Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 23:13:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/08_2023/7u0h_26259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/08_2023/7u0h_26259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/08_2023/7u0h_26259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/08_2023/7u0h_26259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/08_2023/7u0h_26259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/08_2023/7u0h_26259.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 2939 5.49 5 Mg 1 5.21 5 S 145 5.16 5 C 67408 2.51 5 N 22856 2.21 5 O 31579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 124932 Number of models: 1 Model: "" Number of chains: 54 Chain: "1" Number of atoms: 58236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2722, 58236 Classifications: {'RNA': 2722} Modifications used: {'rna2p_pur': 277, 'rna2p_pyr': 201, 'rna3p_pur': 1230, 'rna3p_pyr': 1014} Link IDs: {'rna2p': 478, 'rna3p': 2243} Chain breaks: 13 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 16, 'rna3p_pur': 60, 'rna3p_pyr': 64} Link IDs: {'rna2p': 33, 'rna3p': 124} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1247 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 16, 'rna3p_pur': 20, 'rna3p_pyr': 15} Link IDs: {'rna2p': 24, 'rna3p': 34} Chain breaks: 2 Chain: "A" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1356 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "B" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2700 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 328} Chain breaks: 1 Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} 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: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1470 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "K" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "L" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 173} 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: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1604 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1341 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain breaks: 2 Chain: "Q" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1132 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} 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, 'TRANS': 163} Chain: "T" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 3 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: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} 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: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1087 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "b" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4430 Classifications: {'peptide': 546} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 520} Chain breaks: 1 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': 4, 'TRANS': 102} Chain: "e" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1012 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} 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: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} 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: "m" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "n" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3001 Classifications: {'peptide': 368} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 346} 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, 'TRANS': 129} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1588 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain breaks: 2 Chain: "r" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1341 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 3 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': 10, 'TRANS': 276} Chain breaks: 1 Chain: "u" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "w" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2610 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 6, 'TRANS': 314} Chain breaks: 4 Chain: "y" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1849 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} 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: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A03R2 SG CYS g 44 119.346 68.342 119.439 1.00 4.47 S ATOM A03RK SG CYS g 47 118.662 65.813 122.040 1.00 9.85 S ATOM A03YM SG CYS g 81 121.245 64.988 119.347 1.00 4.47 S ATOM A03Z5 SG CYS g 84 117.655 65.161 118.310 1.00 9.32 S ATOM A05LX SG CYS j 19 108.028 120.375 144.311 1.00 4.47 S ATOM A05MM SG CYS j 22 107.426 122.918 147.079 1.00 4.47 S ATOM A05PE SG CYS j 34 105.374 119.735 146.951 1.00 4.47 S ATOM A05PW SG CYS j 37 104.942 122.433 144.186 1.00 4.47 S ATOM A09YP SG CYS p 39 107.487 54.529 127.971 1.00 17.04 S ATOM A09ZC SG CYS p 42 110.802 52.944 127.397 1.00 15.01 S ATOM A0A2D SG CYS p 57 110.086 55.679 130.036 1.00 17.24 S ATOM A0A2V SG CYS p 60 110.318 56.528 126.158 1.00 18.74 S ATOM A0ERF SG CYS u 36 140.655 63.789 215.253 1.00 4.47 S Residues with excluded nonbonded symmetry interactions: 197 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 185 not shown) Time building chain proxies: 43.64, per 1000 atoms: 0.35 Number of scatterers: 124932 At special positions: 0 Unit cell: (206.799, 235.607, 324.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 145 16.00 P 2939 15.00 Mg 1 11.99 O 31579 8.00 N 22856 7.00 C 67408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.40 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb=" ZN p 501 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 60 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " Number of angles added : 18 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14662 Finding SS restraints... Secondary structure from input PDB file: 304 helices and 83 sheets defined 46.1% alpha, 14.7% beta 915 base pairs and 1439 stacking pairs defined. Time for finding SS restraints: 35.45 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.599A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.191A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.665A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 214 through 220 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: 4.523A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.883A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.480A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 removed outlier: 4.050A pdb=" N LYS C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.713A 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 24 through 73 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 131 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.864A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' 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 46 through 50 removed outlier: 3.525A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.510A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 117 removed outlier: 3.808A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.511A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) 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 227 removed outlier: 4.518A pdb=" N ASP G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.558A pdb=" N LYS G 231 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.740A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.845A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.662A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 76 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'K' and resid 136 through 145 Processing helix chain 'K' and resid 156 through 162 Processing helix chain 'K' and resid 166 through 177 removed outlier: 3.824A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 195 removed outlier: 3.667A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.958A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 255 through 275 removed outlier: 4.246A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA K 273 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN K 275 " --> pdb=" O ILE K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 305 removed outlier: 4.428A pdb=" N GLU K 302 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA K 303 " --> pdb=" O ASP K 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 61 through 66 removed outlier: 4.079A pdb=" N TYR L 65 " --> pdb=" O PRO L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 165 through 193 removed outlier: 5.226A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.637A 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 96 Processing helix chain 'M' and resid 97 through 112 Processing helix chain 'M' and resid 113 through 138 Processing helix chain 'N' and resid 3 through 13 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 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.519A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (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 183 through 195 Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 184 Processing helix chain 'O' and resid 188 through 198 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 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 77 removed outlier: 3.998A 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 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' 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 52 removed outlier: 3.816A 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 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 34 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 113 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 114 Processing helix chain 'S' and resid 131 through 135 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'T' and resid 102 through 122 Processing helix chain 'U' and resid 19 through 26 Processing helix chain 'U' and resid 29 through 41 Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'U' and resid 89 through 93 removed outlier: 3.592A pdb=" N TRP U 92 " --> pdb=" O LEU U 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.830A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.969A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 6 through 16 Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 79 Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 131 through 140 Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.906A 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 123 Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 89 through 93 removed outlier: 3.631A pdb=" N LYS Z 93 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 102 removed outlier: 3.512A pdb=" N PHE Z 101 " --> pdb=" O THR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'a' and resid 76 through 82 removed outlier: 5.224A pdb=" N TRP a 79 " --> pdb=" O ASP a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 93 removed outlier: 4.066A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 5.039A 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 142 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 68 removed outlier: 3.528A pdb=" N PHE b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) 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 143 Processing helix chain 'b' and resid 143 through 160 Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 4.104A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 275 Processing helix chain 'b' and resid 276 through 278 No H-bonds generated for 'chain 'b' and resid 276 through 278' Processing helix chain 'b' and resid 294 through 298 removed outlier: 3.572A pdb=" N LEU b 298 " --> pdb=" O PRO b 295 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.955A pdb=" N LEU b 305 " --> pdb=" O GLU b 301 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 350 removed outlier: 3.631A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 353 through 362 removed outlier: 3.565A pdb=" N VAL b 357 " --> pdb=" O ARG b 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU b 358 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN b 359 " --> pdb=" O ASN b 355 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 Processing helix chain 'b' and resid 398 through 407 Processing helix chain 'b' and resid 425 through 430 removed outlier: 3.915A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 445 Processing helix chain 'b' and resid 448 through 467 Processing helix chain 'b' and resid 482 through 511 Processing helix chain 'b' and resid 527 through 538 removed outlier: 4.056A pdb=" N GLU b 533 " --> pdb=" O GLY b 529 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS b 534 " --> pdb=" O LYS b 530 " (cutoff:3.500A) Processing helix chain 'b' and resid 542 through 551 Processing helix chain 'c' and resid 10 through 21 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 21 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 45 Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'e' and resid 40 through 45 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: 3.865A 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 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'f' and resid 90 through 94 Processing helix chain 'g' and resid 58 through 64 removed outlier: 3.531A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 71 removed outlier: 3.822A pdb=" N THR g 71 " --> pdb=" O THR g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 112 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 36 removed outlier: 3.769A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 3.898A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 25 through 29 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 99 Processing helix chain 'j' and resid 4 through 9 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' 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 'm' and resid 157 through 164 Processing helix chain 'n' and resid 10 through 14 Processing helix chain 'n' and resid 18 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 65 through 72 Processing helix chain 'n' and resid 74 through 97 removed outlier: 4.000A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (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 144 removed outlier: 4.715A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 241 removed outlier: 3.807A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 258 through 262 removed outlier: 3.551A pdb=" N SER n 261 " --> pdb=" O GLY n 258 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 383 Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 428 through 439 removed outlier: 3.617A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 113 removed outlier: 4.133A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 removed outlier: 4.349A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS o 213 " --> pdb=" O LYS o 209 " (cutoff:3.500A) Processing helix chain 'p' and resid 8 through 15 removed outlier: 3.890A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY p 15 " --> pdb=" O GLY p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 34 removed outlier: 3.790A pdb=" N LYS p 28 " --> pdb=" O ARG p 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 204 through 208 Processing helix chain 'q' and resid 222 through 226 removed outlier: 3.565A pdb=" N SER q 226 " --> pdb=" O ALA q 223 " (cutoff:3.500A) Processing helix chain 'q' and resid 230 through 264 Processing helix chain 'q' and resid 265 through 267 No H-bonds generated for 'chain 'q' and resid 265 through 267' Processing helix chain 'q' and resid 321 through 356 removed outlier: 3.660A pdb=" N ASP q 349 " --> pdb=" O GLN q 345 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU q 350 " --> pdb=" O ARG q 346 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU q 351 " --> pdb=" O VAL q 347 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU q 352 " --> pdb=" O LYS q 348 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER q 356 " --> pdb=" O GLU q 352 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 427 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.532A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 74 removed outlier: 3.586A pdb=" N GLY r 47 " --> pdb=" O THR r 43 " (cutoff:3.500A) Processing helix chain 'r' and resid 174 through 178 removed outlier: 3.566A pdb=" N LEU r 177 " --> pdb=" O PRO r 174 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 248 through 253 removed outlier: 3.590A pdb=" N ASP r 252 " --> pdb=" O GLU r 248 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 36 Processing helix chain 't' and resid 16 through 52 removed outlier: 3.847A pdb=" N LYS t 38 " --> pdb=" O GLN t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 191 Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 232 through 240 removed outlier: 3.639A pdb=" N GLU t 236 " --> pdb=" O ASN t 232 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 268 Processing helix chain 't' and resid 281 through 299 Processing helix chain 't' and resid 313 through 322 Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 82 through 113 removed outlier: 3.775A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 130 Processing helix chain 'u' and resid 131 through 141 removed outlier: 3.762A pdb=" N ARG u 135 " --> pdb=" O PRO u 131 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) Processing helix chain 'w' and resid 259 through 265 Processing helix chain 'w' and resid 267 through 274 removed outlier: 4.337A pdb=" N MET w 271 " --> pdb=" O ASP w 267 " (cutoff:3.500A) Processing helix chain 'w' and resid 284 through 291 Processing helix chain 'w' and resid 299 through 306 removed outlier: 4.011A pdb=" N ASP w 306 " --> pdb=" O SER w 302 " (cutoff:3.500A) Processing helix chain 'w' and resid 311 through 329 Processing helix chain 'w' and resid 348 through 388 Processing helix chain 'w' and resid 393 through 407 removed outlier: 3.651A pdb=" N GLU w 405 " --> pdb=" O SER w 401 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER w 406 " --> pdb=" O LEU w 402 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 416 Processing helix chain 'w' and resid 419 through 425 Processing helix chain 'w' and resid 460 through 472 Processing helix chain 'w' and resid 696 through 706 removed outlier: 3.771A pdb=" N HIS w 706 " --> pdb=" O ASP w 702 " (cutoff:3.500A) Processing helix chain 'w' and resid 714 through 730 Processing helix chain 'w' and resid 733 through 763 Processing helix chain 'w' and resid 768 through 782 Processing helix chain 'w' and resid 799 through 803 Processing helix chain 'w' and resid 820 through 837 Processing helix chain 'y' and resid 12 through 16 removed outlier: 3.594A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 12 through 16' Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.919A 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 107 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 147 through 151 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 211 through 222 Processing helix chain 'y' and resid 229 through 231 No H-bonds generated for 'chain 'y' and resid 229 through 231' Processing helix chain 'y' and resid 232 through 244 removed outlier: 5.718A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR y 239 " --> pdb=" O ASN y 235 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 19 Processing helix chain 'z' and resid 20 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.269A pdb=" N LEU A 58 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE A 48 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG A 64 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG A 42 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.746A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N HIS A 139 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 145 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.343A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.343A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.455A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 282 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG B 70 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP B 59 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 227 removed outlier: 5.567A pdb=" N ARG B 270 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 226 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY B 268 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 21 removed outlier: 5.178A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB1, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.920A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR E 89 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE E 41 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR E 87 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.044A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG F 232 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N TYR F 136 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'G' and resid 177 through 180 Processing sheet with id=AB6, first strand: chain 'H' and resid 5 through 11 Processing sheet with id=AB7, first strand: chain 'H' and resid 32 through 37 removed outlier: 3.615A pdb=" N GLY H 32 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.859A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 100 through 106 Processing sheet with id=AC1, first strand: chain 'K' and resid 243 through 250 removed outlier: 7.035A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 291 " --> pdb=" O ILE K 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AC3, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.107A pdb=" N GLU K 153 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 155 " --> pdb=" O LEU K 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AC5, first strand: chain 'L' and resid 21 through 24 removed outlier: 6.384A pdb=" N ARG L 21 " --> pdb=" O LEU N 197 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU N 199 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AC7, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC8, first strand: chain 'L' and resid 156 through 157 removed outlier: 7.395A pdb=" N LYS a 126 " --> pdb=" O PRO a 100 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE a 102 " --> pdb=" O LYS a 126 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL a 125 " --> pdb=" O GLU a 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.513A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 53 through 59 removed outlier: 4.819A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU M 68 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU M 22 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR M 66 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 36 through 38 removed outlier: 5.875A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AD4, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AD5, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.799A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'P' and resid 125 through 127 removed outlier: 3.821A pdb=" N GLN P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR P 139 " --> pdb=" O ARG P 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.308A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE1, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AE2, first strand: chain 'S' and resid 56 through 63 removed outlier: 5.312A pdb=" N ILE S 58 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG S 12 " --> pdb=" O ILE S 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 88 through 96 removed outlier: 6.886A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 60 through 62 Processing sheet with id=AE5, first strand: chain 'U' and resid 54 through 57 removed outlier: 8.140A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 42 through 43 Processing sheet with id=AE7, first strand: chain 'V' and resid 17 through 18 Processing sheet with id=AE8, first strand: chain 'V' and resid 22 through 25 removed outlier: 5.508A pdb=" N ILE V 36 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR V 61 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 85 through 87 removed outlier: 3.511A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE V 92 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL u 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR V 94 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 114 through 118 removed outlier: 5.817A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 64 through 68 removed outlier: 4.347A pdb=" N GLY W 68 " --> pdb=" O THR W 100 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR W 100 " --> pdb=" O GLY W 68 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE W 233 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA W 219 " --> pdb=" O THR W 231 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR W 231 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR W 221 " --> pdb=" O GLU W 229 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU W 229 " --> pdb=" O TYR W 221 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 121 through 123 Processing sheet with id=AF4, first strand: chain 'W' and resid 135 through 137 removed outlier: 7.026A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AF6, first strand: chain 'X' and resid 21 through 24 removed outlier: 3.954A pdb=" N LYS q 444 " --> pdb=" O LEU X 24 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 63 through 66 removed outlier: 4.016A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS X 121 " --> pdb=" O THR X 112 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR X 112 " --> pdb=" O LYS X 121 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR X 123 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL X 110 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG X 125 " --> pdb=" O LEU X 108 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AF9, first strand: chain 'Y' and resid 94 through 99 removed outlier: 9.705A pdb=" N VAL Y 95 " --> pdb=" O LYS Y 84 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LYS Y 84 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE Y 97 " --> pdb=" O VAL Y 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL Y 82 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.384A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL Z 23 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.089A pdb=" N LEU a 73 " --> pdb=" O LEU a 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 205 through 211 removed outlier: 6.293A pdb=" N LEU b 170 " --> pdb=" O ILE b 219 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU b 251 " --> pdb=" O THR b 169 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU b 171 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE b 253 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS b 173 " --> pdb=" O PHE b 253 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASP b 255 " --> pdb=" O CYS b 173 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASN b 288 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET b 254 " --> pdb=" O ASN b 288 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL b 285 " --> pdb=" O MET b 318 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AG5, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.071A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 49 through 51 removed outlier: 6.686A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.936A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.576A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.628A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AH2, first strand: chain 'k' and resid 3 through 4 removed outlier: 4.731A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'n' and resid 15 through 17 Processing sheet with id=AH4, first strand: chain 'n' and resid 176 through 182 removed outlier: 6.614A pdb=" N VAL n 176 " --> pdb=" O ASN n 191 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN n 191 " --> pdb=" O VAL n 176 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY n 185 " --> pdb=" O SER n 182 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 386 through 389 removed outlier: 6.301A pdb=" N VAL n 364 " --> pdb=" O HIS n 409 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE n 411 " --> pdb=" O VAL n 364 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR n 366 " --> pdb=" O ILE n 411 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN n 410 " --> pdb=" O ILE n 427 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'o' and resid 117 through 124 removed outlier: 3.932A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'o' and resid 156 through 157 Processing sheet with id=AH8, first strand: chain 'p' and resid 47 through 51 removed outlier: 5.322A pdb=" N ARG p 49 " --> pdb=" O THR p 56 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR p 56 " --> pdb=" O ARG p 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA p 51 " --> pdb=" O ILE p 54 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'r' and resid 181 through 186 removed outlier: 3.650A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ALA r 257 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN r 183 " --> pdb=" O ALA r 257 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU r 259 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR r 185 " --> pdb=" O LEU r 259 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 't' and resid 129 through 134 removed outlier: 7.013A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 't' and resid 194 through 197 removed outlier: 4.207A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 't' and resid 213 through 216 Processing sheet with id=AI4, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AI5, first strand: chain 'w' and resid 256 through 258 removed outlier: 7.096A pdb=" N THR w 257 " --> pdb=" O THR w 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'w' and resid 794 through 797 Processing sheet with id=AI7, first strand: chain 'y' and resid 2 through 5 Processing sheet with id=AI8, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AI9, first strand: chain 'y' and resid 64 through 65 removed outlier: 6.287A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AJ2, first strand: chain 'y' and resid 152 through 154 2903 hydrogen bonds defined for protein. 8280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2248 hydrogen bonds 3590 hydrogen bond angles 0 basepair planarities 915 basepair parallelities 1439 stacking parallelities Total time for adding SS restraints: 144.45 Time building geometry restraints manager: 47.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 19559 1.33 - 1.45: 50338 1.45 - 1.58: 57424 1.58 - 1.70: 5859 1.70 - 1.83: 239 Bond restraints: 133419 Sorted by residual: bond pdb=" C1' A 12373 " pdb=" N9 A 12373 " ideal model delta sigma weight residual 1.465 1.395 0.070 1.50e-02 4.44e+03 2.16e+01 bond pdb=" C1' U 12861 " pdb=" N1 U 12861 " ideal model delta sigma weight residual 1.480 1.521 -0.041 1.50e-02 4.44e+03 7.35e+00 bond pdb=" C1' C 11199 " pdb=" N1 C 11199 " ideal model delta sigma weight residual 1.480 1.514 -0.034 1.50e-02 4.44e+03 5.28e+00 bond pdb=" N PRO b 376 " pdb=" CD PRO b 376 " ideal model delta sigma weight residual 1.473 1.504 -0.031 1.40e-02 5.10e+03 4.78e+00 bond pdb=" C1' U 12771 " pdb=" N1 U 12771 " ideal model delta sigma weight residual 1.480 1.509 -0.029 1.50e-02 4.44e+03 3.65e+00 ... (remaining 133414 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.44: 18429 106.44 - 113.37: 77112 113.37 - 120.29: 48238 120.29 - 127.22: 43706 127.22 - 134.14: 6801 Bond angle restraints: 194286 Sorted by residual: angle pdb=" O4' G 1 406 " pdb=" C1' G 1 406 " pdb=" N9 G 1 406 " ideal model delta sigma weight residual 108.20 115.01 -6.81 1.50e+00 4.44e-01 2.06e+01 angle pdb=" C3' U 11568 " pdb=" O3' U 11568 " pdb=" P U 11569 " ideal model delta sigma weight residual 120.20 126.52 -6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" O3' U 11568 " pdb=" C3' U 11568 " pdb=" C2' U 11568 " ideal model delta sigma weight residual 109.50 115.62 -6.12 1.50e+00 4.44e-01 1.67e+01 angle pdb=" C2' A 11303 " pdb=" C1' A 11303 " pdb=" N9 A 11303 " ideal model delta sigma weight residual 112.00 117.13 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" C3' C 1 480 " pdb=" O3' C 1 480 " pdb=" P U 1 481 " ideal model delta sigma weight residual 120.20 125.21 -5.01 1.50e+00 4.44e-01 1.12e+01 ... (remaining 194281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 72110 35.69 - 71.38: 2086 71.38 - 107.07: 177 107.07 - 142.76: 14 142.76 - 178.45: 41 Dihedral angle restraints: 74428 sinusoidal: 51819 harmonic: 22609 Sorted by residual: dihedral pdb=" O4' C 12899 " pdb=" C1' C 12899 " pdb=" N1 C 12899 " pdb=" C2 C 12899 " ideal model delta sinusoidal sigma weight residual 200.00 26.54 173.46 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 13306 " pdb=" C1' U 13306 " pdb=" N1 U 13306 " pdb=" C2 U 13306 " ideal model delta sinusoidal sigma weight residual 200.00 26.72 173.28 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 200.00 30.48 169.52 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 74425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 21191 0.057 - 0.115: 2627 0.115 - 0.172: 301 0.172 - 0.230: 35 0.230 - 0.287: 3 Chirality restraints: 24157 Sorted by residual: chirality pdb=" C1' A 11303 " pdb=" O4' A 11303 " pdb=" C2' A 11303 " pdb=" N9 A 11303 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C3' G 1 283 " pdb=" C4' G 1 283 " pdb=" O3' G 1 283 " pdb=" C2' G 1 283 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1' U 13302 " pdb=" O4' U 13302 " pdb=" C2' U 13302 " pdb=" N1 U 13302 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 24154 not shown) Planarity restraints: 13679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 406 " -0.065 2.00e-02 2.50e+03 2.69e-02 2.18e+01 pdb=" N9 G 1 406 " 0.058 2.00e-02 2.50e+03 pdb=" C8 G 1 406 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 1 406 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G 1 406 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 1 406 " -0.012 2.00e-02 2.50e+03 pdb=" O6 G 1 406 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G 1 406 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G 1 406 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 1 406 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G 1 406 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G 1 406 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " 0.055 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 G 2 39 " -0.053 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 835 " -0.049 2.00e-02 2.50e+03 2.14e-02 1.38e+01 pdb=" N9 G 1 835 " 0.053 2.00e-02 2.50e+03 pdb=" C8 G 1 835 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 835 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 835 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G 1 835 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G 1 835 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G 1 835 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 1 835 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G 1 835 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 835 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G 1 835 " 0.006 2.00e-02 2.50e+03 ... (remaining 13676 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 2718 2.64 - 3.21: 104304 3.21 - 3.77: 236448 3.77 - 4.34: 317189 4.34 - 4.90: 441840 Nonbonded interactions: 1102499 Sorted by model distance: nonbonded pdb=" O2' A 11200 " pdb=" O2 C 11201 " model vdw 2.076 2.440 nonbonded pdb=" O2' G 12874 " pdb=" O4' U 12875 " model vdw 2.140 2.440 nonbonded pdb=" O2' U 11568 " pdb=" OP2 U 11569 " model vdw 2.146 2.440 nonbonded pdb=" N2 G 12393 " pdb=" O6 G 12394 " model vdw 2.177 2.520 nonbonded pdb=" N1 A 11200 " pdb=" O6 G 12824 " model vdw 2.200 2.496 ... (remaining 1102494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 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: 21.610 Check model and map are aligned: 1.330 Set scattering table: 0.780 Process input model: 369.600 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 410.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 133419 Z= 0.247 Angle : 0.619 11.092 194286 Z= 0.322 Chirality : 0.039 0.287 24157 Planarity : 0.005 0.056 13679 Dihedral : 14.670 178.448 59766 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 7630 helix: 1.63 (0.09), residues: 3204 sheet: -0.18 (0.15), residues: 1030 loop : -0.53 (0.10), residues: 3396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1533 time to evaluate : 6.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 27 residues processed: 1578 average time/residue: 2.1942 time to fit residues: 4709.4728 Evaluate side-chains 1155 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1128 time to evaluate : 6.580 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 5 average time/residue: 1.1953 time to fit residues: 18.1035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 883 optimal weight: 0.0010 chunk 792 optimal weight: 3.9990 chunk 439 optimal weight: 0.0770 chunk 270 optimal weight: 10.0000 chunk 534 optimal weight: 8.9990 chunk 423 optimal weight: 20.0000 chunk 819 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 498 optimal weight: 3.9990 chunk 610 optimal weight: 7.9990 chunk 949 optimal weight: 20.0000 overall best weight: 2.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 115 ASN C 296 GLN G 59 GLN G 79 GLN G 221 ASN L 114 GLN M 41 GLN M 62 GLN O 55 HIS O 182 ASN R 27 ASN R 36 ASN S 63 GLN S 122 HIS S 157 GLN V 81 GLN X 65 GLN Z 57 HIS Z 123 GLN b 90 HIS b 107 GLN b 124 GLN b 166 ASN b 323 GLN g 52 GLN g 61 GLN h 16 GLN n 69 GLN p 32 GLN q 230 ASN r 13 GLN r 154 HIS s 7 GLN t 274 ASN t 291 GLN u 115 ASN ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 133419 Z= 0.176 Angle : 0.550 9.061 194286 Z= 0.287 Chirality : 0.036 0.276 24157 Planarity : 0.004 0.051 13679 Dihedral : 14.372 179.861 43792 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.09), residues: 7630 helix: 1.86 (0.09), residues: 3182 sheet: -0.08 (0.15), residues: 1003 loop : -0.41 (0.10), residues: 3445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1154 time to evaluate : 6.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 104 residues processed: 1265 average time/residue: 2.1010 time to fit residues: 3655.2143 Evaluate side-chains 1181 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1077 time to evaluate : 6.632 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 59 residues processed: 47 average time/residue: 1.1792 time to fit residues: 100.7003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 527 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 790 optimal weight: 0.9980 chunk 646 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 951 optimal weight: 0.9990 chunk 1027 optimal weight: 10.0000 chunk 847 optimal weight: 20.0000 chunk 943 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 763 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN G 59 GLN G 79 GLN G 221 ASN L 114 GLN M 41 GLN M 62 GLN ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN R 27 ASN R 36 ASN S 122 HIS S 157 GLN V 24 ASN X 65 GLN Z 123 GLN a 65 GLN b 26 GLN b 124 GLN b 166 ASN b 323 GLN c 75 ASN g 61 GLN n 69 GLN n 428 GLN q 355 ASN q 381 HIS s 7 GLN t 291 GLN u 110 ASN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 133419 Z= 0.246 Angle : 0.608 10.165 194286 Z= 0.315 Chirality : 0.039 0.280 24157 Planarity : 0.005 0.060 13679 Dihedral : 14.439 179.174 43792 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 7630 helix: 1.71 (0.09), residues: 3193 sheet: -0.19 (0.15), residues: 1034 loop : -0.46 (0.10), residues: 3403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1072 time to evaluate : 6.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 259 outliers final: 143 residues processed: 1218 average time/residue: 2.1655 time to fit residues: 3624.9531 Evaluate side-chains 1180 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1037 time to evaluate : 6.606 Switching outliers to nearest non-outliers outliers start: 143 outliers final: 95 residues processed: 51 average time/residue: 1.1685 time to fit residues: 108.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 940 optimal weight: 7.9990 chunk 715 optimal weight: 7.9990 chunk 493 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 454 optimal weight: 20.0000 chunk 638 optimal weight: 7.9990 chunk 955 optimal weight: 0.9980 chunk 1011 optimal weight: 0.9980 chunk 498 optimal weight: 6.9990 chunk 905 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN C 296 GLN G 79 GLN G 221 ASN L 114 GLN M 41 GLN M 59 ASN M 62 GLN N 195 ASN O 182 ASN R 27 ASN R 36 ASN S 122 HIS S 157 GLN X 65 GLN Z 123 GLN b 26 GLN b 124 GLN b 166 ASN b 323 GLN c 75 ASN e 52 GLN g 3 GLN g 61 GLN n 69 GLN p 32 GLN q 230 ASN q 381 HIS s 7 GLN t 209 GLN u 110 ASN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 133419 Z= 0.245 Angle : 0.607 12.384 194286 Z= 0.314 Chirality : 0.039 0.282 24157 Planarity : 0.005 0.071 13679 Dihedral : 14.462 179.316 43792 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 4.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 7630 helix: 1.68 (0.09), residues: 3189 sheet: -0.17 (0.15), residues: 1018 loop : -0.50 (0.10), residues: 3423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1055 time to evaluate : 6.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 288 outliers final: 161 residues processed: 1230 average time/residue: 2.1504 time to fit residues: 3673.7773 Evaluate side-chains 1187 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1026 time to evaluate : 6.613 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 115 residues processed: 46 average time/residue: 1.2064 time to fit residues: 100.4553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 842 optimal weight: 7.9990 chunk 573 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 752 optimal weight: 5.9990 chunk 417 optimal weight: 8.9990 chunk 862 optimal weight: 6.9990 chunk 698 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 516 optimal weight: 3.9990 chunk 907 optimal weight: 0.0050 chunk 255 optimal weight: 20.0000 overall best weight: 3.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN G 59 GLN G 79 GLN G 221 ASN H 183 HIS L 114 GLN M 41 GLN O 182 ASN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN U 87 ASN X 19 ASN X 65 GLN Z 123 GLN a 65 GLN b 26 GLN b 124 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN n 69 GLN p 25 GLN p 32 GLN q 230 ASN s 7 GLN t 25 ASN t 209 GLN t 291 GLN u 110 ASN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 133419 Z= 0.201 Angle : 0.565 11.728 194286 Z= 0.294 Chirality : 0.037 0.279 24157 Planarity : 0.004 0.051 13679 Dihedral : 14.400 179.186 43792 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 7630 helix: 1.82 (0.09), residues: 3169 sheet: -0.17 (0.15), residues: 1031 loop : -0.45 (0.10), residues: 3430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1054 time to evaluate : 6.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 271 outliers final: 169 residues processed: 1234 average time/residue: 2.1088 time to fit residues: 3594.5108 Evaluate side-chains 1190 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1021 time to evaluate : 6.568 Switching outliers to nearest non-outliers outliers start: 169 outliers final: 127 residues processed: 42 average time/residue: 1.2509 time to fit residues: 94.3300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 340 optimal weight: 4.9990 chunk 910 optimal weight: 4.9990 chunk 199 optimal weight: 30.0000 chunk 593 optimal weight: 30.0000 chunk 249 optimal weight: 10.0000 chunk 1012 optimal weight: 5.9990 chunk 840 optimal weight: 10.0000 chunk 468 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 531 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN C 237 GLN G 59 GLN G 79 GLN G 221 ASN H 183 HIS L 114 GLN M 41 GLN O 182 ASN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN X 19 ASN X 65 GLN Z 123 GLN a 65 GLN b 26 GLN b 124 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 428 GLN p 25 GLN q 230 ASN s 7 GLN u 110 ASN ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 133419 Z= 0.277 Angle : 0.637 11.643 194286 Z= 0.328 Chirality : 0.040 0.283 24157 Planarity : 0.005 0.059 13679 Dihedral : 14.517 179.220 43792 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 7630 helix: 1.63 (0.09), residues: 3185 sheet: -0.19 (0.15), residues: 1017 loop : -0.53 (0.10), residues: 3428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1026 time to evaluate : 6.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 280 outliers final: 187 residues processed: 1214 average time/residue: 2.0978 time to fit residues: 3524.0756 Evaluate side-chains 1191 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1004 time to evaluate : 6.569 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 143 residues processed: 44 average time/residue: 1.1940 time to fit residues: 96.2144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 975 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 576 optimal weight: 0.3980 chunk 739 optimal weight: 7.9990 chunk 572 optimal weight: 8.9990 chunk 851 optimal weight: 0.8980 chunk 565 optimal weight: 7.9990 chunk 1008 optimal weight: 0.9990 chunk 630 optimal weight: 0.3980 chunk 614 optimal weight: 20.0000 chunk 465 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN G 59 GLN G 79 GLN G 221 ASN H 183 HIS L 114 GLN M 41 GLN O 182 ASN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN X 19 ASN X 65 GLN Z 103 GLN Z 123 GLN b 26 GLN b 124 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN n 69 GLN n 428 GLN p 25 GLN q 230 ASN s 7 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 133419 Z= 0.148 Angle : 0.520 11.217 194286 Z= 0.273 Chirality : 0.035 0.269 24157 Planarity : 0.004 0.053 13679 Dihedral : 14.317 178.849 43792 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 7630 helix: 1.94 (0.09), residues: 3174 sheet: -0.14 (0.16), residues: 1023 loop : -0.39 (0.10), residues: 3433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1050 time to evaluate : 7.047 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 237 outliers final: 156 residues processed: 1223 average time/residue: 2.1530 time to fit residues: 3663.2907 Evaluate side-chains 1165 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1009 time to evaluate : 6.673 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 133 residues processed: 24 average time/residue: 1.0986 time to fit residues: 53.9460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 623 optimal weight: 9.9990 chunk 402 optimal weight: 0.6980 chunk 602 optimal weight: 9.9990 chunk 303 optimal weight: 30.0000 chunk 198 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 640 optimal weight: 9.9990 chunk 686 optimal weight: 9.9990 chunk 498 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 792 optimal weight: 3.9990 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN F 225 GLN G 59 GLN G 79 GLN G 221 ASN H 183 HIS L 114 GLN M 41 GLN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN X 65 GLN Z 123 GLN a 65 GLN b 26 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN n 428 GLN p 25 GLN p 32 GLN q 230 ASN s 7 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 133419 Z= 0.343 Angle : 0.699 11.695 194286 Z= 0.356 Chirality : 0.043 0.285 24157 Planarity : 0.006 0.064 13679 Dihedral : 14.583 179.187 43792 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.57 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 7630 helix: 1.53 (0.09), residues: 3184 sheet: -0.17 (0.16), residues: 995 loop : -0.58 (0.10), residues: 3451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1010 time to evaluate : 6.703 Fit side-chains revert: symmetry clash outliers start: 255 outliers final: 188 residues processed: 1192 average time/residue: 2.1371 time to fit residues: 3519.2623 Evaluate side-chains 1191 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1003 time to evaluate : 6.588 Switching outliers to nearest non-outliers outliers start: 188 outliers final: 150 residues processed: 39 average time/residue: 1.1850 time to fit residues: 85.6809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 917 optimal weight: 20.0000 chunk 965 optimal weight: 20.0000 chunk 881 optimal weight: 8.9990 chunk 939 optimal weight: 10.0000 chunk 565 optimal weight: 5.9990 chunk 409 optimal weight: 5.9990 chunk 737 optimal weight: 2.9990 chunk 288 optimal weight: 30.0000 chunk 848 optimal weight: 8.9990 chunk 888 optimal weight: 4.9990 chunk 936 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN G 79 GLN G 221 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN H 183 HIS L 114 GLN M 41 GLN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN V 98 ASN X 65 GLN Z 123 GLN b 26 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN p 25 GLN p 32 GLN q 230 ASN r 244 GLN s 7 GLN u 110 ASN y 145 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 133419 Z= 0.296 Angle : 0.659 11.683 194286 Z= 0.339 Chirality : 0.041 0.288 24157 Planarity : 0.005 0.065 13679 Dihedral : 14.585 179.436 43792 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.00 % Favored : 96.99 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 7630 helix: 1.49 (0.09), residues: 3181 sheet: -0.18 (0.16), residues: 991 loop : -0.61 (0.10), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1002 time to evaluate : 6.702 Fit side-chains revert: symmetry clash outliers start: 222 outliers final: 178 residues processed: 1171 average time/residue: 2.1296 time to fit residues: 3439.9617 Evaluate side-chains 1166 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 988 time to evaluate : 5.966 Switching outliers to nearest non-outliers outliers start: 178 outliers final: 153 residues processed: 27 average time/residue: 0.9402 time to fit residues: 54.1012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 616 optimal weight: 5.9990 chunk 993 optimal weight: 9.9990 chunk 606 optimal weight: 10.0000 chunk 471 optimal weight: 7.9990 chunk 690 optimal weight: 0.0040 chunk 1042 optimal weight: 4.9990 chunk 959 optimal weight: 1.9990 chunk 829 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 640 optimal weight: 9.9990 chunk 508 optimal weight: 5.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN G 79 GLN G 221 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 183 HIS L 114 GLN M 41 GLN R 27 ASN R 34 GLN R 36 ASN S 122 HIS V 98 ASN X 19 ASN X 65 GLN Z 123 GLN b 26 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN p 25 GLN p 32 GLN q 230 ASN s 7 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 133419 Z= 0.215 Angle : 0.599 11.953 194286 Z= 0.313 Chirality : 0.038 0.291 24157 Planarity : 0.005 0.076 13679 Dihedral : 14.555 179.045 43792 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.09), residues: 7630 helix: 1.62 (0.09), residues: 3175 sheet: -0.17 (0.16), residues: 997 loop : -0.57 (0.10), residues: 3458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15260 Ramachandran restraints generated. 7630 Oldfield, 0 Emsley, 7630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 992 time to evaluate : 6.693 Fit side-chains revert: symmetry clash outliers start: 206 outliers final: 176 residues processed: 1160 average time/residue: 2.1620 time to fit residues: 3467.6412 Evaluate side-chains 1159 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 983 time to evaluate : 6.610 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 154 residues processed: 24 average time/residue: 1.2475 time to fit residues: 57.6875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 659 optimal weight: 9.9990 chunk 883 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 765 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 30.0000 chunk 831 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 chunk 853 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN G 79 GLN G 221 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS L 114 GLN M 41 GLN R 27 ASN R 34 GLN R 36 ASN S 122 HIS V 98 ASN X 19 ASN X 65 GLN Z 123 GLN b 26 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN g 61 GLN p 25 GLN p 32 GLN q 230 ASN s 7 GLN t 252 HIS u 110 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.181723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.132954 restraints weight = 107303.088| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.67 r_work: 0.3097 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 133419 Z= 0.289 Angle : 0.661 12.105 194286 Z= 0.340 Chirality : 0.041 0.289 24157 Planarity : 0.006 0.065 13679 Dihedral : 14.584 179.294 43792 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.72 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.09), residues: 7630 helix: 1.50 (0.09), residues: 3180 sheet: -0.20 (0.16), residues: 997 loop : -0.62 (0.10), residues: 3453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47455.31 seconds wall clock time: 820 minutes 49.44 seconds (49249.44 seconds total)