Starting phenix.real_space_refine (version: dev) on Sat May 14 09:46:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/05_2022/6ylx_10841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/05_2022/6ylx_10841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/05_2022/6ylx_10841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/05_2022/6ylx_10841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/05_2022/6ylx_10841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/05_2022/6ylx_10841.pdb" } resolution = 3.9 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= -0.000 sd= 0.013 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 118882 Number of models: 1 Model: "" Number of chains: 47 Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 371, 'PCIS': 2} Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 343, 'PCIS': 1} Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 147, 'PCIS': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1515 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'CIS': 1, 'TRANS': 181} Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'CIS': 2, 'TRANS': 184} Chain: "K" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'CIS': 1, 'TRANS': 244} Chain breaks: 1 Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1499 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "N" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1543 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 188, 'PCIS': 1} Chain: "P" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1397 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain breaks: 1 Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 162} Chain: "T" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 50, 'PCIS': 1} Chain: "U" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 844 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1885 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'CIS': 1, 'TRANS': 222} Chain: "X" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1100 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 127} Chain: "a" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "b" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3814 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'CIS': 1, 'TRANS': 445} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 102, 'PCIS': 1} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 101, 'PCIS': 1} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 84, 'PCIS': 1} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "n" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3030 Classifications: {'peptide': 371} Link IDs: {'CIS': 3, 'PTRANS': 19, 'TRANS': 346, 'PCIS': 2} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'CIS': 2, 'TRANS': 127} Chain: "q" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 723 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Chain: "r" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1760 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 2 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "t" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2306 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'CIS': 1, 'TRANS': 275, 'PCIS': 1} Chain breaks: 1 Chain: "u" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1040 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "y" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1849 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'CIS': 1, 'TRANS': 234} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "1" Number of atoms: 54232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2534, 54232 Classifications: {'RNA': 2534} Modifications used: {'rna3p_pyr': 932, 'rna2p_pur': 274, 'rna3p_pur': 1140, 'rna2p_pyr': 188} Link IDs: {'rna3p': 2071, 'rna2p': 462} Chain breaks: 10 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna3p_pyr': 63, 'rna2p_pur': 15, 'rna3p_pur': 63, 'rna2p_pyr': 17} Link IDs: {'rna3p': 126, 'rna2p': 31} Chain: "6" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1370 Classifications: {'RNA': 65} Modifications used: {'rna3p_pyr': 19, 'rna2p_pur': 8, 'rna3p_pur': 21, 'rna2p_pyr': 17} Link IDs: {'rna3p': 40, 'rna2p': 24} Chain breaks: 1 Chain: "w" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2898 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 15, 'TRANS': 344} Chain breaks: 4 Residues with excluded nonbonded symmetry interactions: 199 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 187 not shown) Time building chain proxies: 48.39, per 1000 atoms: 0.41 Number of scatterers: 118882 At special positions: 0 Unit cell: (215.716, 196.204, 321.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 P 2757 15.00 O 29860 8.00 N 21739 7.00 C 64385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.08 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.04 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.06 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.00 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 9 " distance=2.06 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.02 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 36 " distance=1.96 Simple disulfide: pdb=" SG CYS u 32 " - pdb=" SG CYS u 36 " distance=2.08 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: 44.76 Conformation dependent library (CDL) restraints added in 7.8 seconds 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14156 Finding SS restraints... Secondary structure from input PDB file: 266 helices and 74 sheets defined 42.4% alpha, 12.7% beta 790 base pairs and 1268 stacking pairs defined. Time for finding SS restraints: 33.16 Creating SS restraints... Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.539A pdb=" N GLY B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.661A pdb=" N LEU B 351 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 44 removed outlier: 4.215A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.793A pdb=" N ILE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.681A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 299 Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.035A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 4.022A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 27 through 72 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.903A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 83 through 95 removed outlier: 3.778A pdb=" N ALA G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 removed outlier: 4.253A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 223 Processing helix chain 'G' and resid 226 through 230 removed outlier: 3.752A pdb=" N VAL G 229 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 226 through 230' Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.875A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 50 removed outlier: 3.795A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 106 through 115 Processing helix chain 'K' and resid 130 through 134 removed outlier: 3.914A pdb=" N LYS K 133 " --> pdb=" O SER K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 148 removed outlier: 4.241A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER K 146 " --> pdb=" O ASP K 142 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU K 147 " --> pdb=" O GLN K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 176 removed outlier: 4.303A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 193 removed outlier: 3.968A pdb=" N THR K 188 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU K 190 " --> pdb=" O VAL K 187 " (cutoff:3.500A) Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.857A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 224 Processing helix chain 'K' and resid 224 through 232 Processing helix chain 'K' and resid 255 through 271 removed outlier: 3.658A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 299 No H-bonds generated for 'chain 'K' and resid 297 through 299' Processing helix chain 'K' and resid 300 through 305 removed outlier: 3.806A pdb=" N LYS K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 4.316A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 166 through 193 removed outlier: 5.174A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.913A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.824A pdb=" N HIS N 156 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 186 through 195 Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 75 through 88 Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 186 removed outlier: 3.555A pdb=" N VAL O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 removed outlier: 4.944A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.891A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 76 removed outlier: 4.102A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 169 through 183 Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.538A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 22 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 98 through 115 Processing helix chain 'S' and resid 140 through 145 removed outlier: 4.222A pdb=" N THR S 145 " --> pdb=" O GLN S 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 122 Processing helix chain 'U' and resid 19 through 25 Processing helix chain 'U' and resid 29 through 41 removed outlier: 4.034A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 removed outlier: 3.909A pdb=" N ALA V 130 " --> pdb=" O TRP V 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.870A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.753A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.150A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 17 Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.645A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 132 through 140 Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 4.372A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 105 through 123 removed outlier: 3.832A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 113 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 83 through 92 removed outlier: 4.185A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 108 Processing helix chain 'a' and resid 131 through 141 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 66 Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 117 Processing helix chain 'b' and resid 121 through 142 Processing helix chain 'b' and resid 143 through 159 removed outlier: 4.067A pdb=" N LEU b 147 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA b 148 " --> pdb=" O ARG b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 Processing helix chain 'b' and resid 263 through 274 Processing helix chain 'b' and resid 294 through 298 removed outlier: 3.576A pdb=" N ASP b 297 " --> pdb=" O ARG b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 311 Processing helix chain 'b' and resid 325 through 348 Processing helix chain 'b' and resid 353 through 362 removed outlier: 4.439A pdb=" N LEU b 358 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASN b 359 " --> pdb=" O ASN b 355 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 385 Processing helix chain 'b' and resid 399 through 407 removed outlier: 4.429A pdb=" N GLY b 407 " --> pdb=" O GLU b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 425 through 429 removed outlier: 3.835A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 444 removed outlier: 3.711A pdb=" N ASP b 443 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 3.832A pdb=" N GLU b 466 " --> pdb=" O LYS b 462 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 20 removed outlier: 3.709A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 61 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.213A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'g' and resid 58 through 62 Processing helix chain 'g' and resid 67 through 71 Processing helix chain 'g' and resid 82 through 113 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 35 Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.783A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 90 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 77 removed outlier: 7.600A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 100 Processing helix chain 'j' and resid 4 through 10 Processing helix chain 'j' and resid 50 through 58 removed outlier: 4.021A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 76 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'l' and resid 6 through 20 Processing helix chain 'l' and resid 24 through 28 Processing helix chain 'n' and resid 5 through 9 removed outlier: 3.578A pdb=" N THR n 8 " --> pdb=" O LYS n 5 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG n 9 " --> pdb=" O LYS n 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 5 through 9' Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 removed outlier: 4.443A pdb=" N GLY n 40 " --> pdb=" O CYS n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 74 removed outlier: 4.358A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU n 74 " --> pdb=" O TYR n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 97 removed outlier: 4.184A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS n 79 " --> pdb=" O PRO n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 131 Processing helix chain 'n' and resid 132 through 145 removed outlier: 3.527A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 153 through 174 Processing helix chain 'n' and resid 215 through 241 Processing helix chain 'n' and resid 249 through 256 removed outlier: 3.801A pdb=" N ILE n 255 " --> pdb=" O LYS n 251 " (cutoff:3.500A) Processing helix chain 'n' and resid 376 through 383 Processing helix chain 'n' and resid 391 through 394 removed outlier: 3.516A pdb=" N ASP n 394 " --> pdb=" O ALA n 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 391 through 394' Processing helix chain 'n' and resid 429 through 439 Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 removed outlier: 4.616A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'q' and resid 230 through 266 removed outlier: 3.680A pdb=" N TRP q 234 " --> pdb=" O ASN q 230 " (cutoff:3.500A) Processing helix chain 'q' and resid 405 through 409 Processing helix chain 'q' and resid 414 through 427 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 20 through 41 removed outlier: 4.510A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 73 Processing helix chain 'r' and resid 187 through 190 removed outlier: 3.651A pdb=" N GLY r 190 " --> pdb=" O PRO r 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 187 through 190' Processing helix chain 'r' and resid 207 through 213 removed outlier: 3.855A pdb=" N GLN r 211 " --> pdb=" O PRO r 207 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 35 removed outlier: 4.148A pdb=" N LYS s 35 " --> pdb=" O LYS s 31 " (cutoff:3.500A) Processing helix chain 't' and resid 16 through 53 removed outlier: 4.305A pdb=" N LEU t 20 " --> pdb=" O PRO t 16 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER t 50 " --> pdb=" O LYS t 46 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS t 52 " --> pdb=" O LYS t 48 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN t 53 " --> pdb=" O ARG t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 167 removed outlier: 5.292A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 183 through 191 removed outlier: 3.598A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.561A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 241 through 243 No H-bonds generated for 'chain 't' and resid 241 through 243' Processing helix chain 't' and resid 247 through 256 Processing helix chain 't' and resid 261 through 268 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.666A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.680A pdb=" N ALA t 319 " --> pdb=" O ASP t 315 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 59 removed outlier: 4.032A pdb=" N ALA u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.850A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 113 removed outlier: 4.060A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 123 removed outlier: 4.294A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) Processing helix chain 'y' and resid 33 through 43 removed outlier: 3.920A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 46 No H-bonds generated for 'chain 'y' and resid 44 through 46' Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 removed outlier: 3.749A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'y' and resid 230 through 236 Processing helix chain 'y' and resid 237 through 244 removed outlier: 3.508A pdb=" N ILE y 241 " --> pdb=" O ARG y 237 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 20 Processing helix chain 'z' and resid 20 through 56 removed outlier: 4.046A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA z 25 " --> pdb=" O VAL z 21 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) Processing helix chain 'w' and resid 27 through 31 removed outlier: 3.673A pdb=" N SER w 30 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE w 31 " --> pdb=" O ARG w 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 27 through 31' Processing helix chain 'w' and resid 32 through 40 removed outlier: 3.792A pdb=" N ILE w 36 " --> pdb=" O LYS w 32 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU w 38 " --> pdb=" O ILE w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 58 through 68 removed outlier: 3.740A pdb=" N VAL w 63 " --> pdb=" O SER w 59 " (cutoff:3.500A) Processing helix chain 'w' and resid 97 through 108 removed outlier: 3.837A pdb=" N ARG w 101 " --> pdb=" O THR w 97 " (cutoff:3.500A) Processing helix chain 'w' and resid 129 through 150 Processing helix chain 'w' and resid 165 through 177 Processing helix chain 'w' and resid 209 through 213 removed outlier: 3.738A pdb=" N LEU w 213 " --> pdb=" O PRO w 210 " (cutoff:3.500A) Processing helix chain 'w' and resid 259 through 265 Processing helix chain 'w' and resid 284 through 291 Processing helix chain 'w' and resid 299 through 304 Processing helix chain 'w' and resid 311 through 329 Processing helix chain 'w' and resid 696 through 705 removed outlier: 4.351A pdb=" N ASP w 702 " --> pdb=" O TRP w 698 " (cutoff:3.500A) Processing helix chain 'w' and resid 714 through 726 Processing helix chain 'w' and resid 820 through 838 removed outlier: 3.818A pdb=" N LYS w 824 " --> pdb=" O ASP w 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.317A pdb=" N SER B 355 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 320 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 81 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 106 removed outlier: 6.305A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 88 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 162 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 179 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 removed outlier: 4.177A pdb=" N GLY B 225 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 270 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 268 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 8 removed outlier: 6.994A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.635A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 79 removed outlier: 7.332A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.689A pdb=" N VAL F 77 " --> pdb=" O ARG T 139 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG T 139 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.318A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.332A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.882A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 48 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.885A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AB7, first strand: chain 'K' and resid 243 through 249 removed outlier: 5.364A pdb=" N ASN K 245 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL K 83 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N HIS K 247 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE K 81 " --> pdb=" O HIS K 247 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY K 249 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR K 292 " --> pdb=" O ILE K 279 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE K 281 " --> pdb=" O PRO K 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AB9, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AC1, first strand: chain 'L' and resid 22 through 25 Processing sheet with id=AC2, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AC3, first strand: chain 'L' and resid 123 through 126 removed outlier: 4.166A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 156 through 157 removed outlier: 7.875A pdb=" N LYS a 126 " --> pdb=" O PRO a 100 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE a 102 " --> pdb=" O LYS a 126 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL a 125 " --> pdb=" O GLU a 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 14 through 16 Processing sheet with id=AC6, first strand: chain 'M' and resid 55 through 59 removed outlier: 5.484A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 37 through 39 removed outlier: 3.767A pdb=" N ALA N 39 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR N 62 " --> pdb=" O VAL N 132 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 6 through 10 removed outlier: 3.507A pdb=" N LYS O 103 " --> pdb=" O ILE O 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AD1, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.883A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 58 through 59 removed outlier: 3.817A pdb=" N ILE P 58 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 128 through 130 removed outlier: 4.265A pdb=" N THR P 129 " --> pdb=" O ASN P 137 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN P 137 " --> pdb=" O THR P 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AD5, first strand: chain 'Q' and resid 120 through 122 removed outlier: 6.432A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL Q 81 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA Q 102 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR Q 80 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU Q 140 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL Q 82 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 58 through 63 removed outlier: 6.850A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 88 through 96 removed outlier: 4.424A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 54 through 58 removed outlier: 8.566A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 17 through 18 Processing sheet with id=AE1, first strand: chain 'V' and resid 22 through 24 removed outlier: 6.901A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL V 78 " --> pdb=" O VAL V 101 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL V 101 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 85 through 87 removed outlier: 4.214A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 117 through 118 Processing sheet with id=AE4, first strand: chain 'W' and resid 64 through 66 removed outlier: 3.815A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS W 216 " --> pdb=" O ILE W 233 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE W 233 " --> pdb=" O LYS W 216 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 121 through 123 Processing sheet with id=AE6, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=AE7, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.739A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AE9, first strand: chain 'Y' and resid 79 through 82 removed outlier: 7.107A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AF2, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.386A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 72 through 73 Processing sheet with id=AF4, first strand: chain 'b' and resid 205 through 211 removed outlier: 3.849A pdb=" N CYS b 249 " --> pdb=" O THR b 169 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 363 through 364 removed outlier: 3.677A pdb=" N LEU y 181 " --> pdb=" O ALA b 364 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 21 through 25 removed outlier: 6.545A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE c 70 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE c 44 " --> pdb=" O PHE c 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 49 through 50 removed outlier: 6.719A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE d 90 " --> pdb=" O LYS d 78 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS d 78 " --> pdb=" O PHE d 90 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.794A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'f' and resid 8 through 15 removed outlier: 6.907A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS f 75 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.493A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG3, first strand: chain 'k' and resid 3 through 4 removed outlier: 6.557A pdb=" N ARG k 3 " --> pdb=" O THR k 53 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL k 55 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'n' and resid 178 through 181 Processing sheet with id=AG5, first strand: chain 'n' and resid 386 through 389 Processing sheet with id=AG6, first strand: chain 'o' and resid 119 through 124 removed outlier: 4.422A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU o 167 " --> pdb=" O SER o 90 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE o 92 " --> pdb=" O ARG o 165 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG o 165 " --> pdb=" O ILE o 92 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR o 94 " --> pdb=" O GLN o 163 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN o 163 " --> pdb=" O TYR o 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'r' and resid 149 through 150 removed outlier: 7.264A pdb=" N ARG r 149 " --> pdb=" O ILE r 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'r' and resid 181 through 185 removed outlier: 3.738A pdb=" N LYS r 201 " --> pdb=" O ILE r 220 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 129 through 133 Processing sheet with id=AH1, first strand: chain 't' and resid 194 through 195 removed outlier: 4.051A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 't' and resid 213 through 215 Processing sheet with id=AH3, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AH4, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AH5, first strand: chain 'y' and resid 2 through 4 removed outlier: 6.345A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU y 203 " --> pdb=" O ASN y 200 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AH7, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.822A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'y' and resid 109 through 110 removed outlier: 3.770A pdb=" N CYS y 109 " --> pdb=" O LEU y 116 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'y' and resid 152 through 154 Processing sheet with id=AI1, first strand: chain 'w' and resid 88 through 92 removed outlier: 5.989A pdb=" N ILE w 74 " --> pdb=" O ILE w 89 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE w 91 " --> pdb=" O ILE w 74 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY w 76 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE w 51 " --> pdb=" O LEU w 117 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL w 116 " --> pdb=" O VAL w 157 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LYS w 159 " --> pdb=" O VAL w 116 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS w 118 " --> pdb=" O LYS w 159 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N PHE w 161 " --> pdb=" O HIS w 118 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'w' and resid 795 through 797 2527 hydrogen bonds defined for protein. 7275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1971 hydrogen bonds 3294 hydrogen bond angles 0 basepair planarities 790 basepair parallelities 1268 stacking parallelities Total time for adding SS restraints: 137.94 Time building geometry restraints manager: 49.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 14979 1.30 - 1.45: 55888 1.45 - 1.60: 53558 1.60 - 1.74: 2294 1.74 - 1.89: 223 Bond restraints: 126942 Sorted by residual: bond pdb=" CA ALA N 146 " pdb=" C ALA N 146 " ideal model delta sigma weight residual 1.522 1.383 0.139 1.72e-02 3.38e+03 6.50e+01 bond pdb=" C LEU f 102 " pdb=" N TYR f 103 " ideal model delta sigma weight residual 1.327 1.159 0.168 2.31e-02 1.87e+03 5.32e+01 bond pdb=" C PRO B 96 " pdb=" N ARG B 97 " ideal model delta sigma weight residual 1.332 1.241 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" C ASP N 153 " pdb=" N PRO N 154 " ideal model delta sigma weight residual 1.337 1.265 0.072 1.11e-02 8.12e+03 4.16e+01 bond pdb=" CB PRO f 104 " pdb=" CG PRO f 104 " ideal model delta sigma weight residual 1.506 1.256 0.250 3.90e-02 6.57e+02 4.11e+01 ... (remaining 126937 not shown) Histogram of bond angle deviations from ideal: 91.98 - 102.01: 3815 102.01 - 112.04: 72399 112.04 - 122.06: 78884 122.06 - 132.09: 28922 132.09 - 142.11: 721 Bond angle restraints: 184741 Sorted by residual: angle pdb=" C ILE F 156 " pdb=" N ASN F 157 " pdb=" CA ASN F 157 " ideal model delta sigma weight residual 121.54 139.63 -18.09 1.91e+00 2.74e-01 8.97e+01 angle pdb=" N LYS n 5 " pdb=" CA LYS n 5 " pdb=" C LYS n 5 " ideal model delta sigma weight residual 110.91 119.41 -8.50 1.17e+00 7.31e-01 5.27e+01 angle pdb=" N VAL E 35 " pdb=" CA VAL E 35 " pdb=" C VAL E 35 " ideal model delta sigma weight residual 109.19 103.52 5.67 8.20e-01 1.49e+00 4.79e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 134.40 -12.86 1.91e+00 2.74e-01 4.53e+01 angle pdb=" C LYS r 16 " pdb=" CA LYS r 16 " pdb=" CB LYS r 16 " ideal model delta sigma weight residual 110.42 97.15 13.27 1.99e+00 2.53e-01 4.45e+01 ... (remaining 184736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 67693 36.00 - 72.00: 2841 72.00 - 108.00: 227 108.00 - 144.00: 37 144.00 - 180.00: 58 Dihedral angle restraints: 70856 sinusoidal: 49024 harmonic: 21832 Sorted by residual: dihedral pdb=" CA PRO n 123 " pdb=" C PRO n 123 " pdb=" N SER n 124 " pdb=" CA SER n 124 " ideal model delta harmonic sigma weight residual -180.00 -59.05 -120.95 0 5.00e+00 4.00e-02 5.85e+02 dihedral pdb=" CA ILE n 375 " pdb=" C ILE n 375 " pdb=" N LEU n 376 " pdb=" CA LEU n 376 " ideal model delta harmonic sigma weight residual 180.00 119.73 60.27 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLY n 55 " pdb=" C GLY n 55 " pdb=" N SER n 56 " pdb=" CA SER n 56 " ideal model delta harmonic sigma weight residual -180.00 -120.85 -59.15 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 70853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 19915 0.120 - 0.240: 2688 0.240 - 0.360: 276 0.360 - 0.480: 40 0.480 - 0.600: 9 Chirality restraints: 22928 Sorted by residual: chirality pdb=" CB VAL P 119 " pdb=" CA VAL P 119 " pdb=" CG1 VAL P 119 " pdb=" CG2 VAL P 119 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CB VAL O 145 " pdb=" CA VAL O 145 " pdb=" CG1 VAL O 145 " pdb=" CG2 VAL O 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" CB VAL Y 8 " pdb=" CA VAL Y 8 " pdb=" CG1 VAL Y 8 " pdb=" CG2 VAL Y 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 22925 not shown) Planarity restraints: 13136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 15 " 0.083 2.00e-02 2.50e+03 3.63e-02 3.94e+01 pdb=" N9 G 2 15 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G 2 15 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 2 15 " -0.016 2.00e-02 2.50e+03 pdb=" C5 G 2 15 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G 2 15 " 0.030 2.00e-02 2.50e+03 pdb=" O6 G 2 15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G 2 15 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G 2 15 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G 2 15 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G 2 15 " -0.021 2.00e-02 2.50e+03 pdb=" C4 G 2 15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA g 82 " -0.030 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ALA g 82 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA g 82 " -0.038 2.00e-02 2.50e+03 pdb=" N ASN g 83 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 166 " -0.030 2.00e-02 2.50e+03 5.95e-02 3.53e+01 pdb=" C ALA L 166 " 0.103 2.00e-02 2.50e+03 pdb=" O ALA L 166 " -0.038 2.00e-02 2.50e+03 pdb=" N PHE L 167 " -0.035 2.00e-02 2.50e+03 ... (remaining 13133 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 3489 2.61 - 3.18: 104730 3.18 - 3.75: 229630 3.75 - 4.33: 285447 4.33 - 4.90: 416905 Nonbonded interactions: 1040201 Sorted by model distance: nonbonded pdb=" O2' A 11303 " pdb=" O4' A 11304 " model vdw 2.033 2.440 nonbonded pdb=" OP1 C 1 339 " pdb=" O2' G 11380 " model vdw 2.042 2.440 nonbonded pdb=" O2' A 11433 " pdb=" O4' G 11434 " model vdw 2.048 2.440 nonbonded pdb=" O ASN e 99 " pdb=" O2' U 11388 " model vdw 2.053 2.440 nonbonded pdb=" O2' A 11524 " pdb=" OP2 U 11526 " model vdw 2.059 2.440 ... (remaining 1040196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2757 5.49 5 S 141 5.16 5 C 64385 2.51 5 N 21739 2.21 5 O 29860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.430 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: 0.110 Extract box with map and model: 19.190 Check model and map are aligned: 1.420 Convert atoms to be neutral: 0.790 Process input model: 358.290 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 389.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.019 0.286 126942 Z= 1.201 Angle : 1.572 18.094 184741 Z= 0.794 Chirality : 0.085 0.600 22928 Planarity : 0.010 0.120 13136 Dihedral : 17.825 179.997 56676 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.21 % Twisted Proline : 2.41 % Twisted General : 1.06 % 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: -3.91 (0.08), residues: 7377 helix: -2.20 (0.07), residues: 2863 sheet: -2.35 (0.15), residues: 916 loop : -2.99 (0.08), residues: 3598 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1871 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1829 time to evaluate : 7.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 42 outliers final: 26 residues processed: 1864 average time/residue: 1.1974 time to fit residues: 3704.2713 Evaluate side-chains 1377 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1351 time to evaluate : 6.953 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.8091 time to fit residues: 48.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 846 optimal weight: 0.9990 chunk 760 optimal weight: 0.9980 chunk 421 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 512 optimal weight: 0.9980 chunk 406 optimal weight: 9.9990 chunk 786 optimal weight: 4.9990 chunk 304 optimal weight: 20.0000 chunk 478 optimal weight: 0.9990 chunk 585 optimal weight: 8.9990 chunk 910 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 231 HIS C 58 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN F 37 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 93 ASN F 146 GLN G 77 GLN G 192 GLN H 5 GLN H 50 ASN H 102 ASN H 116 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN H 183 HIS K 42 ASN K 84 ASN K 262 ASN L 37 ASN L 103 ASN L 112 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 ASN O 42 ASN O 55 HIS O 182 ASN P 121 GLN S 138 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 57 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN b 288 ASN b 454 GLN c 75 ASN d 17 HIS d 43 HIS f 42 GLN f 77 ASN g 33 GLN h 59 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 437 ASN ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 GLN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN ** t 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 225 HIS u 37 HIS u 115 ASN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN y 235 ASN ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN w 71 ASN w 92 GLN w 174 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 126942 Z= 0.208 Angle : 0.760 14.953 184741 Z= 0.382 Chirality : 0.040 0.321 22928 Planarity : 0.006 0.120 13136 Dihedral : 16.301 179.918 41320 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.87 % Favored : 94.02 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.34 % Twisted General : 0.24 % 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: -2.46 (0.09), residues: 7377 helix: -0.74 (0.09), residues: 2862 sheet: -1.67 (0.16), residues: 923 loop : -2.39 (0.09), residues: 3592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1887 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1734 time to evaluate : 7.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 153 outliers final: 70 residues processed: 1809 average time/residue: 1.1286 time to fit residues: 3468.5460 Evaluate side-chains 1498 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1428 time to evaluate : 7.086 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 70 outliers final: 1 residues processed: 70 average time/residue: 0.8924 time to fit residues: 127.2155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 506 optimal weight: 0.9990 chunk 282 optimal weight: 20.0000 chunk 758 optimal weight: 10.0000 chunk 620 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 912 optimal weight: 10.0000 chunk 985 optimal weight: 0.9980 chunk 812 optimal weight: 6.9990 chunk 904 optimal weight: 30.0000 chunk 311 optimal weight: 5.9990 chunk 732 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 198 HIS B 279 ASN B 319 ASN C 43 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN F 37 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN H 50 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 162 GLN K 200 ASN ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 57 GLN O 42 ASN O 182 ASN P 54 HIS ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 ASN V 7 GLN W 205 GLN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 91 ASN Z 127 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN c 75 ASN d 21 HIS e 49 ASN f 88 ASN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 GLN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 ASN ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 228 ASN q 231 ASN r 10 HIS r 14 HIS r 49 GLN ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN t 91 GLN t 230 ASN u 73 GLN y 6 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.160 126942 Z= 0.260 Angle : 0.715 15.971 184741 Z= 0.364 Chirality : 0.040 0.304 22928 Planarity : 0.006 0.126 13136 Dihedral : 15.992 179.867 41320 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.34 % Twisted General : 0.22 % 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: -1.99 (0.09), residues: 7377 helix: -0.28 (0.09), residues: 2885 sheet: -1.35 (0.16), residues: 924 loop : -2.21 (0.09), residues: 3568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1822 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1632 time to evaluate : 6.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 190 outliers final: 85 residues processed: 1737 average time/residue: 1.1768 time to fit residues: 3519.5176 Evaluate side-chains 1527 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1442 time to evaluate : 7.261 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 85 outliers final: 1 residues processed: 85 average time/residue: 0.9451 time to fit residues: 160.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 901 optimal weight: 10.0000 chunk 686 optimal weight: 9.9990 chunk 473 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 435 optimal weight: 0.6980 chunk 612 optimal weight: 50.0000 chunk 915 optimal weight: 10.0000 chunk 969 optimal weight: 10.0000 chunk 478 optimal weight: 0.0060 chunk 867 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 198 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 136 ASN S 62 ASN U 40 HIS V 7 GLN ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 81 GLN Z 127 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 75 ASN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 163 GLN ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN t 303 ASN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 126942 Z= 0.218 Angle : 0.668 16.363 184741 Z= 0.340 Chirality : 0.038 0.309 22928 Planarity : 0.005 0.129 13136 Dihedral : 15.809 179.840 41320 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.70 (0.09), residues: 7377 helix: -0.04 (0.09), residues: 2885 sheet: -1.22 (0.16), residues: 894 loop : -2.03 (0.10), residues: 3598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1588 time to evaluate : 7.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 167 outliers final: 93 residues processed: 1676 average time/residue: 1.0899 time to fit residues: 3141.4118 Evaluate side-chains 1502 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1409 time to evaluate : 6.686 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 93 outliers final: 1 residues processed: 93 average time/residue: 0.8612 time to fit residues: 158.5002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 807 optimal weight: 20.0000 chunk 550 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 721 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 827 optimal weight: 10.0000 chunk 670 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 495 optimal weight: 4.9990 chunk 870 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 61 ASN F 225 GLN G 123 GLN G 192 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 175 ASN O 182 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN W 54 GLN W 223 ASN X 94 GLN X 137 ASN Y 4 GLN Y 81 GLN Z 127 ASN b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 GLN h 59 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN z 31 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.188 126942 Z= 0.306 Angle : 0.710 17.025 184741 Z= 0.361 Chirality : 0.040 0.358 22928 Planarity : 0.006 0.104 13136 Dihedral : 15.835 179.854 41320 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.73 % Favored : 92.15 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.61 (0.09), residues: 7377 helix: 0.02 (0.09), residues: 2885 sheet: -1.22 (0.16), residues: 953 loop : -1.97 (0.10), residues: 3539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1521 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 175 outliers final: 89 residues processed: 1621 average time/residue: 1.1180 time to fit residues: 3124.5845 Evaluate side-chains 1503 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1414 time to evaluate : 7.164 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.9098 time to fit residues: 162.0539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 326 optimal weight: 2.9990 chunk 873 optimal weight: 50.0000 chunk 191 optimal weight: 8.9990 chunk 569 optimal weight: 30.0000 chunk 239 optimal weight: 5.9990 chunk 970 optimal weight: 1.9990 chunk 805 optimal weight: 30.0000 chunk 449 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 321 optimal weight: 20.0000 chunk 509 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN F 225 GLN G 192 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 23 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN V 7 GLN V 98 ASN W 44 HIS X 137 ASN Z 106 GLN b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 126942 Z= 0.190 Angle : 0.655 15.154 184741 Z= 0.332 Chirality : 0.037 0.374 22928 Planarity : 0.005 0.105 13136 Dihedral : 15.671 179.458 41320 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.09 % Favored : 92.77 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.41 (0.09), residues: 7377 helix: 0.16 (0.09), residues: 2884 sheet: -1.03 (0.16), residues: 925 loop : -1.84 (0.10), residues: 3568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1575 time to evaluate : 7.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 111 outliers final: 62 residues processed: 1625 average time/residue: 1.1700 time to fit residues: 3282.7704 Evaluate side-chains 1521 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1459 time to evaluate : 7.091 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 1.0105 time to fit residues: 123.6602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 935 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 552 optimal weight: 6.9990 chunk 708 optimal weight: 10.0000 chunk 549 optimal weight: 4.9990 chunk 816 optimal weight: 10.0000 chunk 541 optimal weight: 0.3980 chunk 966 optimal weight: 20.0000 chunk 604 optimal weight: 0.9980 chunk 589 optimal weight: 9.9990 chunk 446 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 184 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN F 146 GLN F 225 GLN G 192 GLN H 5 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN L 120 GLN M 119 GLN N 23 GLN O 182 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN W 44 HIS X 137 ASN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 HIS l 11 GLN l 19 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 160 GLN n 165 GLN ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 92 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.119 126942 Z= 0.240 Angle : 0.669 17.104 184741 Z= 0.340 Chirality : 0.038 0.509 22928 Planarity : 0.005 0.114 13136 Dihedral : 15.647 179.600 41320 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.60 % Favored : 92.27 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.09), residues: 7377 helix: 0.19 (0.09), residues: 2892 sheet: -0.97 (0.16), residues: 955 loop : -1.82 (0.10), residues: 3530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1625 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1528 time to evaluate : 7.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 97 outliers final: 50 residues processed: 1579 average time/residue: 1.1471 time to fit residues: 3114.1088 Evaluate side-chains 1490 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1440 time to evaluate : 7.075 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.9448 time to fit residues: 98.0454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 598 optimal weight: 10.0000 chunk 386 optimal weight: 8.9990 chunk 577 optimal weight: 0.2980 chunk 291 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 614 optimal weight: 6.9990 chunk 658 optimal weight: 8.9990 chunk 477 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 759 optimal weight: 10.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 225 GLN H 50 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN P 116 HIS ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN W 44 HIS ** X 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 HIS b 89 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 454 GLN ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS r 183 ASN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 92 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.319 126942 Z= 0.298 Angle : 0.708 19.861 184741 Z= 0.360 Chirality : 0.039 0.528 22928 Planarity : 0.006 0.146 13136 Dihedral : 15.700 179.938 41320 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.07 % Favored : 91.83 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.38 (0.09), residues: 7377 helix: 0.18 (0.09), residues: 2892 sheet: -0.97 (0.16), residues: 941 loop : -1.84 (0.10), residues: 3544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1487 time to evaluate : 7.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 110 outliers final: 60 residues processed: 1536 average time/residue: 1.1083 time to fit residues: 2915.3564 Evaluate side-chains 1477 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1417 time to evaluate : 7.030 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.8828 time to fit residues: 107.1357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 879 optimal weight: 30.0000 chunk 926 optimal weight: 10.0000 chunk 844 optimal weight: 20.0000 chunk 900 optimal weight: 10.0000 chunk 925 optimal weight: 8.9990 chunk 542 optimal weight: 0.6980 chunk 392 optimal weight: 10.0000 chunk 707 optimal weight: 8.9990 chunk 276 optimal weight: 3.9990 chunk 814 optimal weight: 5.9990 chunk 852 optimal weight: 20.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 279 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 275 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 156 HIS O 29 ASN O 182 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** X 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 430 GLN ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 92 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.143 126942 Z= 0.451 Angle : 0.812 16.224 184741 Z= 0.414 Chirality : 0.044 0.446 22928 Planarity : 0.007 0.129 13136 Dihedral : 16.002 179.875 41320 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.12 % Favored : 90.74 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.61 (0.09), residues: 7377 helix: 0.01 (0.09), residues: 2886 sheet: -1.21 (0.16), residues: 963 loop : -1.96 (0.10), residues: 3528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1491 time to evaluate : 7.112 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 90 outliers final: 52 residues processed: 1526 average time/residue: 1.1709 time to fit residues: 3083.2970 Evaluate side-chains 1486 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1434 time to evaluate : 7.057 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.9181 time to fit residues: 98.8089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 897 optimal weight: 20.0000 chunk 591 optimal weight: 10.0000 chunk 952 optimal weight: 5.9990 chunk 581 optimal weight: 10.0000 chunk 451 optimal weight: 40.0000 chunk 662 optimal weight: 10.0000 chunk 999 optimal weight: 2.9990 chunk 919 optimal weight: 7.9990 chunk 795 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 614 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN O 182 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN W 44 HIS X 65 GLN Z 79 HIS ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 59 ASN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.385 126942 Z= 0.457 Angle : 0.854 73.898 184741 Z= 0.430 Chirality : 0.045 0.600 22928 Planarity : 0.007 0.176 13136 Dihedral : 16.012 179.992 41320 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.19 % Favored : 90.66 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.71 (0.09), residues: 7377 helix: -0.05 (0.09), residues: 2878 sheet: -1.25 (0.16), residues: 957 loop : -2.03 (0.10), residues: 3542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1506 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1457 time to evaluate : 7.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 49 outliers final: 36 residues processed: 1472 average time/residue: 1.1058 time to fit residues: 2800.0576 Evaluate side-chains 1461 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1425 time to evaluate : 6.958 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.9074 time to fit residues: 69.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 487 optimal weight: 0.8980 chunk 632 optimal weight: 5.9990 chunk 847 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 733 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 796 optimal weight: 4.9990 chunk 333 optimal weight: 0.9980 chunk 818 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 319 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** X 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 59 ASN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN y 9 ASN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.145985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103649 restraints weight = 267108.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104335 restraints weight = 204301.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105038 restraints weight = 122836.114| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.478 126942 Z= 0.234 Angle : 0.742 48.690 184741 Z= 0.374 Chirality : 0.039 0.554 22928 Planarity : 0.006 0.164 13136 Dihedral : 15.774 179.474 41320 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.98 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.51 (0.09), residues: 7377 helix: 0.06 (0.09), residues: 2884 sheet: -1.13 (0.16), residues: 954 loop : -1.87 (0.10), residues: 3539 =============================================================================== Job complete usr+sys time: 40688.93 seconds wall clock time: 698 minutes 24.26 seconds (41904.26 seconds total)