Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 14:29:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_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_2787/07_2023/4v19_2787_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v19_2787/07_2023/4v19_2787_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 Unresolved non-hydrogen dihedrals: 61 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: 25.40, per 1000 atoms: 0.37 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: 26.80 Conformation dependent library (CDL) restraints added in 4.1 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: 21.76 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: 54.91 Time building geometry restraints manager: 29.07 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 1.493 1.328 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" C5 Y5P B 13 " pdb=" C6 Y5P B 13 " ideal model delta sigma weight residual 1.493 1.328 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C5 Y5P B 8 " pdb=" C6 Y5P B 8 " ideal model delta sigma weight residual 1.493 1.332 0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C5 Y5P B 26 " pdb=" C6 Y5P B 26 " ideal model delta sigma weight residual 1.493 1.333 0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" C5 Y5P B 3 " pdb=" C6 Y5P B 3 " ideal model delta sigma weight residual 1.493 1.335 0.158 2.00e-02 2.50e+03 6.27e+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=" C1' P5P B 29 " pdb=" N9 P5P B 29 " pdb=" C8 P5P B 29 " ideal model delta sigma weight residual 103.63 129.74 -26.11 3.00e+00 1.11e-01 7.57e+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 45 " pdb=" N9 P5P B 45 " pdb=" C8 P5P B 45 " ideal model delta sigma weight residual 103.63 129.28 -25.65 3.00e+00 1.11e-01 7.31e+01 ... (remaining 107458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 38359 35.99 - 71.99: 2594 71.99 - 107.98: 212 107.98 - 143.98: 34 143.98 - 179.97: 44 Dihedral angle restraints: 41243 sinusoidal: 28642 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 41240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 10796 0.065 - 0.131: 1815 0.131 - 0.196: 184 0.196 - 0.262: 20 0.262 - 0.327: 14 Chirality restraints: 12829 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 12826 not shown) Planarity restraints: 7962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' P5P B 23 " 0.077 2.00e-02 2.50e+03 6.16e-01 8.54e+03 pdb=" C4' P5P B 23 " 0.442 2.00e-02 2.50e+03 pdb=" O4' P5P B 23 " 0.656 2.00e-02 2.50e+03 pdb=" C3' P5P B 23 " -0.598 2.00e-02 2.50e+03 pdb=" O3' P5P B 23 " -0.661 2.00e-02 2.50e+03 pdb=" C2' P5P B 23 " -0.168 2.00e-02 2.50e+03 pdb=" O2' P5P B 23 " 0.995 2.00e-02 2.50e+03 pdb=" C1' P5P B 23 " 0.217 2.00e-02 2.50e+03 pdb=" N9 P5P B 23 " -0.960 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' P5P B 50 " -0.064 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' P5P B 50 " -0.445 2.00e-02 2.50e+03 pdb=" O4' P5P B 50 " -0.671 2.00e-02 2.50e+03 pdb=" C3' P5P B 50 " 0.593 2.00e-02 2.50e+03 pdb=" O3' P5P B 50 " 0.652 2.00e-02 2.50e+03 pdb=" C2' P5P B 50 " 0.174 2.00e-02 2.50e+03 pdb=" O2' P5P B 50 " -0.990 2.00e-02 2.50e+03 pdb=" C1' P5P B 50 " -0.211 2.00e-02 2.50e+03 pdb=" N9 P5P B 50 " 0.963 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' P5P B 67 " -0.062 2.00e-02 2.50e+03 6.15e-01 8.51e+03 pdb=" C4' P5P B 67 " -0.470 2.00e-02 2.50e+03 pdb=" O4' P5P B 67 " -0.736 2.00e-02 2.50e+03 pdb=" C3' P5P B 67 " 0.582 2.00e-02 2.50e+03 pdb=" O3' P5P B 67 " 0.622 2.00e-02 2.50e+03 pdb=" C2' P5P B 67 " 0.209 2.00e-02 2.50e+03 pdb=" O2' P5P B 67 " -0.932 2.00e-02 2.50e+03 pdb=" C1' P5P B 67 " -0.194 2.00e-02 2.50e+03 pdb=" N9 P5P B 67 " 0.981 2.00e-02 2.50e+03 ... (remaining 7959 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 7.530 Check model and map are aligned: 0.790 Set scattering table: 0.480 Process input model: 190.760 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.260 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.740 ------------------------------------------------------------------------------- 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 0.165 73904 Z= 0.563 Angle : 1.324 26.110 107463 Z= 0.745 Chirality : 0.049 0.327 12829 Planarity : 0.051 0.616 7962 Dihedral : 20.284 179.972 33111 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 % 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 *********************** 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 : 4.112 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 outliers start: 266 outliers final: 60 residues processed: 1486 average time/residue: 0.7836 time to fit residues: 1850.0316 Evaluate side-chains 825 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 765 time to evaluate : 4.113 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.5086 time to fit residues: 63.0944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 243 optimal weight: 9.9990 chunk 150 optimal weight: 40.0000 chunk 296 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 454 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 276 optimal weight: 0.7980 chunk 338 optimal weight: 20.0000 chunk 526 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** 0 86 ASN 1 27 HIS 1 42 HIS 1 111 GLN 2 101 HIS 2 112 ASN 2 149 GLN 2 197 ASN 3 67 HIS 4 47 GLN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 65 HIS 8 118 HIS D 183 HIS D 250 ASN D 272 ASN E 88 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 J 41 HIS J 100 GLN J 150 HIS K 103 HIS K 126 GLN N 49 GLN O 33 GLN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN P 71 GLN P 84 ASN P 87 HIS P 91 HIS P 123 ASN P 130 GLN P 219 ASN P 264 GLN Q 98 HIS Q 149 HIS Q 209 ASN Q 210 GLN R 39 HIS R 112 ASN R 129 ASN ** 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 86 GLN V 104 HIS ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 122 ASN V 175 ASN ** V 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 GLN W 171 HIS ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 103 GLN Y 117 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 73904 Z= 0.276 Angle : 1.128 17.436 107463 Z= 0.662 Chirality : 0.042 0.285 12829 Planarity : 0.012 0.130 7962 Dihedral : 20.937 179.924 23844 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % Favored : 97.26 % Rotamer Outliers : 4.19 % 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: -1.24 (0.11), residues: 4303 helix: -1.10 (0.13), residues: 1240 sheet: -0.51 (0.18), residues: 652 loop : -0.67 (0.12), residues: 2411 *********************** 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 979 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 819 time to evaluate : 4.202 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 outliers start: 160 outliers final: 85 residues processed: 915 average time/residue: 0.7101 time to fit residues: 1085.5197 Evaluate side-chains 794 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 709 time to evaluate : 4.151 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.5262 time to fit residues: 88.8917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 292 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 527 optimal weight: 8.9990 chunk 570 optimal weight: 9.9990 chunk 469 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 423 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** 0 86 ASN 2 75 ASN ** 5 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 23 GLN 7 80 GLN D 196 ASN D 206 GLN D 250 ASN E 88 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN J 100 GLN J 101 HIS N 80 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 96 HIS ** S 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN T 212 ASN V 86 GLN ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 HIS ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 135 HIS Y 84 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.102 73904 Z= 0.435 Angle : 1.103 14.978 107463 Z= 0.649 Chirality : 0.046 0.364 12829 Planarity : 0.012 0.132 7962 Dihedral : 20.406 179.990 23844 Min Nonbonded Distance : 1.086 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.32 % Favored : 96.56 % Rotamer Outliers : 3.22 % 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: -0.91 (0.12), residues: 4303 helix: -0.52 (0.14), residues: 1228 sheet: -0.50 (0.19), residues: 638 loop : -0.58 (0.12), residues: 2437 *********************** 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 837 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 714 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 74 residues processed: 796 average time/residue: 0.7300 time to fit residues: 975.5935 Evaluate side-chains 734 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 660 time to evaluate : 4.180 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.5337 time to fit residues: 79.7490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 521 optimal weight: 1.9990 chunk 396 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 354 optimal weight: 7.9990 chunk 529 optimal weight: 3.9990 chunk 560 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 501 optimal weight: 10.0000 chunk 151 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 76 HIS 2 75 ASN 2 149 GLN 5 83 ASN ** 6 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 80 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 ASN D 90 GLN E 88 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN F 83 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 GLN J 101 HIS J 150 HIS ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 HIS ** 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 175 GLN T 212 ASN U 98 ASN V 86 GLN V 109 GLN ** V 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 103 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 73904 Z= 0.293 Angle : 1.029 14.368 107463 Z= 0.620 Chirality : 0.041 0.398 12829 Planarity : 0.011 0.128 7962 Dihedral : 20.100 179.956 23844 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Rotamer Outliers : 2.46 % 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: -0.59 (0.12), residues: 4303 helix: -0.05 (0.15), residues: 1212 sheet: -0.49 (0.19), residues: 651 loop : -0.45 (0.12), residues: 2440 *********************** 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 835 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 741 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 52 residues processed: 796 average time/residue: 0.7341 time to fit residues: 972.4979 Evaluate side-chains 730 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 678 time to evaluate : 4.405 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5644 time to fit residues: 58.4737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 466 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 417 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 478 optimal weight: 8.9990 chunk 387 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 503 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 overall best weight: 7.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 86 ASN ** 1 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 ASN ** 2 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 149 GLN 6 23 GLN ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 178 GLN 9 92 ASN D 253 HIS E 88 HIS E 128 HIS E 197 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 HIS N 64 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** 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 60 GLN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.112 73904 Z= 0.441 Angle : 1.092 14.100 107463 Z= 0.645 Chirality : 0.046 0.282 12829 Planarity : 0.012 0.133 7962 Dihedral : 19.923 179.072 23844 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer Outliers : 3.17 % 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: -0.67 (0.12), residues: 4303 helix: -0.07 (0.15), residues: 1201 sheet: -0.64 (0.19), residues: 669 loop : -0.49 (0.12), residues: 2433 *********************** 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 826 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 705 time to evaluate : 4.157 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 outliers start: 121 outliers final: 69 residues processed: 772 average time/residue: 0.7296 time to fit residues: 943.2555 Evaluate side-chains 718 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 649 time to evaluate : 4.107 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.5398 time to fit residues: 74.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 110 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 561 optimal weight: 20.0000 chunk 465 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 86 ASN 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 ASN D 90 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** 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** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 HIS K 116 HIS ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 GLN R 155 GLN ** 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 V 183 ASN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 103 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 73904 Z= 0.187 Angle : 0.987 13.828 107463 Z= 0.602 Chirality : 0.037 0.261 12829 Planarity : 0.011 0.128 7962 Dihedral : 19.617 179.848 23844 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer Outliers : 1.23 % 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: -0.30 (0.12), residues: 4303 helix: 0.29 (0.15), residues: 1203 sheet: -0.51 (0.19), residues: 684 loop : -0.26 (0.12), residues: 2416 *********************** 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 771 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 724 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 20 residues processed: 746 average time/residue: 0.7313 time to fit residues: 906.3907 Evaluate side-chains 685 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 665 time to evaluate : 4.076 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5312 time to fit residues: 24.8860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 541 optimal weight: 6.9990 chunk 63 optimal weight: 0.0370 chunk 319 optimal weight: 0.0980 chunk 409 optimal weight: 9.9990 chunk 317 optimal weight: 0.9990 chunk 472 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 559 optimal weight: 7.9990 chunk 349 optimal weight: 30.0000 chunk 340 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 overall best weight: 2.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 112 ASN 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 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** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS K 84 GLN K 103 HIS N 49 GLN O 89 HIS ** R 147 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 77 GLN U 94 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN V 122 ASN V 183 ASN W 60 GLN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 73904 Z= 0.190 Angle : 0.975 13.541 107463 Z= 0.595 Chirality : 0.037 0.252 12829 Planarity : 0.011 0.129 7962 Dihedral : 19.326 179.953 23844 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer Outliers : 1.31 % 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: -0.05 (0.13), residues: 4303 helix: 0.51 (0.15), residues: 1193 sheet: -0.33 (0.19), residues: 671 loop : -0.13 (0.12), residues: 2439 *********************** 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 762 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 712 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 737 average time/residue: 0.7251 time to fit residues: 893.0646 Evaluate side-chains 692 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 668 time to evaluate : 4.112 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.6400 time to fit residues: 32.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 345 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 333 optimal weight: 0.3980 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: 0.9990 chunk 276 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 439 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 112 ASN 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** F 63 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS K 103 HIS ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN T 212 ASN U 77 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 ASN X 103 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 73904 Z= 0.226 Angle : 0.981 13.271 107463 Z= 0.598 Chirality : 0.037 0.255 12829 Planarity : 0.011 0.130 7962 Dihedral : 19.235 179.964 23844 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer Outliers : 1.23 % 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: -0.09 (0.13), residues: 4303 helix: 0.52 (0.15), residues: 1195 sheet: -0.47 (0.19), residues: 696 loop : -0.12 (0.13), residues: 2412 *********************** 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 723 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 676 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 23 residues processed: 697 average time/residue: 0.7094 time to fit residues: 826.5596 Evaluate side-chains 679 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 656 time to evaluate : 4.085 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5187 time to fit residues: 27.6679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 508 optimal weight: 10.0000 chunk 535 optimal weight: 7.9990 chunk 488 optimal weight: 5.9990 chunk 520 optimal weight: 0.9990 chunk 313 optimal weight: 0.0070 chunk 226 optimal weight: 10.0000 chunk 409 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 492 optimal weight: 0.4980 chunk 519 optimal weight: 7.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 112 ASN 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 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** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS O 111 ASN ** 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 ** T 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 ASN U 77 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN V 200 ASN W 60 GLN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 73904 Z= 0.166 Angle : 0.964 13.209 107463 Z= 0.591 Chirality : 0.035 0.245 12829 Planarity : 0.011 0.129 7962 Dihedral : 19.139 179.991 23844 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.56 % Rotamer Outliers : 0.31 % 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: 0.04 (0.13), residues: 4303 helix: 0.60 (0.15), residues: 1195 sheet: -0.24 (0.20), residues: 668 loop : -0.08 (0.12), residues: 2440 *********************** 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 700 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 688 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 695 average time/residue: 0.7426 time to fit residues: 869.9730 Evaluate side-chains 671 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 664 time to evaluate : 4.508 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5058 time to fit residues: 11.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 342 optimal weight: 0.0070 chunk 550 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 577 optimal weight: 9.9990 chunk 531 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 355 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 overall best weight: 2.7404 ------------------------------------------------------------------------------- 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** 2 149 GLN 5 83 ASN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 154 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** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 HIS S 96 HIS S 162 GLN ** T 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 ASN U 77 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN W 60 GLN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 ASN X 103 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 73904 Z= 0.205 Angle : 0.971 13.053 107463 Z= 0.594 Chirality : 0.036 0.248 12829 Planarity : 0.011 0.130 7962 Dihedral : 19.063 179.957 23844 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer Outliers : 0.45 % 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: 0.03 (0.13), residues: 4303 helix: 0.60 (0.15), residues: 1193 sheet: -0.32 (0.19), residues: 680 loop : -0.07 (0.13), residues: 2430 ********************** 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 688 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 671 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 678 average time/residue: 0.7287 time to fit residues: 828.3463 Evaluate side-chains 666 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 655 time to evaluate : 4.295 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6929 time to fit residues: 18.3702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 365 optimal weight: 6.9990 chunk 490 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 460 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 473 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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** 2 149 GLN ** 5 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 31 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** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 HIS J 119 HIS N 160 GLN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 HIS S 162 GLN ** T 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 ASN U 77 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN W 60 GLN ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 ASN X 98 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.095492 restraints weight = 126253.461| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.37 r_work: 0.2917 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 73904 Z= 0.209 Angle : 0.972 13.071 107463 Z= 0.594 Chirality : 0.036 0.248 12829 Planarity : 0.011 0.129 7962 Dihedral : 19.010 179.910 23844 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer Outliers : 0.52 % 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: 0.02 (0.13), residues: 4303 helix: 0.57 (0.15), residues: 1193 sheet: -0.33 (0.19), residues: 685 loop : -0.06 (0.13), residues: 2425 =============================================================================== Job complete usr+sys time: 15385.20 seconds wall clock time: 271 minutes 53.29 seconds (16313.29 seconds total)