144 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8300 (tt0) REVERT: 7 64 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8430 (mttt) REVERT: 7 91 LYS cc_start: 0.9094 (tttt) cc_final: 0.8640 (ttpt) REVERT: 9 84 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8277 (mtm-85) REVERT: D 90 GLN cc_start: 0.9100 (mt0) cc_final: 0.8880 (mt0) REVERT: D 126 LYS cc_start: 0.8572 (tttt) cc_final: 0.8115 (mptt) REVERT: D 207 TYR cc_start: 0.9064 (m-80) cc_final: 0.8716 (m-80) REVERT: D 209 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8688 (mtm-85) REVERT: E 96 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7070 (ttp-110) REVERT: E 257 MET cc_start: 0.9195 (mtp) cc_final: 0.8763 (mtp) REVERT: F 76 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7312 (ptt180) REVERT: F 202 TYR cc_start: 0.8928 (t80) cc_final: 0.8706 (t80) REVERT: F 238 LYS cc_start: 0.8863 (mttt) cc_final: 0.8097 (mmmt) REVERT: F 284 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8439 (p90) REVERT: I 139 LEU cc_start: 0.7744 (tp) cc_final: 0.7050 (mp) REVERT: J 63 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7042 (tmm160) REVERT: J 74 GLU cc_start: 0.6241 (mp0) cc_final: 0.4955 (tp30) REVERT: J 100 GLN cc_start: 0.5941 (tt0) cc_final: 0.5427 (tp40) REVERT: J 150 HIS cc_start: 0.3559 (OUTLIER) cc_final: 0.2680 (m90) REVERT: K 46 ILE cc_start: 0.0969 (OUTLIER) cc_final: 0.0624 (tp) REVERT: N 154 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7024 (mmm160) REVERT: O 35 MET cc_start: 0.8898 (mmm) cc_final: 0.8412 (mtt) REVERT: O 37 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7059 (mtt90) REVERT: O 48 THR cc_start: 0.7853 (m) cc_final: 0.7011 (t) REVERT: O 72 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8187 (ttp-110) REVERT: O 104 ASN cc_start: 0.8862 (m-40) cc_final: 0.8567 (m-40) REVERT: O 131 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: P 28 LYS cc_start: 0.8199 (tttt) cc_final: 0.7328 (mtmt) REVERT: P 186 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.8823 (mp) REVERT: P 240 TYR cc_start: 0.8246 (m-80) cc_final: 0.8001 (m-80) REVERT: Q 104 MET cc_start: 0.9015 (tmm) cc_final: 0.8679 (tmm) REVERT: Q 118 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8576 (mpp) REVERT: Q 149 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7835 (t-170) REVERT: R 30 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: R 57 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8584 (mm-30) REVERT: R 105 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8281 (p) REVERT: S 141 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7962 (mt) REVERT: S 163 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8149 (t-90) REVERT: T 86 ARG cc_start: 0.8320 (ptt180) cc_final: 0.7877 (ptp-170) REVERT: T 98 ASP cc_start: 0.8936 (m-30) cc_final: 0.8710 (m-30) REVERT: T 239 ASN cc_start: 0.8498 (t0) cc_final: 0.8230 (t0) REVERT: T 255 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8163 (mtm-85) REVERT: T 268 ASP cc_start: 0.8917 (t0) cc_final: 0.8619 (t0) REVERT: T 283 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (m100) REVERT: U 55 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8626 (mtm180) REVERT: U 122 ARG cc_start: 0.9015 (tpt170) cc_final: 0.7896 (mmt180) REVERT: U 126 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8436 (mt-10) REVERT: V 59 SER cc_start: 0.9065 (m) cc_final: 0.8837 (p) REVERT: V 150 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8441 (mtpt) REVERT: W 80 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8722 (t80) REVERT: W 98 ASP cc_start: 0.8783 (p0) cc_final: 0.8506 (p0) REVERT: X 84 ASN cc_start: 0.9436 (t0) cc_final: 0.9201 (t0) REVERT: X 140 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7132 (mmt180) REVERT: X 150 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6263 (mt) REVERT: Y 25 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7027 (tmt-80) REVERT: Y 98 VAL cc_start: 0.7288 (OUTLIER) cc_final: 0.6870 (m) REVERT: Y 105 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.5913 (ptt90) REVERT: Y 142 GLU cc_start: 0.6196 (pt0) cc_final: 0.5944 (mm-30) REVERT: Y 149 ARG cc_start: 0.6950 (ttp-110) cc_final: 0.6737 (ttp80) REVERT: Y 161 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.4547 (ptt180) REVERT: Y 204 ILE cc_start: 0.8313 (tp) cc_final: 0.7973 (tp) outliers start: 204 outliers final: 150 residues processed: 823 average time/residue: 0.6831 time to fit residues: 945.7410 Evaluate side-chains 845 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 668 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 129 THR Chi-restraints excluded: chain 0 residue 131 VAL Chi-restraints excluded: chain 1 residue 46 HIS Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 2 residue 88 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 159 GLN Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 213 MET Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 118 ARG Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 5 residue 91 ARG Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 154 THR Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain 9 residue 87 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 160 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 234 LEU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LYS Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 112 ILE Chi-restraints excluded: chain S residue 137 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 157 SER Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 282 ILE Chi-restraints excluded: chain T residue 283 TRP Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 132 ILE Chi-restraints excluded: chain V residue 150 LYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 127 ASP Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 161 ARG Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 199 MET Chi-restraints excluded: chain Y residue 207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 508 optimal weight: 7.9990 chunk 535 optimal weight: 4.9990 chunk 488 optimal weight: 6.9990 chunk 520 optimal weight: 7.9990 chunk 313 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 409 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 470 optimal weight: 5.9990 chunk 492 optimal weight: 7.9990 chunk 519 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: ** 1 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 112 ASN 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 187 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN T 212 ASN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN W 60 GLN X 62 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 73904 Z= 0.304 Angle : 0.673 10.327 107463 Z= 0.338 Chirality : 0.040 0.275 13077 Planarity : 0.005 0.109 7900 Dihedral : 23.368 179.670 28166 Min Nonbonded Distance : 1.078 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 4.74 % Allowed : 21.36 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4303 helix: 0.24 (0.15), residues: 1197 sheet: -0.46 (0.20), residues: 632 loop : -0.37 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 7 69 HIS 0.007 0.001 HIS F 153 PHE 0.021 0.002 PHE U 31 TYR 0.043 0.002 TYR Y 216 ARG 0.015 0.001 ARG E 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 679 time to evaluate : 4.070 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: 1 139 CYS cc_start: 0.7725 (m) cc_final: 0.7348 (p) REVERT: 1 148 THR cc_start: 0.9361 (m) cc_final: 0.9127 (p) REVERT: 1 165 MET cc_start: 0.8390 (ptp) cc_final: 0.8120 (ptp) REVERT: 2 159 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: 2 195 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7904 (tttp) REVERT: 2 220 ARG cc_start: 0.8510 (mtt180) cc_final: 0.7588 (mmt180) REVERT: 3 56 TYR cc_start: 0.8935 (m-80) cc_final: 0.8616 (m-80) REVERT: 5 91 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8886 (mtt90) REVERT: 5 105 ASN cc_start: 0.8282 (p0) cc_final: 0.7984 (p0) REVERT: 5 143 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8592 (ttpp) REVERT: 5 144 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8331 (tt0) REVERT: 6 21 MET cc_start: 0.6662 (mpp) cc_final: 0.5781 (mtt) REVERT: 7 64 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8409 (mttt) REVERT: 7 91 LYS cc_start: 0.9074 (tttt) cc_final: 0.8615 (ttpt) REVERT: 9 84 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8308 (mtm-85) REVERT: D 126 LYS cc_start: 0.8545 (tttt) cc_final: 0.8104 (mptt) REVERT: D 207 TYR cc_start: 0.9058 (m-80) cc_final: 0.8737 (m-80) REVERT: D 209 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8670 (mtm-85) REVERT: E 141 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7872 (mtp-110) REVERT: E 257 MET cc_start: 0.9136 (mtp) cc_final: 0.8694 (mtp) REVERT: F 76 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7300 (ptt180) REVERT: F 238 LYS cc_start: 0.8850 (mttt) cc_final: 0.8089 (mmmt) REVERT: F 284 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8412 (p90) REVERT: I 72 ARG cc_start: 0.8364 (ttt90) cc_final: 0.7999 (ttt90) REVERT: I 100 GLN cc_start: 0.5502 (mp-120) cc_final: 0.4980 (mp-120) REVERT: I 131 TYR cc_start: 0.7670 (m-10) cc_final: 0.7279 (m-10) REVERT: I 139 LEU cc_start: 0.7765 (tp) cc_final: 0.7100 (mp) REVERT: J 63 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7038 (tmm160) REVERT: J 74 GLU cc_start: 0.6227 (mp0) cc_final: 0.4996 (tp30) REVERT: J 100 GLN cc_start: 0.5739 (tt0) cc_final: 0.5262 (tp40) REVERT: J 150 HIS cc_start: 0.3278 (OUTLIER) cc_final: 0.2379 (m90) REVERT: J 158 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6806 (mm-30) REVERT: K 46 ILE cc_start: 0.0968 (OUTLIER) cc_final: 0.0632 (tp) REVERT: N 111 MET cc_start: 0.9403 (mmt) cc_final: 0.9024 (mmm) REVERT: N 154 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7349 (mmm160) REVERT: O 35 MET cc_start: 0.8898 (mmm) cc_final: 0.8410 (mtt) REVERT: O 37 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.7066 (mtt90) REVERT: O 48 THR cc_start: 0.7857 (m) cc_final: 0.7049 (t) REVERT: O 72 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8080 (ttp-110) REVERT: O 104 ASN cc_start: 0.8840 (m-40) cc_final: 0.8549 (m-40) REVERT: P 28 LYS cc_start: 0.8171 (tttt) cc_final: 0.7282 (mtmt) REVERT: P 186 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.8793 (mp) REVERT: Q 104 MET cc_start: 0.9029 (tmm) cc_final: 0.8714 (tmm) REVERT: Q 118 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8572 (mpp) REVERT: Q 149 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7654 (t-170) REVERT: R 30 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: R 57 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8541 (mm-30) REVERT: R 105 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8202 (p) REVERT: S 88 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6588 (m170) REVERT: S 141 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7916 (mt) REVERT: S 163 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8198 (t-90) REVERT: T 86 ARG cc_start: 0.8307 (ptt180) cc_final: 0.7868 (ptp-170) REVERT: T 98 ASP cc_start: 0.8927 (m-30) cc_final: 0.8702 (m-30) REVERT: T 239 ASN cc_start: 0.8511 (t0) cc_final: 0.8302 (t0) REVERT: T 255 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8185 (mtm-85) REVERT: T 268 ASP cc_start: 0.8911 (t0) cc_final: 0.8610 (t0) REVERT: U 122 ARG cc_start: 0.8977 (tpt170) cc_final: 0.7808 (mmt180) REVERT: U 126 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8485 (mm-30) REVERT: V 59 SER cc_start: 0.9060 (m) cc_final: 0.8803 (p) REVERT: V 135 GLU cc_start: 0.5006 (mp0) cc_final: 0.4615 (mp0) REVERT: V 150 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8423 (mtpt) REVERT: W 80 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8724 (t80) REVERT: W 98 ASP cc_start: 0.8751 (p0) cc_final: 0.8446 (p0) REVERT: X 84 ASN cc_start: 0.9372 (t0) cc_final: 0.9048 (t0) REVERT: X 140 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7137 (mmt180) REVERT: X 150 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6267 (mt) REVERT: Y 25 ARG cc_start: 0.8032 (ttt180) cc_final: 0.6915 (tmt-80) REVERT: Y 66 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6884 (mm-30) REVERT: Y 98 VAL cc_start: 0.7247 (OUTLIER) cc_final: 0.6877 (m) REVERT: Y 105 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.5919 (ptt180) REVERT: Y 142 GLU cc_start: 0.6290 (pt0) cc_final: 0.6025 (mm-30) REVERT: Y 161 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.4678 (ptt180) REVERT: Y 204 ILE cc_start: 0.8319 (tp) cc_final: 0.7996 (tp) outliers start: 181 outliers final: 145 residues processed: 801 average time/residue: 0.6819 time to fit residues: 918.9208 Evaluate side-chains 835 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 666 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 129 THR Chi-restraints excluded: chain 0 residue 131 VAL Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 2 residue 88 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 159 GLN Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 213 MET Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 5 residue 91 ARG Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 104 LYS Chi-restraints excluded: chain 5 residue 141 MET Chi-restraints excluded: chain 5 residue 154 THR Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 38 ARG Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain 9 residue 87 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 160 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 234 LEU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 197 LYS Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 112 ILE Chi-restraints excluded: chain S residue 121 ASN Chi-restraints excluded: chain S residue 137 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 157 SER Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 282 ILE Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 132 ILE Chi-restraints excluded: chain V residue 150 LYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 127 ASP Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 161 ARG Chi-restraints excluded: chain Y residue 163 ASP Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 199 MET Chi-restraints excluded: chain Y residue 207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 342 optimal weight: 6.9990 chunk 550 optimal weight: 0.5980 chunk 336 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 577 optimal weight: 0.9990 chunk 531 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 355 optimal weight: 40.0000 chunk 282 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN T 139 GLN ** T 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 ASN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN V 200 ASN W 60 GLN X 62 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 73904 Z= 0.243 Angle : 0.642 10.358 107463 Z= 0.322 Chirality : 0.038 0.266 13077 Planarity : 0.005 0.112 7900 Dihedral : 23.277 179.930 28162 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 4.40 % Allowed : 21.76 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4303 helix: 0.33 (0.15), residues: 1192 sheet: -0.43 (0.20), residues: 644 loop : -0.28 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 86 HIS 0.006 0.001 HIS F 153 PHE 0.018 0.002 PHE U 31 TYR 0.038 0.002 TYR Y 216 ARG 0.012 0.001 ARG E 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8606 Ramachandran restraints generated. 4303 Oldfield, 0 Emsley, 4303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 692 time to evaluate : 4.183 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: 1 139 CYS cc_start: 0.7653 (m) cc_final: 0.7383 (p) REVERT: 1 165 MET cc_start: 0.8343 (ptp) cc_final: 0.8072 (ptp) REVERT: 2 159 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: 2 195 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7876 (tttp) REVERT: 2 220 ARG cc_start: 0.8485 (mtt180) cc_final: 0.7566 (mmt180) REVERT: 3 56 TYR cc_start: 0.8930 (m-80) cc_final: 0.8617 (m-80) REVERT: 5 91 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8867 (mtt90) REVERT: 5 105 ASN cc_start: 0.8215 (p0) cc_final: 0.7902 (p0) REVERT: 5 143 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8597 (ttpp) REVERT: 5 144 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8324 (tt0) REVERT: 6 21 MET cc_start: 0.7122 (mpp) cc_final: 0.5892 (mtt) REVERT: 7 64 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8383 (mttt) REVERT: 7 91 LYS cc_start: 0.9054 (tttt) cc_final: 0.8596 (ttpt) REVERT: 9 84 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8299 (mtm-85) REVERT: D 126 LYS cc_start: 0.8486 (tttt) cc_final: 0.8105 (mptt) REVERT: D 207 TYR cc_start: 0.9043 (m-80) cc_final: 0.8734 (m-80) REVERT: D 209 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8732 (mtm-85) REVERT: E 141 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7876 (mtp-110) REVERT: E 257 MET cc_start: 0.9134 (mtp) cc_final: 0.8672 (mtp) REVERT: F 76 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7264 (ptt180) REVERT: F 238 LYS cc_start: 0.8815 (mttt) cc_final: 0.8058 (mmmt) REVERT: F 284 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8389 (p90) REVERT: I 72 ARG cc_start: 0.8131 (ttt90) cc_final: 0.7819 (ttt90) REVERT: I 100 GLN cc_start: 0.5521 (mp-120) cc_final: 0.4998 (mp-120) REVERT: I 139 LEU cc_start: 0.7492 (tp) cc_final: 0.6899 (mp) REVERT: J 63 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7055 (tmm160) REVERT: J 74 GLU cc_start: 0.6588 (mp0) cc_final: 0.5597 (tp30) REVERT: J 100 GLN cc_start: 0.5763 (tt0) cc_final: 0.5326 (tp40) REVERT: J 150 HIS cc_start: 0.3266 (OUTLIER) cc_final: 0.2318 (m-70) REVERT: J 158 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6728 (mm-30) REVERT: K 46 ILE cc_start: 0.0975 (OUTLIER) cc_final: 0.0654 (tp) REVERT: N 111 MET cc_start: 0.9400 (mmt) cc_final: 0.9026 (mmm) REVERT: N 154 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7295 (mmm160) REVERT: O 35 MET cc_start: 0.8892 (mmm) cc_final: 0.8352 (mtt) REVERT: O 37 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7042 (mtt90) REVERT: O 48 THR cc_start: 0.7882 (m) cc_final: 0.7085 (t) REVERT: O 72 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8143 (ttp-110) REVERT: O 104 ASN cc_start: 0.8817 (m-40) cc_final: 0.8524 (m-40) REVERT: P 28 LYS cc_start: 0.8152 (tttt) cc_final: 0.7183 (mttt) REVERT: P 186 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.8753 (mp) REVERT: Q 104 MET cc_start: 0.9015 (tmm) cc_final: 0.8695 (tmm) REVERT: Q 118 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8400 (mpp) REVERT: Q 149 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7588 (t-170) REVERT: R 30 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: R 57 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8791 (mm-30) REVERT: R 105 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8823 (t) REVERT: S 88 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6837 (m170) REVERT: S 141 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7766 (mt) REVERT: S 163 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.8200 (t-90) REVERT: T 86 ARG cc_start: 0.8261 (ptt180) cc_final: 0.7833 (ptp-170) REVERT: T 98 ASP cc_start: 0.8923 (m-30) cc_final: 0.8708 (m-30) REVERT: T 224 MET cc_start: 0.8343 (mmp) cc_final: 0.8081 (mmm) REVERT: T 239 ASN cc_start: 0.8481 (t0) cc_final: 0.8269 (t0) REVERT: T 268 ASP cc_start: 0.8863 (t0) cc_final: 0.8567 (t0) REVERT: U 122 ARG cc_start: 0.8945 (tpt170) cc_final: 0.7676 (mmt180) REVERT: U 126 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8476 (mm-30) REVERT: V 59 SER cc_start: 0.9095 (m) cc_final: 0.8791 (p) REVERT: V 71 PRO cc_start: 0.8814 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: V 135 GLU cc_start: 0.4955 (mp0) cc_final: 0.4526 (mp0) REVERT: V 150 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: W 80 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8767 (t80) REVERT: W 98 ASP cc_start: 0.8715 (p0) cc_final: 0.8421 (p0) REVERT: X 84 ASN cc_start: 0.9342 (t0) cc_final: 0.9014 (t0) REVERT: X 140 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7133 (mmt180) REVERT: X 150 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6808 (tp) REVERT: Y 25 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7041 (tmt-80) REVERT: Y 66 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6964 (mm-30) REVERT: Y 98 VAL cc_start: 0.7233 (t) cc_final: 0.6966 (m) REVERT: Y 105 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.5914 (ptt180) REVERT: Y 142 GLU cc_start: 0.6312 (pt0) cc_final: 0.5809 (tm-30) REVERT: Y 161 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.4581 (ptt180) REVERT: Y 204 ILE cc_start: 0.8279 (tp) cc_final: 0.7955 (tp) outliers start: 168 outliers final: 137 residues processed: 803 average time/residue: 0.6948 time to fit residues: 936.4100 Evaluate side-chains 831 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 671 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 97 VAL Chi-restraints excluded: chain 0 residue 112 GLU Chi-restraints excluded: chain 0 residue 125 VAL Chi-restraints excluded: chain 0 residue 131 VAL Chi-restraints excluded: chain 1 residue 46 HIS Chi-restraints excluded: chain 1 residue 69 VAL Chi-restraints excluded: chain 1 residue 92 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 VAL Chi-restraints excluded: chain 1 residue 124 THR Chi-restraints excluded: chain 1 residue 169 LEU Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 196 ILE Chi-restraints excluded: chain 1 residue 207 THR Chi-restraints excluded: chain 1 residue 209 ASP Chi-restraints excluded: chain 2 residue 88 THR Chi-restraints excluded: chain 2 residue 94 ASN Chi-restraints excluded: chain 2 residue 145 ASP Chi-restraints excluded: chain 2 residue 159 GLN Chi-restraints excluded: chain 2 residue 188 ILE Chi-restraints excluded: chain 2 residue 211 VAL Chi-restraints excluded: chain 2 residue 213 MET Chi-restraints excluded: chain 2 residue 228 LEU Chi-restraints excluded: chain 3 residue 75 THR Chi-restraints excluded: chain 3 residue 86 ILE Chi-restraints excluded: chain 3 residue 133 ASP Chi-restraints excluded: chain 3 residue 142 ASN Chi-restraints excluded: chain 3 residue 148 ARG Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 5 residue 91 ARG Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 141 MET Chi-restraints excluded: chain 5 residue 158 VAL Chi-restraints excluded: chain 6 residue 54 VAL Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 137 THR Chi-restraints excluded: chain 8 residue 162 THR Chi-restraints excluded: chain 8 residue 163 THR Chi-restraints excluded: chain 8 residue 184 THR Chi-restraints excluded: chain 9 residue 87 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 311 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 284 TYR Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 150 HIS Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 91 MET Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain P residue 160 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 234 LEU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 284 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 197 LYS Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 30 GLN Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 121 ASN Chi-restraints excluded: chain S residue 137 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 163 HIS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain T residue 139 GLN Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 247 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 36 ASN Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 132 ILE Chi-restraints excluded: chain V residue 150 LYS Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 80 TYR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 117 HIS Chi-restraints excluded: chain Y residue 127 ASP Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 161 ARG Chi-restraints excluded: chain Y residue 163 ASP Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 365 optimal weight: 20.0000 chunk 490 optimal weight: 0.3980 chunk 140 optimal weight: 10.0000 chunk 424 optimal weight: 0.0870 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 473 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 overall best weight: 3.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN T 212 ASN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN W 60 GLN X 62 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091252 restraints weight = 126661.799| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.19 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 73904 Z= 0.253 Angle : 0.682 59.200 107463 Z= 0.355 Chirality : 0.038 0.550 13077 Planarity : 0.005 0.112 7900 Dihedral : 23.277 179.936 28162 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 4.40 % Allowed : 21.86 % Favored : 73.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4303 helix: 0.34 (0.15), residues: 1192 sheet: -0.43 (0.20), residues: 644 loop : -0.28 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 86 HIS 0.005 0.001 HIS F 153 PHE 0.024 0.001 PHE X 24 TYR 0.031 0.001 TYR Y 216 ARG 0.012 0.000 ARG T 255 =============================================================================== Job complete usr+sys time: 16832.43 seconds wall clock time: 296 minutes 26.71 seconds (17786.71 seconds total)