Starting phenix.real_space_refine on Sat Feb 17 02:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/02_2024/7u0h_26259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/02_2024/7u0h_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_26259/02_2024/7u0h_26259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/02_2024/7u0h_26259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/02_2024/7u0h_26259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0h_26259/02_2024/7u0h_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-dev-5238/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: 46.46, per 1000 atoms: 0.37 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: 47.07 Conformation dependent library (CDL) restraints added in 9.1 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: 41.45 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: 154.28 Time building geometry restraints manager: 51.19 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: 76898 35.69 - 71.38: 7017 71.38 - 107.07: 742 107.07 - 142.76: 14 142.76 - 178.45: 41 Dihedral angle restraints: 84712 sinusoidal: 62103 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 84709 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 18.400 Check model and map are aligned: 1.330 Set scattering table: 0.840 Process input model: 395.160 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.280 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 433.890 ------------------------------------------------------------------------------- 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 : 21.440 178.448 70050 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 % Allowed : 6.43 % Favored : 92.61 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP e 32 HIS 0.007 0.001 HIS C 311 PHE 0.032 0.002 PHE F 229 TYR 0.021 0.002 TYR o 110 ARG 0.006 0.001 ARG g 74 *********************** 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 : 6.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.5914 (mttt) cc_final: 0.5554 (mtpm) REVERT: A 168 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7970 (t) REVERT: B 324 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8378 (t) REVERT: C 73 ARG cc_start: 0.8403 (mtt180) cc_final: 0.8147 (mtt180) REVERT: C 272 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8264 (m) REVERT: E 89 THR cc_start: 0.8182 (t) cc_final: 0.7818 (m) REVERT: E 148 GLU cc_start: 0.5943 (tp30) cc_final: 0.5137 (tp30) REVERT: F 55 TYR cc_start: 0.8304 (m-10) cc_final: 0.7582 (m-10) REVERT: G 65 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7992 (mt) REVERT: G 100 GLU cc_start: 0.7282 (tt0) cc_final: 0.6961 (tt0) REVERT: G 171 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7851 (mttp) REVERT: G 219 ASP cc_start: 0.6447 (m-30) cc_final: 0.6160 (m-30) REVERT: H 90 MET cc_start: 0.8460 (mtp) cc_final: 0.8230 (mtp) REVERT: L 52 ASP cc_start: 0.8444 (p0) cc_final: 0.7977 (p0) REVERT: L 106 GLN cc_start: 0.7779 (tp40) cc_final: 0.7371 (mm-40) REVERT: L 114 GLN cc_start: 0.7476 (tp40) cc_final: 0.7107 (tp-100) REVERT: M 82 SER cc_start: 0.8561 (t) cc_final: 0.8303 (m) REVERT: M 92 GLU cc_start: 0.6990 (mp0) cc_final: 0.6605 (mp0) REVERT: M 106 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7402 (mtm110) REVERT: P 75 GLU cc_start: 0.8296 (tt0) cc_final: 0.8069 (tt0) REVERT: P 127 ARG cc_start: 0.6371 (ptt180) cc_final: 0.6094 (pmm-80) REVERT: P 140 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6833 (mt-10) REVERT: P 152 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6770 (mt-10) REVERT: R 59 SER cc_start: 0.8784 (p) cc_final: 0.8427 (t) REVERT: R 82 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7850 (mppt) REVERT: S 60 SER cc_start: 0.7080 (t) cc_final: 0.6504 (p) REVERT: S 110 MET cc_start: 0.8016 (mmm) cc_final: 0.7594 (mmm) REVERT: V 12 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7653 (ttt180) REVERT: V 24 ASN cc_start: 0.7987 (m-40) cc_final: 0.7763 (m-40) REVERT: V 32 ARG cc_start: 0.6650 (mmt-90) cc_final: 0.6308 (mtp85) REVERT: V 109 MET cc_start: 0.7388 (mmp) cc_final: 0.7136 (mmp) REVERT: V 120 LYS cc_start: 0.7485 (ttpt) cc_final: 0.7147 (ttpp) REVERT: W 109 VAL cc_start: 0.5341 (OUTLIER) cc_final: 0.5084 (p) REVERT: W 129 THR cc_start: 0.5517 (p) cc_final: 0.5152 (m) REVERT: W 211 SER cc_start: 0.4964 (t) cc_final: 0.4746 (p) REVERT: X 22 LYS cc_start: 0.7304 (tptt) cc_final: 0.7096 (tmtt) REVERT: X 27 ARG cc_start: 0.6865 (mtt-85) cc_final: 0.6547 (mtp85) REVERT: Z 27 LYS cc_start: 0.7378 (mttt) cc_final: 0.6843 (tppp) REVERT: a 135 GLU cc_start: 0.7377 (tt0) cc_final: 0.7094 (tt0) REVERT: b 82 MET cc_start: 0.6194 (mtt) cc_final: 0.5458 (mmt) REVERT: b 87 GLU cc_start: 0.5443 (tt0) cc_final: 0.5136 (mm-30) REVERT: b 106 GLU cc_start: 0.6194 (tt0) cc_final: 0.5865 (tt0) REVERT: b 135 ARG cc_start: 0.7377 (mtt-85) cc_final: 0.7080 (mtt180) REVERT: b 141 LYS cc_start: 0.6936 (mtmt) cc_final: 0.6469 (mttt) REVERT: b 142 LYS cc_start: 0.6261 (mttt) cc_final: 0.6008 (mtpt) REVERT: b 146 PRO cc_start: 0.6565 (Cg_exo) cc_final: 0.6060 (Cg_endo) REVERT: b 166 ASN cc_start: 0.5663 (m-40) cc_final: 0.5451 (m110) REVERT: b 220 ASP cc_start: 0.6637 (t0) cc_final: 0.6186 (t0) REVERT: b 241 TYR cc_start: 0.5463 (m-80) cc_final: 0.5169 (m-10) REVERT: b 328 VAL cc_start: 0.5550 (m) cc_final: 0.5240 (p) REVERT: b 401 ASP cc_start: 0.6049 (m-30) cc_final: 0.5644 (m-30) REVERT: b 442 TYR cc_start: 0.7503 (m-80) cc_final: 0.7259 (m-80) REVERT: b 490 LYS cc_start: 0.5970 (mttp) cc_final: 0.5342 (mmtt) REVERT: b 501 LYS cc_start: 0.6210 (mtmm) cc_final: 0.5873 (mptp) REVERT: b 506 GLU cc_start: 0.6378 (mt-10) cc_final: 0.6177 (mt-10) REVERT: b 519 MET cc_start: 0.4937 (mmm) cc_final: 0.4216 (mmm) REVERT: b 531 MET cc_start: 0.3569 (ttt) cc_final: 0.3159 (ttm) REVERT: c 16 LEU cc_start: 0.6214 (tp) cc_final: 0.5922 (tt) REVERT: c 35 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7852 (ttp80) REVERT: c 84 LEU cc_start: 0.7213 (mt) cc_final: 0.6870 (mt) REVERT: d 7 VAL cc_start: 0.7253 (t) cc_final: 0.6787 (t) REVERT: d 74 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7278 (ttm170) REVERT: e 67 SER cc_start: 0.7962 (m) cc_final: 0.7730 (p) REVERT: f 3 GLU cc_start: 0.6996 (pt0) cc_final: 0.6642 (pm20) REVERT: f 92 LYS cc_start: 0.8220 (pttm) cc_final: 0.7956 (tttt) REVERT: g 19 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7941 (mttm) REVERT: g 29 ILE cc_start: 0.8728 (pt) cc_final: 0.8524 (pp) REVERT: g 61 GLN cc_start: 0.8455 (mt0) cc_final: 0.8198 (mt0) REVERT: g 64 THR cc_start: 0.7796 (m) cc_final: 0.7448 (p) REVERT: h 20 GLN cc_start: 0.8430 (tt0) cc_final: 0.8130 (tt0) REVERT: i 9 ILE cc_start: 0.8260 (pt) cc_final: 0.8056 (tt) REVERT: i 26 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.6160 (tt) REVERT: i 42 SER cc_start: 0.8349 (p) cc_final: 0.8131 (m) REVERT: j 64 MET cc_start: 0.8076 (mtm) cc_final: 0.7872 (mtm) REVERT: n 69 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7244 (tp-100) REVERT: n 120 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6505 (mt-10) REVERT: n 205 PHE cc_start: 0.7452 (m-80) cc_final: 0.7209 (m-80) REVERT: o 104 GLU cc_start: 0.6700 (mp0) cc_final: 0.6279 (mp0) REVERT: p 11 THR cc_start: 0.8140 (m) cc_final: 0.7882 (m) REVERT: p 29 LEU cc_start: 0.8157 (mp) cc_final: 0.7953 (mp) REVERT: q 210 GLU cc_start: 0.5390 (pt0) cc_final: 0.5064 (pt0) REVERT: q 216 GLU cc_start: 0.5309 (tt0) cc_final: 0.4982 (tp30) REVERT: q 227 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.6079 (p90) REVERT: q 245 GLU cc_start: 0.4757 (tp30) cc_final: 0.4433 (mp0) REVERT: q 351 GLU cc_start: 0.3635 (mt-10) cc_final: 0.1851 (mm-30) REVERT: q 452 LYS cc_start: 0.5710 (ttmm) cc_final: 0.5428 (tptm) REVERT: r 35 ILE cc_start: 0.8779 (mt) cc_final: 0.8547 (mm) REVERT: r 55 TYR cc_start: 0.8144 (t80) cc_final: 0.7923 (t80) REVERT: r 150 MET cc_start: 0.4189 (ptm) cc_final: 0.3847 (tmm) REVERT: s 1 MET cc_start: 0.5066 (tpt) cc_final: 0.4829 (tpt) REVERT: s 7 GLN cc_start: 0.7257 (mm110) cc_final: 0.6908 (mt0) REVERT: t 41 ARG cc_start: 0.5990 (ptp90) cc_final: 0.5323 (ttp-110) REVERT: t 267 PHE cc_start: 0.7088 (t80) cc_final: 0.6813 (t80) REVERT: u 104 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7201 (tm-30) REVERT: w 310 LEU cc_start: 0.7285 (mt) cc_final: 0.7051 (mt) REVERT: w 387 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.5751 (mtp) REVERT: w 815 LYS cc_start: 0.5924 (mmmt) cc_final: 0.5513 (mtmt) REVERT: y 131 ASP cc_start: 0.7075 (t0) cc_final: 0.6826 (t0) REVERT: y 223 ARG cc_start: 0.5798 (mtp-110) cc_final: 0.5523 (ttp-110) outliers start: 64 outliers final: 27 residues processed: 1578 average time/residue: 2.1455 time to fit residues: 4607.3240 Evaluate side-chains 1182 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1147 time to evaluate : 5.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain w residue 387 MET 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: 10.0000 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: 3.6150 ------------------------------------------------------------------------------- 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 M 41 GLN M 62 GLN 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 323 GLN e 52 GLN g 52 GLN h 16 GLN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 32 GLN q 230 ASN r 13 GLN ** r 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 133419 Z= 0.208 Angle : 0.580 8.990 194286 Z= 0.302 Chirality : 0.038 0.290 24157 Planarity : 0.005 0.052 13679 Dihedral : 22.672 179.967 54128 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.48 % Allowed : 13.50 % Favored : 83.02 % 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: 0.76 (0.09), residues: 7630 helix: 1.76 (0.09), residues: 3192 sheet: -0.19 (0.15), residues: 1035 loop : -0.45 (0.10), residues: 3403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 32 HIS 0.007 0.001 HIS C 311 PHE 0.027 0.002 PHE F 229 TYR 0.027 0.002 TYR C 120 ARG 0.008 0.001 ARG j 24 *********************** 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 1377 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1145 time to evaluate : 6.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6452 (ttt-90) cc_final: 0.6240 (ttt-90) REVERT: A 93 LYS cc_start: 0.5937 (mttt) cc_final: 0.5521 (mtpm) REVERT: A 168 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7926 (t) REVERT: C 73 ARG cc_start: 0.8431 (mtt180) cc_final: 0.8219 (mtt180) REVERT: C 272 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8266 (m) REVERT: C 319 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7048 (tttt) REVERT: E 89 THR cc_start: 0.8148 (t) cc_final: 0.7807 (m) REVERT: E 148 GLU cc_start: 0.5858 (tp30) cc_final: 0.5066 (tp30) REVERT: F 55 TYR cc_start: 0.8308 (m-10) cc_final: 0.7582 (m-10) REVERT: F 59 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5632 (tp30) REVERT: G 51 LYS cc_start: 0.7391 (tttm) cc_final: 0.7165 (tttt) REVERT: G 100 GLU cc_start: 0.7228 (tt0) cc_final: 0.6881 (tt0) REVERT: G 171 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7837 (mttp) REVERT: G 208 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6370 (mm-30) REVERT: G 219 ASP cc_start: 0.6327 (m-30) cc_final: 0.6042 (m-30) REVERT: H 42 ASP cc_start: 0.7429 (m-30) cc_final: 0.7113 (m-30) REVERT: K 76 LYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4612 (tppp) REVERT: K 80 LEU cc_start: 0.5120 (tt) cc_final: 0.4774 (tt) REVERT: K 153 GLU cc_start: 0.4642 (mt-10) cc_final: 0.4308 (mt-10) REVERT: K 160 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7526 (mp) REVERT: L 52 ASP cc_start: 0.8420 (p0) cc_final: 0.7972 (p0) REVERT: L 106 GLN cc_start: 0.7829 (tp40) cc_final: 0.7441 (mm-40) REVERT: L 114 GLN cc_start: 0.7437 (tp40) cc_final: 0.7067 (tp-100) REVERT: M 82 SER cc_start: 0.8439 (t) cc_final: 0.8216 (m) REVERT: M 92 GLU cc_start: 0.7039 (mp0) cc_final: 0.6706 (mp0) REVERT: M 106 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7692 (mtp180) REVERT: N 11 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: P 23 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7404 (mpp-170) REVERT: P 75 GLU cc_start: 0.8315 (tt0) cc_final: 0.8023 (tt0) REVERT: P 140 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6751 (mt-10) REVERT: P 152 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6757 (mt-10) REVERT: Q 116 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6736 (tttt) REVERT: R 59 SER cc_start: 0.8782 (p) cc_final: 0.8403 (t) REVERT: R 82 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7820 (mppt) REVERT: S 13 ARG cc_start: 0.5245 (ttm110) cc_final: 0.4985 (ttm110) REVERT: S 60 SER cc_start: 0.7108 (t) cc_final: 0.6722 (t) REVERT: S 110 MET cc_start: 0.8062 (mmm) cc_final: 0.7698 (mmm) REVERT: U 74 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6518 (tppp) REVERT: V 32 ARG cc_start: 0.6725 (mmt-90) cc_final: 0.6348 (mtp85) REVERT: V 59 MET cc_start: 0.8228 (mmm) cc_final: 0.7977 (mmp) REVERT: V 109 MET cc_start: 0.7405 (mmp) cc_final: 0.7065 (mmp) REVERT: V 120 LYS cc_start: 0.7524 (ttpt) cc_final: 0.7263 (ttpp) REVERT: W 46 ASP cc_start: 0.4273 (OUTLIER) cc_final: 0.3992 (m-30) REVERT: W 85 TYR cc_start: 0.4839 (OUTLIER) cc_final: 0.2827 (t80) REVERT: W 109 VAL cc_start: 0.5280 (OUTLIER) cc_final: 0.5015 (p) REVERT: W 121 ARG cc_start: 0.5211 (mmp80) cc_final: 0.4837 (mmm160) REVERT: W 129 THR cc_start: 0.5528 (p) cc_final: 0.5124 (m) REVERT: W 205 GLN cc_start: 0.7031 (tp40) cc_final: 0.6655 (tp40) REVERT: X 27 ARG cc_start: 0.6853 (mtt-85) cc_final: 0.6538 (mtp85) REVERT: Z 27 LYS cc_start: 0.7440 (mttt) cc_final: 0.6868 (tppp) REVERT: a 135 GLU cc_start: 0.7417 (tt0) cc_final: 0.7099 (tt0) REVERT: b 3 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.4853 (mp) REVERT: b 82 MET cc_start: 0.6200 (mtt) cc_final: 0.5497 (mmt) REVERT: b 87 GLU cc_start: 0.5449 (tt0) cc_final: 0.5146 (mm-30) REVERT: b 106 GLU cc_start: 0.6159 (tt0) cc_final: 0.5856 (tt0) REVERT: b 135 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.7042 (mtt180) REVERT: b 141 LYS cc_start: 0.6903 (mtmt) cc_final: 0.6533 (mttt) REVERT: b 146 PRO cc_start: 0.6522 (Cg_exo) cc_final: 0.6135 (Cg_endo) REVERT: b 185 ARG cc_start: 0.5320 (ptt180) cc_final: 0.4934 (ptt90) REVERT: b 220 ASP cc_start: 0.6572 (t0) cc_final: 0.6119 (t0) REVERT: b 328 VAL cc_start: 0.5569 (m) cc_final: 0.5250 (p) REVERT: b 401 ASP cc_start: 0.6067 (m-30) cc_final: 0.5731 (m-30) REVERT: b 442 TYR cc_start: 0.7495 (m-80) cc_final: 0.7252 (m-80) REVERT: b 490 LYS cc_start: 0.5828 (mttp) cc_final: 0.5276 (mmmt) REVERT: b 501 LYS cc_start: 0.6240 (mtmm) cc_final: 0.5881 (mptp) REVERT: b 519 MET cc_start: 0.4870 (mmm) cc_final: 0.4060 (mmm) REVERT: b 531 MET cc_start: 0.3552 (ttt) cc_final: 0.3261 (ttm) REVERT: b 535 MET cc_start: 0.2481 (mmt) cc_final: 0.2165 (mmt) REVERT: c 74 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6970 (p0) REVERT: d 7 VAL cc_start: 0.7358 (t) cc_final: 0.6859 (t) REVERT: e 67 SER cc_start: 0.7931 (m) cc_final: 0.7723 (p) REVERT: e 90 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7917 (mtmm) REVERT: f 92 LYS cc_start: 0.8076 (pttm) cc_final: 0.7788 (tttt) REVERT: g 19 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7942 (mttm) REVERT: g 61 GLN cc_start: 0.8413 (mt0) cc_final: 0.8109 (mt0) REVERT: g 64 THR cc_start: 0.7900 (m) cc_final: 0.7533 (p) REVERT: h 20 GLN cc_start: 0.8436 (tt0) cc_final: 0.8161 (tt0) REVERT: h 84 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7754 (mtpt) REVERT: i 42 SER cc_start: 0.8321 (p) cc_final: 0.8118 (m) REVERT: k 13 GLU cc_start: 0.6482 (mm-30) cc_final: 0.5799 (mm-30) REVERT: k 74 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6530 (tttp) REVERT: n 54 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7833 (mtpt) REVERT: n 120 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6593 (mt-10) REVERT: n 198 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.6755 (ttp-170) REVERT: n 205 PHE cc_start: 0.7423 (m-80) cc_final: 0.7197 (m-80) REVERT: n 215 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: o 104 GLU cc_start: 0.6723 (mp0) cc_final: 0.6321 (mp0) REVERT: p 7 LYS cc_start: 0.6959 (ttpt) cc_final: 0.6577 (ttpt) REVERT: p 29 LEU cc_start: 0.8202 (mp) cc_final: 0.7966 (mp) REVERT: p 89 MET cc_start: 0.4106 (tpt) cc_final: 0.3847 (tmm) REVERT: q 210 GLU cc_start: 0.5377 (pt0) cc_final: 0.5065 (pt0) REVERT: q 351 GLU cc_start: 0.3593 (mt-10) cc_final: 0.1838 (mm-30) REVERT: q 452 LYS cc_start: 0.5776 (ttmm) cc_final: 0.5448 (tptm) REVERT: r 35 ILE cc_start: 0.8775 (mt) cc_final: 0.8511 (mm) REVERT: r 55 TYR cc_start: 0.8187 (t80) cc_final: 0.7975 (t80) REVERT: r 150 MET cc_start: 0.4155 (ptm) cc_final: 0.3808 (tmm) REVERT: s 1 MET cc_start: 0.5059 (tpt) cc_final: 0.4815 (tpt) REVERT: s 5 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7139 (tttm) REVERT: s 7 GLN cc_start: 0.7255 (mm110) cc_final: 0.6901 (mt0) REVERT: t 207 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7708 (mp) REVERT: t 237 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: t 267 PHE cc_start: 0.7106 (t80) cc_final: 0.6829 (t80) REVERT: u 104 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7149 (tm-30) REVERT: w 380 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5980 (mtpt) REVERT: w 429 MET cc_start: 0.2203 (OUTLIER) cc_final: 0.0975 (mmt) REVERT: w 815 LYS cc_start: 0.6077 (mmmt) cc_final: 0.5767 (mtmt) REVERT: y 8 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: y 99 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6467 (tm-30) outliers start: 232 outliers final: 107 residues processed: 1265 average time/residue: 2.0734 time to fit residues: 3597.6083 Evaluate side-chains 1217 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1083 time to evaluate : 6.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 215 PHE Chi-restraints excluded: chain n residue 218 MET Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 429 MET Chi-restraints excluded: chain w residue 714 THR Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 209 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 527 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 chunk 790 optimal weight: 0.7980 chunk 646 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 951 optimal weight: 0.9990 chunk 1027 optimal weight: 9.9990 chunk 847 optimal weight: 8.9990 chunk 943 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 763 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 M 41 GLN M 62 GLN 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 e 52 GLN n 69 GLN n 428 GLN q 230 ASN q 355 ASN q 381 HIS ** r 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 GLN u 110 ASN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 133419 Z= 0.211 Angle : 0.576 9.134 194286 Z= 0.300 Chirality : 0.037 0.278 24157 Planarity : 0.005 0.053 13679 Dihedral : 22.610 179.384 54111 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.05 % Allowed : 14.76 % Favored : 81.19 % 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: 1.79 (0.09), residues: 3183 sheet: -0.16 (0.15), residues: 1035 loop : -0.45 (0.10), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 32 HIS 0.007 0.001 HIS C 311 PHE 0.028 0.002 PHE F 229 TYR 0.019 0.002 TYR C 194 ARG 0.008 0.001 ARG j 24 *********************** 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 1386 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1116 time to evaluate : 6.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6596 (ttt-90) cc_final: 0.6243 (ttt-90) REVERT: A 93 LYS cc_start: 0.5920 (mttt) cc_final: 0.5495 (mtpm) REVERT: B 34 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7412 (tppp) REVERT: B 74 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: B 318 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7397 (mttp) REVERT: C 73 ARG cc_start: 0.8449 (mtt180) cc_final: 0.8195 (mtt180) REVERT: C 272 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8264 (m) REVERT: C 319 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7085 (tttt) REVERT: E 77 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7309 (mtp-110) REVERT: E 89 THR cc_start: 0.8212 (t) cc_final: 0.7803 (m) REVERT: E 148 GLU cc_start: 0.5860 (tp30) cc_final: 0.5070 (tp30) REVERT: F 55 TYR cc_start: 0.8316 (m-10) cc_final: 0.7576 (m-10) REVERT: G 51 LYS cc_start: 0.7455 (tttm) cc_final: 0.7205 (tttt) REVERT: G 65 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7955 (mt) REVERT: G 100 GLU cc_start: 0.7324 (tt0) cc_final: 0.6977 (tt0) REVERT: G 107 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6335 (tp30) REVERT: G 171 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7826 (mttp) REVERT: G 208 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6362 (mm-30) REVERT: G 219 ASP cc_start: 0.6407 (m-30) cc_final: 0.6086 (m-30) REVERT: K 76 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4683 (tppp) REVERT: K 80 LEU cc_start: 0.5059 (tt) cc_final: 0.4795 (tt) REVERT: K 153 GLU cc_start: 0.4788 (mt-10) cc_final: 0.4542 (tp30) REVERT: K 219 LEU cc_start: 0.5438 (pt) cc_final: 0.5229 (tp) REVERT: L 52 ASP cc_start: 0.8381 (p0) cc_final: 0.7953 (p0) REVERT: L 106 GLN cc_start: 0.7828 (tp40) cc_final: 0.7447 (mm-40) REVERT: M 82 SER cc_start: 0.8437 (t) cc_final: 0.8203 (m) REVERT: M 92 GLU cc_start: 0.7191 (mp0) cc_final: 0.6848 (mp0) REVERT: M 106 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7686 (mtp180) REVERT: M 128 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: N 11 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7130 (mm-40) REVERT: N 192 LYS cc_start: 0.7560 (ptpp) cc_final: 0.6967 (pttp) REVERT: N 193 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6568 (ttt90) REVERT: P 75 GLU cc_start: 0.8275 (tt0) cc_final: 0.8010 (tt0) REVERT: P 140 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6776 (mt-10) REVERT: P 152 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6748 (mt-10) REVERT: Q 116 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6862 (tttt) REVERT: R 59 SER cc_start: 0.8793 (p) cc_final: 0.8418 (t) REVERT: R 82 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7794 (mppt) REVERT: S 8 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: S 26 ARG cc_start: 0.5965 (mtp180) cc_final: 0.5604 (mtp180) REVERT: S 60 SER cc_start: 0.7208 (t) cc_final: 0.6778 (t) REVERT: S 110 MET cc_start: 0.8070 (mmm) cc_final: 0.7732 (mmm) REVERT: U 74 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6598 (tppp) REVERT: V 32 ARG cc_start: 0.6748 (mmt-90) cc_final: 0.6374 (mtp85) REVERT: V 59 MET cc_start: 0.8267 (mmm) cc_final: 0.7952 (mmp) REVERT: V 109 MET cc_start: 0.7393 (mmp) cc_final: 0.7062 (mmp) REVERT: V 120 LYS cc_start: 0.7434 (ttpt) cc_final: 0.7119 (ttpp) REVERT: W 46 ASP cc_start: 0.4303 (OUTLIER) cc_final: 0.4018 (m-30) REVERT: W 85 TYR cc_start: 0.4813 (OUTLIER) cc_final: 0.2809 (t80) REVERT: W 121 ARG cc_start: 0.5191 (mmp80) cc_final: 0.4957 (mmm160) REVERT: W 129 THR cc_start: 0.5559 (p) cc_final: 0.5080 (m) REVERT: X 27 ARG cc_start: 0.6816 (mtt-85) cc_final: 0.6509 (mtp85) REVERT: Y 6 LEU cc_start: 0.8071 (mt) cc_final: 0.7782 (mp) REVERT: Z 27 LYS cc_start: 0.7262 (mttt) cc_final: 0.6766 (tppp) REVERT: a 135 GLU cc_start: 0.7406 (tt0) cc_final: 0.7137 (tt0) REVERT: b 3 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.4843 (mp) REVERT: b 82 MET cc_start: 0.6279 (mtt) cc_final: 0.5481 (mmt) REVERT: b 106 GLU cc_start: 0.6204 (tt0) cc_final: 0.5882 (tt0) REVERT: b 135 ARG cc_start: 0.7395 (mtt-85) cc_final: 0.7068 (mtt180) REVERT: b 141 LYS cc_start: 0.6922 (mtmt) cc_final: 0.6605 (mttt) REVERT: b 146 PRO cc_start: 0.6514 (Cg_exo) cc_final: 0.6099 (Cg_endo) REVERT: b 220 ASP cc_start: 0.6626 (t0) cc_final: 0.6147 (t0) REVERT: b 318 MET cc_start: 0.4676 (ttp) cc_final: 0.4426 (ttt) REVERT: b 328 VAL cc_start: 0.5550 (m) cc_final: 0.5233 (p) REVERT: b 442 TYR cc_start: 0.7498 (m-80) cc_final: 0.7237 (m-80) REVERT: b 490 LYS cc_start: 0.5724 (mttp) cc_final: 0.5374 (mmmt) REVERT: b 519 MET cc_start: 0.4829 (mmm) cc_final: 0.4050 (mmm) REVERT: c 74 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7099 (p0) REVERT: d 7 VAL cc_start: 0.7361 (t) cc_final: 0.6856 (t) REVERT: e 67 SER cc_start: 0.7959 (m) cc_final: 0.7740 (p) REVERT: f 92 LYS cc_start: 0.8153 (pttm) cc_final: 0.7878 (tttt) REVERT: g 19 LYS cc_start: 0.8182 (mmtm) cc_final: 0.7952 (mttm) REVERT: g 61 GLN cc_start: 0.8419 (mt0) cc_final: 0.8119 (mt0) REVERT: g 64 THR cc_start: 0.7830 (m) cc_final: 0.7459 (p) REVERT: h 20 GLN cc_start: 0.8429 (tt0) cc_final: 0.8128 (tt0) REVERT: h 84 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7679 (mtpt) REVERT: i 42 SER cc_start: 0.8319 (p) cc_final: 0.8116 (m) REVERT: k 29 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7249 (mtpt) REVERT: k 74 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6571 (tttp) REVERT: n 120 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6556 (mt-10) REVERT: n 133 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6062 (p0) REVERT: n 205 PHE cc_start: 0.7418 (m-80) cc_final: 0.7202 (m-80) REVERT: n 453 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6017 (tp) REVERT: o 104 GLU cc_start: 0.6696 (mp0) cc_final: 0.6291 (mp0) REVERT: p 28 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6742 (ttmt) REVERT: p 29 LEU cc_start: 0.8241 (mp) cc_final: 0.7960 (mp) REVERT: q 210 GLU cc_start: 0.5171 (pt0) cc_final: 0.4938 (pt0) REVERT: q 351 GLU cc_start: 0.3552 (mt-10) cc_final: 0.1764 (mm-30) REVERT: q 386 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5129 (pttm) REVERT: q 452 LYS cc_start: 0.5707 (ttmm) cc_final: 0.5433 (tptm) REVERT: r 55 TYR cc_start: 0.8129 (t80) cc_final: 0.7857 (t80) REVERT: r 150 MET cc_start: 0.4162 (ptm) cc_final: 0.3812 (tmm) REVERT: s 1 MET cc_start: 0.4966 (tpt) cc_final: 0.4735 (tpt) REVERT: s 5 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7143 (tttm) REVERT: s 7 GLN cc_start: 0.7258 (mm110) cc_final: 0.6901 (mt0) REVERT: t 48 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6636 (tttt) REVERT: t 73 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6208 (mm-30) REVERT: t 207 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7716 (mp) REVERT: t 267 PHE cc_start: 0.7121 (t80) cc_final: 0.6813 (t80) REVERT: u 104 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7141 (tm-30) REVERT: w 380 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5934 (mtpt) REVERT: w 429 MET cc_start: 0.2137 (OUTLIER) cc_final: 0.0996 (mmt) REVERT: w 815 LYS cc_start: 0.6011 (mmmt) cc_final: 0.5741 (mtmt) REVERT: y 1 MET cc_start: 0.4748 (mtm) cc_final: 0.3864 (mpt) REVERT: y 8 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: y 99 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: y 126 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6116 (mt-10) outliers start: 270 outliers final: 144 residues processed: 1261 average time/residue: 2.0778 time to fit residues: 3605.6056 Evaluate side-chains 1245 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1067 time to evaluate : 6.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 35 GLU Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 291 GLN Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 385 MET Chi-restraints excluded: chain w residue 429 MET Chi-restraints excluded: chain w residue 714 THR Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 209 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 940 optimal weight: 8.9990 chunk 715 optimal weight: 10.0000 chunk 493 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 454 optimal weight: 20.0000 chunk 638 optimal weight: 1.9990 chunk 955 optimal weight: 7.9990 chunk 1011 optimal weight: 3.9990 chunk 498 optimal weight: 5.9990 chunk 905 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 55 HIS O 182 ASN R 27 ASN R 36 ASN S 122 HIS S 157 GLN U 87 ASN V 24 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 n 69 GLN q 230 ASN q 381 HIS ** r 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 209 GLN u 110 ASN ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7552 moved from start: 0.1018 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 : 0.607 9.761 194286 Z= 0.314 Chirality : 0.039 0.279 24157 Planarity : 0.005 0.059 13679 Dihedral : 22.617 179.333 54105 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.58 % Allowed : 15.39 % Favored : 80.03 % 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: 0.68 (0.09), residues: 7630 helix: 1.71 (0.09), residues: 3182 sheet: -0.20 (0.15), residues: 1037 loop : -0.50 (0.10), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 32 HIS 0.008 0.001 HIS C 311 PHE 0.030 0.002 PHE F 229 TYR 0.020 0.002 TYR C 194 ARG 0.009 0.001 ARG j 24 *********************** 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 1366 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1061 time to evaluate : 6.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.5943 (mttt) cc_final: 0.5503 (mtpm) REVERT: B 34 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7395 (tppp) REVERT: B 74 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: B 318 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7348 (mttp) REVERT: C 272 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8269 (m) REVERT: C 319 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7112 (tttt) REVERT: C 338 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7343 (mmpt) REVERT: E 77 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7230 (mtp-110) REVERT: E 89 THR cc_start: 0.8230 (t) cc_final: 0.7752 (m) REVERT: E 143 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5565 (mmmt) REVERT: E 148 GLU cc_start: 0.5897 (tp30) cc_final: 0.5109 (tp30) REVERT: F 55 TYR cc_start: 0.8318 (m-10) cc_final: 0.7588 (m-10) REVERT: F 59 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5741 (tp30) REVERT: G 51 LYS cc_start: 0.7476 (tttm) cc_final: 0.7230 (tttt) REVERT: G 65 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7955 (mt) REVERT: G 208 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6354 (mm-30) REVERT: H 69 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7111 (tpt90) REVERT: H 135 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6189 (mt-10) REVERT: H 183 HIS cc_start: 0.6847 (t-90) cc_final: 0.6619 (t70) REVERT: K 76 LYS cc_start: 0.5348 (OUTLIER) cc_final: 0.4578 (tppp) REVERT: K 80 LEU cc_start: 0.4986 (tt) cc_final: 0.4776 (tt) REVERT: K 133 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5617 (ptpp) REVERT: K 153 GLU cc_start: 0.4756 (mt-10) cc_final: 0.4445 (tt0) REVERT: L 52 ASP cc_start: 0.8376 (p0) cc_final: 0.7944 (p0) REVERT: L 106 GLN cc_start: 0.7828 (tp40) cc_final: 0.7430 (mm-40) REVERT: M 82 SER cc_start: 0.8436 (t) cc_final: 0.8212 (m) REVERT: M 92 GLU cc_start: 0.7132 (mp0) cc_final: 0.6837 (mp0) REVERT: M 106 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7685 (mtp180) REVERT: N 11 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7136 (mm-40) REVERT: N 192 LYS cc_start: 0.7570 (ptpp) cc_final: 0.6952 (pttp) REVERT: N 193 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.6594 (ttt90) REVERT: P 23 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7555 (mpp-170) REVERT: P 75 GLU cc_start: 0.8277 (tt0) cc_final: 0.8021 (tt0) REVERT: P 140 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6833 (mt-10) REVERT: P 152 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6759 (mt-10) REVERT: R 59 SER cc_start: 0.8809 (p) cc_final: 0.8426 (t) REVERT: R 82 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7754 (mppt) REVERT: S 60 SER cc_start: 0.7120 (t) cc_final: 0.6684 (t) REVERT: S 110 MET cc_start: 0.8096 (mmm) cc_final: 0.7648 (mmm) REVERT: U 74 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6598 (tppp) REVERT: V 59 MET cc_start: 0.8277 (mmm) cc_final: 0.7977 (mmp) REVERT: V 109 MET cc_start: 0.7376 (mmp) cc_final: 0.7041 (mmp) REVERT: V 120 LYS cc_start: 0.7421 (ttpt) cc_final: 0.7078 (ttpp) REVERT: W 46 ASP cc_start: 0.4513 (OUTLIER) cc_final: 0.4246 (m-30) REVERT: W 85 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.2809 (t80) REVERT: W 121 ARG cc_start: 0.5301 (mmp80) cc_final: 0.4960 (mmm160) REVERT: W 205 GLN cc_start: 0.7053 (tp40) cc_final: 0.6728 (tp40) REVERT: X 27 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.6480 (mtp85) REVERT: Y 87 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7528 (ptpt) REVERT: Z 27 LYS cc_start: 0.7331 (mttt) cc_final: 0.6895 (tppp) REVERT: a 135 GLU cc_start: 0.7439 (tt0) cc_final: 0.7130 (tt0) REVERT: b 3 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4804 (mp) REVERT: b 38 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6428 (mtmm) REVERT: b 60 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6606 (tptp) REVERT: b 82 MET cc_start: 0.6257 (mtt) cc_final: 0.5431 (mmt) REVERT: b 88 LYS cc_start: 0.5997 (tttp) cc_final: 0.5771 (tttp) REVERT: b 106 GLU cc_start: 0.6225 (tt0) cc_final: 0.5961 (tt0) REVERT: b 135 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.7029 (mtt180) REVERT: b 141 LYS cc_start: 0.6926 (mtmt) cc_final: 0.6617 (mttt) REVERT: b 146 PRO cc_start: 0.6531 (Cg_exo) cc_final: 0.6134 (Cg_endo) REVERT: b 251 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5975 (mp) REVERT: b 328 VAL cc_start: 0.5585 (m) cc_final: 0.5286 (p) REVERT: b 442 TYR cc_start: 0.7499 (m-80) cc_final: 0.7243 (m-80) REVERT: b 448 GLU cc_start: 0.5031 (pm20) cc_final: 0.4534 (pt0) REVERT: b 490 LYS cc_start: 0.5740 (mttp) cc_final: 0.5359 (mmmt) REVERT: b 519 MET cc_start: 0.4888 (mmm) cc_final: 0.3942 (mmm) REVERT: b 531 MET cc_start: 0.3376 (ttt) cc_final: 0.3054 (ttm) REVERT: c 14 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6201 (tt) REVERT: c 16 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6417 (tt) REVERT: c 74 ASN cc_start: 0.7405 (p0) cc_final: 0.7161 (p0) REVERT: d 7 VAL cc_start: 0.7280 (t) cc_final: 0.6860 (t) REVERT: e 67 SER cc_start: 0.7960 (m) cc_final: 0.7739 (p) REVERT: f 92 LYS cc_start: 0.8151 (pttm) cc_final: 0.7879 (tttt) REVERT: g 19 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7941 (mttm) REVERT: g 51 LEU cc_start: 0.7806 (pt) cc_final: 0.7286 (mp) REVERT: g 61 GLN cc_start: 0.8421 (mt0) cc_final: 0.8110 (mt0) REVERT: g 64 THR cc_start: 0.7908 (m) cc_final: 0.7546 (p) REVERT: i 42 SER cc_start: 0.8321 (p) cc_final: 0.8116 (m) REVERT: j 32 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: k 16 ARG cc_start: 0.6254 (mtm110) cc_final: 0.5879 (mtm110) REVERT: k 29 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7229 (mtpt) REVERT: k 74 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6514 (tttp) REVERT: n 34 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8006 (mtm180) REVERT: n 120 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6633 (mt-10) REVERT: n 133 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6101 (p0) REVERT: n 205 PHE cc_start: 0.7383 (m-80) cc_final: 0.7177 (m-80) REVERT: n 453 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.5956 (tp) REVERT: o 104 GLU cc_start: 0.6667 (mp0) cc_final: 0.6219 (mp0) REVERT: o 118 LYS cc_start: 0.5365 (mtpt) cc_final: 0.4911 (tptp) REVERT: o 124 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7147 (mtp85) REVERT: o 196 LEU cc_start: 0.2233 (OUTLIER) cc_final: 0.1948 (mm) REVERT: p 7 LYS cc_start: 0.6869 (ttpt) cc_final: 0.6582 (ttpt) REVERT: p 25 GLN cc_start: 0.7213 (mt0) cc_final: 0.6949 (tt0) REVERT: p 28 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6789 (ttmt) REVERT: p 29 LEU cc_start: 0.8253 (mp) cc_final: 0.7962 (mp) REVERT: q 210 GLU cc_start: 0.5219 (pt0) cc_final: 0.5002 (pt0) REVERT: q 351 GLU cc_start: 0.3569 (mt-10) cc_final: 0.1798 (mm-30) REVERT: q 386 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5194 (pttm) REVERT: q 452 LYS cc_start: 0.5702 (ttmm) cc_final: 0.5423 (tptm) REVERT: r 150 MET cc_start: 0.4144 (ptm) cc_final: 0.3670 (tmm) REVERT: s 1 MET cc_start: 0.5014 (tpt) cc_final: 0.4778 (tpt) REVERT: s 5 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7197 (tttm) REVERT: s 7 GLN cc_start: 0.7225 (mm110) cc_final: 0.6869 (mt0) REVERT: t 48 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6641 (tttt) REVERT: t 73 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6230 (mm-30) REVERT: t 97 LYS cc_start: 0.5388 (OUTLIER) cc_final: 0.4477 (mttm) REVERT: t 207 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7725 (mp) REVERT: t 253 GLU cc_start: 0.4961 (OUTLIER) cc_final: 0.4725 (tp30) REVERT: t 267 PHE cc_start: 0.7134 (t80) cc_final: 0.6855 (t80) REVERT: u 104 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7163 (tm-30) REVERT: w 380 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5973 (mtpt) REVERT: w 429 MET cc_start: 0.2104 (OUTLIER) cc_final: 0.0944 (mmt) REVERT: w 711 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6588 (tttm) REVERT: w 815 LYS cc_start: 0.5991 (mmmt) cc_final: 0.5728 (mtmt) REVERT: y 1 MET cc_start: 0.4736 (mtm) cc_final: 0.4186 (mtt) REVERT: y 4 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6442 (mtt90) REVERT: y 8 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: y 99 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6497 (tm-30) outliers start: 305 outliers final: 170 residues processed: 1243 average time/residue: 2.1381 time to fit residues: 3649.2159 Evaluate side-chains 1258 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1041 time to evaluate : 6.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 251 LEU Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 402 ILE Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 253 GLU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 378 LYS Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 429 MET Chi-restraints excluded: chain w residue 711 LYS Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 136 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain z residue 33 ILE 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: 0.9980 chunk 14 optimal weight: 10.0000 chunk 752 optimal weight: 4.9990 chunk 417 optimal weight: 9.9990 chunk 862 optimal weight: 8.9990 chunk 698 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 516 optimal weight: 5.9990 chunk 907 optimal weight: 0.0570 chunk 255 optimal weight: 20.0000 overall best weight: 4.0104 ------------------------------------------------------------------------------- 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 L 114 GLN M 41 GLN M 62 GLN O 55 HIS O 182 ASN R 27 ASN R 36 ASN S 122 HIS S 157 GLN X 19 ASN 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 n 69 GLN q 230 ASN r 154 HIS t 25 ASN t 209 GLN u 110 ASN y 178 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 133419 Z= 0.220 Angle : 0.583 12.416 194286 Z= 0.303 Chirality : 0.038 0.280 24157 Planarity : 0.005 0.053 13679 Dihedral : 22.591 179.329 54105 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.67 % Allowed : 15.75 % Favored : 79.58 % 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: 1.76 (0.09), residues: 3169 sheet: -0.18 (0.15), residues: 1037 loop : -0.48 (0.10), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 32 HIS 0.008 0.001 HIS C 311 PHE 0.028 0.002 PHE F 229 TYR 0.023 0.002 TYR o 110 ARG 0.008 0.001 ARG j 24 *********************** 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 1386 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1075 time to evaluate : 6.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.5928 (mtt90) cc_final: 0.5334 (mtt90) REVERT: A 93 LYS cc_start: 0.5951 (mttt) cc_final: 0.5499 (mtpm) REVERT: B 34 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7375 (tppp) REVERT: B 74 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: B 318 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7458 (mttp) REVERT: C 272 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8272 (m) REVERT: C 319 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7110 (tttt) REVERT: C 338 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (mmpt) REVERT: E 77 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7318 (mtp-110) REVERT: E 89 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7729 (m) REVERT: E 143 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5716 (mmmt) REVERT: E 148 GLU cc_start: 0.5893 (tp30) cc_final: 0.5106 (tp30) REVERT: F 55 TYR cc_start: 0.8321 (m-10) cc_final: 0.7593 (m-10) REVERT: F 59 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5668 (tp30) REVERT: G 51 LYS cc_start: 0.7489 (tttm) cc_final: 0.7233 (tttt) REVERT: G 65 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7934 (mt) REVERT: G 111 LYS cc_start: 0.6390 (mmtp) cc_final: 0.6135 (mttp) REVERT: G 208 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6360 (mm-30) REVERT: H 183 HIS cc_start: 0.6803 (t-90) cc_final: 0.6563 (t70) REVERT: K 76 LYS cc_start: 0.5331 (OUTLIER) cc_final: 0.4775 (tppp) REVERT: K 133 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5582 (ptpp) REVERT: K 150 LYS cc_start: 0.5050 (tppp) cc_final: 0.4522 (tppt) REVERT: K 153 GLU cc_start: 0.4679 (mt-10) cc_final: 0.4316 (tt0) REVERT: L 52 ASP cc_start: 0.8372 (p0) cc_final: 0.7938 (p0) REVERT: L 106 GLN cc_start: 0.7873 (tp40) cc_final: 0.7579 (mm-40) REVERT: L 160 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6153 (mt0) REVERT: M 82 SER cc_start: 0.8430 (t) cc_final: 0.8205 (m) REVERT: M 92 GLU cc_start: 0.7131 (mp0) cc_final: 0.6839 (mp0) REVERT: M 106 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7702 (mtp180) REVERT: M 137 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5792 (mtpt) REVERT: N 11 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7137 (mm-40) REVERT: N 192 LYS cc_start: 0.7534 (ptpp) cc_final: 0.6930 (pttp) REVERT: N 193 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6617 (ttt90) REVERT: P 23 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7439 (mpp-170) REVERT: P 75 GLU cc_start: 0.8268 (tt0) cc_final: 0.7920 (tt0) REVERT: P 120 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7794 (p0) REVERT: P 140 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6720 (mt-10) REVERT: P 152 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6734 (mt-10) REVERT: R 59 SER cc_start: 0.8795 (p) cc_final: 0.8414 (t) REVERT: R 82 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7740 (mppt) REVERT: S 60 SER cc_start: 0.7079 (t) cc_final: 0.6518 (p) REVERT: S 110 MET cc_start: 0.8102 (mmm) cc_final: 0.7719 (mmm) REVERT: U 74 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6594 (tppp) REVERT: V 59 MET cc_start: 0.8281 (mmm) cc_final: 0.7945 (mmp) REVERT: V 109 MET cc_start: 0.7428 (mmp) cc_final: 0.7144 (mmp) REVERT: V 120 LYS cc_start: 0.7461 (ttpt) cc_final: 0.7102 (ttpp) REVERT: W 46 ASP cc_start: 0.4668 (OUTLIER) cc_final: 0.4393 (m-30) REVERT: W 85 TYR cc_start: 0.4785 (OUTLIER) cc_final: 0.2789 (t80) REVERT: W 121 ARG cc_start: 0.5205 (mmp80) cc_final: 0.4998 (mmm160) REVERT: X 27 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6542 (mtp85) REVERT: Y 87 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7499 (ptpt) REVERT: Z 27 LYS cc_start: 0.7321 (mttt) cc_final: 0.6873 (tppp) REVERT: a 135 GLU cc_start: 0.7441 (tt0) cc_final: 0.7123 (tt0) REVERT: b 3 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4770 (mp) REVERT: b 38 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6418 (mtmm) REVERT: b 60 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6629 (tptp) REVERT: b 82 MET cc_start: 0.6246 (mtt) cc_final: 0.5423 (mmt) REVERT: b 88 LYS cc_start: 0.6002 (tttp) cc_final: 0.5767 (tttp) REVERT: b 106 GLU cc_start: 0.6220 (tt0) cc_final: 0.5986 (tt0) REVERT: b 135 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.7024 (mtt180) REVERT: b 141 LYS cc_start: 0.6932 (mtmt) cc_final: 0.6533 (mttt) REVERT: b 146 PRO cc_start: 0.6523 (Cg_exo) cc_final: 0.6131 (Cg_endo) REVERT: b 168 ARG cc_start: 0.5484 (mtm-85) cc_final: 0.5162 (mmp80) REVERT: b 328 VAL cc_start: 0.5651 (m) cc_final: 0.5321 (p) REVERT: b 442 TYR cc_start: 0.7501 (m-80) cc_final: 0.7236 (m-80) REVERT: b 448 GLU cc_start: 0.5023 (pm20) cc_final: 0.4540 (pt0) REVERT: b 490 LYS cc_start: 0.5794 (mttp) cc_final: 0.5382 (mmmt) REVERT: b 519 MET cc_start: 0.4857 (mmm) cc_final: 0.3921 (mmm) REVERT: c 16 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6448 (tt) REVERT: c 74 ASN cc_start: 0.7451 (p0) cc_final: 0.7251 (p0) REVERT: d 7 VAL cc_start: 0.7303 (t) cc_final: 0.6869 (t) REVERT: e 67 SER cc_start: 0.8008 (m) cc_final: 0.7779 (p) REVERT: e 80 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7508 (ttpt) REVERT: f 92 LYS cc_start: 0.8141 (pttm) cc_final: 0.7884 (tttt) REVERT: g 19 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7945 (mttm) REVERT: g 61 GLN cc_start: 0.8429 (mt0) cc_final: 0.8119 (mt0) REVERT: g 64 THR cc_start: 0.7913 (m) cc_final: 0.7545 (p) REVERT: h 20 GLN cc_start: 0.8426 (tt0) cc_final: 0.8131 (tt0) REVERT: i 42 SER cc_start: 0.8322 (p) cc_final: 0.8113 (m) REVERT: j 32 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8100 (mtpt) REVERT: k 16 ARG cc_start: 0.6333 (mtm110) cc_final: 0.6088 (mtm110) REVERT: k 29 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7219 (mtpt) REVERT: k 74 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6504 (tttp) REVERT: n 34 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.8001 (mtm180) REVERT: n 54 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7663 (mtpp) REVERT: n 120 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6519 (mt-10) REVERT: n 133 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.6056 (p0) REVERT: n 205 PHE cc_start: 0.7350 (m-80) cc_final: 0.7139 (m-80) REVERT: n 453 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.5954 (tp) REVERT: o 104 GLU cc_start: 0.6655 (mp0) cc_final: 0.6205 (mp0) REVERT: o 118 LYS cc_start: 0.5340 (mtpt) cc_final: 0.5009 (tptp) REVERT: o 196 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.1970 (mm) REVERT: p 7 LYS cc_start: 0.6730 (ttpt) cc_final: 0.6448 (ttpt) REVERT: p 25 GLN cc_start: 0.7195 (mt0) cc_final: 0.6934 (tt0) REVERT: p 28 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6806 (ttmt) REVERT: p 29 LEU cc_start: 0.8235 (mp) cc_final: 0.7950 (mp) REVERT: q 210 GLU cc_start: 0.5252 (pt0) cc_final: 0.5045 (pt0) REVERT: q 351 GLU cc_start: 0.3569 (mt-10) cc_final: 0.1793 (mm-30) REVERT: q 383 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5738 (tp) REVERT: q 386 LYS cc_start: 0.5340 (OUTLIER) cc_final: 0.4962 (pttm) REVERT: q 452 LYS cc_start: 0.5701 (ttmm) cc_final: 0.5407 (tptm) REVERT: r 150 MET cc_start: 0.4147 (ptm) cc_final: 0.3732 (tmm) REVERT: s 1 MET cc_start: 0.4983 (tpt) cc_final: 0.4780 (tpt) REVERT: s 5 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7287 (tttm) REVERT: s 7 GLN cc_start: 0.7222 (mm110) cc_final: 0.6851 (mt0) REVERT: t 48 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6639 (tttt) REVERT: t 73 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6216 (mm-30) REVERT: t 97 LYS cc_start: 0.5365 (OUTLIER) cc_final: 0.4503 (mttm) REVERT: t 207 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7726 (mp) REVERT: t 253 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.4691 (tp30) REVERT: t 267 PHE cc_start: 0.7131 (t80) cc_final: 0.6775 (t80) REVERT: u 104 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7133 (tm-30) REVERT: w 380 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.6013 (mtpt) REVERT: w 711 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6586 (tttm) REVERT: w 815 LYS cc_start: 0.6043 (mmmt) cc_final: 0.5762 (mtmt) REVERT: y 4 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6485 (mtt90) REVERT: y 8 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6357 (mp0) REVERT: y 99 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6570 (tm-30) outliers start: 311 outliers final: 185 residues processed: 1267 average time/residue: 2.0810 time to fit residues: 3629.3676 Evaluate side-chains 1263 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1028 time to evaluate : 6.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 137 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 364 VAL Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 253 GLU Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 293 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 378 LYS Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 711 LYS Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain z residue 33 ILE 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: 40.0000 chunk 249 optimal weight: 10.0000 chunk 1012 optimal weight: 6.9990 chunk 840 optimal weight: 9.9990 chunk 468 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 531 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 L 114 GLN M 41 GLN O 55 HIS O 182 ASN R 27 ASN R 36 ASN S 122 HIS S 157 GLN V 24 ASN W 205 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 n 69 GLN q 230 ASN t 209 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 133419 Z= 0.340 Angle : 0.706 12.092 194286 Z= 0.360 Chirality : 0.043 0.293 24157 Planarity : 0.006 0.066 13679 Dihedral : 22.714 179.262 54103 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.55 % Favored : 96.44 % Rotamer: Outliers : 5.18 % Allowed : 16.24 % Favored : 78.58 % 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: 0.41 (0.09), residues: 7630 helix: 1.42 (0.09), residues: 3182 sheet: -0.24 (0.15), residues: 1005 loop : -0.62 (0.10), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP e 32 HIS 0.010 0.002 HIS C 311 PHE 0.035 0.002 PHE F 229 TYR 0.026 0.003 TYR o 110 ARG 0.013 0.001 ARG j 24 *********************** 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 1382 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1037 time to evaluate : 6.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.6009 (mttt) cc_final: 0.5532 (mtpm) REVERT: B 34 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7409 (tppp) REVERT: B 74 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6978 (mm-30) REVERT: B 318 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7380 (mttp) REVERT: C 272 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8264 (m) REVERT: C 319 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7114 (tttt) REVERT: C 338 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7368 (mmpt) REVERT: E 77 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6998 (mtp-110) REVERT: E 89 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7739 (m) REVERT: E 143 LYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5945 (mmmt) REVERT: E 148 GLU cc_start: 0.5994 (tp30) cc_final: 0.5207 (tp30) REVERT: F 55 TYR cc_start: 0.8353 (m-10) cc_final: 0.7615 (m-10) REVERT: G 65 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (mt) REVERT: G 107 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6344 (tp30) REVERT: G 111 LYS cc_start: 0.6350 (mmtp) cc_final: 0.6023 (mttp) REVERT: G 208 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6480 (mm-30) REVERT: G 219 ASP cc_start: 0.6402 (m-30) cc_final: 0.6089 (m-30) REVERT: H 69 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7254 (tpt90) REVERT: H 135 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6190 (mt-10) REVERT: H 183 HIS cc_start: 0.6727 (t-90) cc_final: 0.6501 (t70) REVERT: K 39 LYS cc_start: 0.4487 (mtmt) cc_final: 0.4005 (mtpm) REVERT: K 76 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.4902 (tppp) REVERT: K 153 GLU cc_start: 0.4640 (mt-10) cc_final: 0.4299 (tt0) REVERT: L 52 ASP cc_start: 0.8355 (p0) cc_final: 0.7916 (p0) REVERT: L 106 GLN cc_start: 0.7830 (tp40) cc_final: 0.7500 (mm-40) REVERT: L 160 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6299 (mt0) REVERT: M 82 SER cc_start: 0.8431 (t) cc_final: 0.8210 (m) REVERT: M 92 GLU cc_start: 0.7113 (mp0) cc_final: 0.6817 (mp0) REVERT: M 137 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5865 (mtpt) REVERT: N 11 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7162 (mm-40) REVERT: N 23 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7317 (mm110) REVERT: N 192 LYS cc_start: 0.7685 (ptpp) cc_final: 0.7039 (pttp) REVERT: N 193 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6483 (ttt90) REVERT: P 23 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7406 (mpp-170) REVERT: P 75 GLU cc_start: 0.8257 (tt0) cc_final: 0.8006 (tt0) REVERT: P 140 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6914 (mt-10) REVERT: R 82 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7678 (mppt) REVERT: S 60 SER cc_start: 0.6995 (t) cc_final: 0.6507 (p) REVERT: S 110 MET cc_start: 0.8075 (mmm) cc_final: 0.7673 (mmm) REVERT: U 74 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6839 (tppp) REVERT: V 59 MET cc_start: 0.8316 (mmm) cc_final: 0.8042 (mmp) REVERT: V 109 MET cc_start: 0.7350 (mmp) cc_final: 0.7008 (mmp) REVERT: V 120 LYS cc_start: 0.7538 (ttpt) cc_final: 0.7293 (ttpp) REVERT: W 46 ASP cc_start: 0.4570 (OUTLIER) cc_final: 0.4270 (m-30) REVERT: W 85 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.2786 (t80) REVERT: W 109 VAL cc_start: 0.5496 (OUTLIER) cc_final: 0.5227 (p) REVERT: W 121 ARG cc_start: 0.5004 (mmp80) cc_final: 0.4758 (mmm160) REVERT: X 27 ARG cc_start: 0.6762 (mtt-85) cc_final: 0.6425 (mtp85) REVERT: X 77 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6570 (tp30) REVERT: Y 87 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7294 (ptpt) REVERT: Z 27 LYS cc_start: 0.7518 (mttt) cc_final: 0.6986 (tppp) REVERT: a 135 GLU cc_start: 0.7446 (tt0) cc_final: 0.7122 (tt0) REVERT: b 3 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4835 (mp) REVERT: b 60 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6614 (tptp) REVERT: b 82 MET cc_start: 0.6202 (mtt) cc_final: 0.5028 (mmt) REVERT: b 88 LYS cc_start: 0.6041 (tttp) cc_final: 0.5777 (tttp) REVERT: b 106 GLU cc_start: 0.6277 (tt0) cc_final: 0.6058 (tt0) REVERT: b 141 LYS cc_start: 0.6864 (mtmt) cc_final: 0.6594 (mttt) REVERT: b 146 PRO cc_start: 0.6546 (Cg_exo) cc_final: 0.6149 (Cg_endo) REVERT: b 328 VAL cc_start: 0.5742 (m) cc_final: 0.5411 (p) REVERT: b 442 TYR cc_start: 0.7540 (m-80) cc_final: 0.7288 (m-80) REVERT: b 448 GLU cc_start: 0.5024 (pm20) cc_final: 0.4545 (pt0) REVERT: b 490 LYS cc_start: 0.5797 (mttp) cc_final: 0.5213 (mmmt) REVERT: b 519 MET cc_start: 0.4923 (mmm) cc_final: 0.3966 (mmm) REVERT: c 16 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6418 (tt) REVERT: d 7 VAL cc_start: 0.7361 (t) cc_final: 0.6894 (t) REVERT: e 67 SER cc_start: 0.8004 (m) cc_final: 0.7767 (p) REVERT: e 80 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7488 (ttpt) REVERT: f 92 LYS cc_start: 0.8168 (pttm) cc_final: 0.7882 (tttt) REVERT: g 19 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7932 (mttm) REVERT: g 51 LEU cc_start: 0.7865 (pt) cc_final: 0.7519 (mp) REVERT: g 61 GLN cc_start: 0.8409 (mt0) cc_final: 0.8091 (mt0) REVERT: g 64 THR cc_start: 0.7815 (m) cc_final: 0.7488 (p) REVERT: h 20 GLN cc_start: 0.8461 (tt0) cc_final: 0.8164 (tt0) REVERT: i 42 SER cc_start: 0.8329 (p) cc_final: 0.8113 (m) REVERT: j 32 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8084 (mtpt) REVERT: k 16 ARG cc_start: 0.6251 (mtm110) cc_final: 0.5949 (mtm110) REVERT: k 29 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6493 (mmtm) REVERT: k 74 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6518 (tttp) REVERT: n 34 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8051 (mtm180) REVERT: n 54 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7649 (mtpp) REVERT: n 120 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6656 (mt-10) REVERT: n 133 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6024 (p0) REVERT: n 154 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7512 (ttpt) REVERT: n 453 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6020 (tp) REVERT: o 104 GLU cc_start: 0.6639 (mp0) cc_final: 0.6178 (mp0) REVERT: o 124 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7158 (mtp85) REVERT: o 196 LEU cc_start: 0.2274 (OUTLIER) cc_final: 0.1841 (mm) REVERT: p 7 LYS cc_start: 0.6828 (ttpt) cc_final: 0.6533 (ttpt) REVERT: p 25 GLN cc_start: 0.7178 (mt0) cc_final: 0.6921 (tt0) REVERT: p 28 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6804 (ttmt) REVERT: p 29 LEU cc_start: 0.8244 (mp) cc_final: 0.7972 (mp) REVERT: q 210 GLU cc_start: 0.5319 (pt0) cc_final: 0.5100 (pt0) REVERT: q 351 GLU cc_start: 0.3573 (mt-10) cc_final: 0.1782 (mm-30) REVERT: q 386 LYS cc_start: 0.5474 (OUTLIER) cc_final: 0.5092 (pttm) REVERT: q 452 LYS cc_start: 0.5668 (ttmm) cc_final: 0.5463 (tptm) REVERT: r 150 MET cc_start: 0.4045 (ptm) cc_final: 0.3707 (tmm) REVERT: s 1 MET cc_start: 0.4995 (tpt) cc_final: 0.4780 (tpt) REVERT: s 5 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7210 (tttm) REVERT: s 7 GLN cc_start: 0.7307 (mm110) cc_final: 0.6872 (mt0) REVERT: t 48 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6580 (tttt) REVERT: t 97 LYS cc_start: 0.5488 (OUTLIER) cc_final: 0.4563 (mttm) REVERT: t 207 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7695 (mp) REVERT: u 104 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7168 (tm-30) REVERT: w 380 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6006 (mtpt) REVERT: w 815 LYS cc_start: 0.5937 (mmmt) cc_final: 0.5657 (mtmt) REVERT: y 1 MET cc_start: 0.5064 (OUTLIER) cc_final: 0.4686 (mtt) REVERT: y 4 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6440 (mtt90) REVERT: y 8 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: y 99 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: y 126 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6285 (mt-10) outliers start: 345 outliers final: 208 residues processed: 1253 average time/residue: 2.0750 time to fit residues: 3581.8497 Evaluate side-chains 1291 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1034 time to evaluate : 6.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 233 GLN Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 137 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 167 THR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 364 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 122 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 293 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 391 THR Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 421 ASP Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 33 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 975 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 576 optimal weight: 0.8980 chunk 739 optimal weight: 9.9990 chunk 572 optimal weight: 7.9990 chunk 851 optimal weight: 5.9990 chunk 565 optimal weight: 5.9990 chunk 1008 optimal weight: 5.9990 chunk 630 optimal weight: 20.0000 chunk 614 optimal weight: 20.0000 chunk 465 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 K 295 GLN L 114 GLN M 41 GLN O 55 HIS 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 a 65 GLN b 26 GLN b 124 GLN b 166 ASN b 323 GLN e 52 GLN g 3 GLN n 69 GLN q 230 ASN t 209 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 133419 Z= 0.254 Angle : 0.625 11.939 194286 Z= 0.323 Chirality : 0.039 0.286 24157 Planarity : 0.005 0.061 13679 Dihedral : 22.646 179.658 54103 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.86 % Favored : 97.13 % Rotamer: Outliers : 4.80 % Allowed : 17.02 % Favored : 78.17 % 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: 0.51 (0.09), residues: 7630 helix: 1.54 (0.09), residues: 3184 sheet: -0.24 (0.15), residues: 1011 loop : -0.59 (0.10), residues: 3435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 32 HIS 0.009 0.001 HIS C 311 PHE 0.030 0.002 PHE F 229 TYR 0.024 0.002 TYR o 110 ARG 0.008 0.001 ARG j 24 *********************** 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 1349 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1029 time to evaluate : 6.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.5958 (mtt90) cc_final: 0.5442 (mtt90) REVERT: A 93 LYS cc_start: 0.5996 (mttt) cc_final: 0.5522 (mtpm) REVERT: A 104 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6976 (mp) REVERT: B 34 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7394 (tppp) REVERT: B 74 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: B 318 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7337 (mttp) REVERT: C 272 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (m) REVERT: C 319 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7130 (tttt) REVERT: C 338 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7343 (mmpt) REVERT: E 77 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7208 (mtp-110) REVERT: E 89 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7690 (m) REVERT: E 143 LYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5752 (mmmt) REVERT: E 148 GLU cc_start: 0.5986 (tp30) cc_final: 0.5211 (tp30) REVERT: F 55 TYR cc_start: 0.8327 (m-10) cc_final: 0.7598 (m-10) REVERT: G 65 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7936 (mt) REVERT: G 111 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6048 (mttp) REVERT: G 208 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6353 (mm-30) REVERT: H 69 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7164 (tpt90) REVERT: H 91 ARG cc_start: 0.7320 (mtm110) cc_final: 0.6779 (mtp-110) REVERT: K 39 LYS cc_start: 0.4502 (mtmt) cc_final: 0.4021 (mtpm) REVERT: K 76 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.4892 (tppp) REVERT: K 133 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5567 (ptpp) REVERT: K 153 GLU cc_start: 0.4751 (mt-10) cc_final: 0.4397 (tt0) REVERT: L 52 ASP cc_start: 0.8355 (p0) cc_final: 0.7912 (p0) REVERT: L 106 GLN cc_start: 0.7858 (tp40) cc_final: 0.7593 (mm-40) REVERT: L 160 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.6225 (mt0) REVERT: M 82 SER cc_start: 0.8420 (t) cc_final: 0.8197 (m) REVERT: M 92 GLU cc_start: 0.7154 (mp0) cc_final: 0.6851 (mp0) REVERT: M 137 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5751 (mtpt) REVERT: N 11 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: N 192 LYS cc_start: 0.7594 (ptpp) cc_final: 0.7016 (pttp) REVERT: N 193 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6576 (ttt90) REVERT: P 23 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7482 (mpp-170) REVERT: P 75 GLU cc_start: 0.8271 (tt0) cc_final: 0.8021 (tt0) REVERT: P 140 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6887 (mt-10) REVERT: R 82 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7693 (mppt) REVERT: S 110 MET cc_start: 0.8092 (mmm) cc_final: 0.7711 (mmm) REVERT: U 74 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6853 (tppp) REVERT: V 59 MET cc_start: 0.8307 (mmm) cc_final: 0.7971 (mmp) REVERT: V 109 MET cc_start: 0.7443 (mmp) cc_final: 0.7161 (mmp) REVERT: V 120 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7169 (ttpp) REVERT: W 43 LEU cc_start: 0.5249 (OUTLIER) cc_final: 0.5036 (mt) REVERT: W 46 ASP cc_start: 0.4523 (OUTLIER) cc_final: 0.4187 (m-30) REVERT: W 56 ILE cc_start: 0.5980 (mm) cc_final: 0.5759 (mm) REVERT: W 85 TYR cc_start: 0.4847 (OUTLIER) cc_final: 0.2759 (t80) REVERT: W 109 VAL cc_start: 0.5397 (OUTLIER) cc_final: 0.5146 (p) REVERT: W 121 ARG cc_start: 0.4987 (mmp80) cc_final: 0.4734 (mmm160) REVERT: X 27 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.6496 (mtp85) REVERT: Y 87 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7320 (ptpt) REVERT: Z 27 LYS cc_start: 0.7503 (mttt) cc_final: 0.6972 (tppp) REVERT: a 135 GLU cc_start: 0.7451 (tt0) cc_final: 0.7120 (tt0) REVERT: b 3 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4842 (mp) REVERT: b 38 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6479 (mtmm) REVERT: b 60 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6599 (tptp) REVERT: b 82 MET cc_start: 0.5968 (mtt) cc_final: 0.5206 (mmt) REVERT: b 88 LYS cc_start: 0.6015 (tttp) cc_final: 0.5767 (tttp) REVERT: b 106 GLU cc_start: 0.6222 (tt0) cc_final: 0.5990 (tt0) REVERT: b 141 LYS cc_start: 0.6921 (mtmt) cc_final: 0.6624 (mttt) REVERT: b 146 PRO cc_start: 0.6514 (Cg_exo) cc_final: 0.6138 (Cg_endo) REVERT: b 220 ASP cc_start: 0.6622 (t0) cc_final: 0.6117 (t0) REVERT: b 328 VAL cc_start: 0.5682 (m) cc_final: 0.5340 (p) REVERT: b 442 TYR cc_start: 0.7501 (m-80) cc_final: 0.7229 (m-80) REVERT: b 448 GLU cc_start: 0.5022 (pm20) cc_final: 0.4546 (pt0) REVERT: b 490 LYS cc_start: 0.5871 (mttp) cc_final: 0.5284 (mmmt) REVERT: b 503 MET cc_start: 0.5743 (mtp) cc_final: 0.5543 (mtp) REVERT: b 519 MET cc_start: 0.4966 (mmm) cc_final: 0.4036 (mmm) REVERT: c 16 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6306 (tt) REVERT: c 55 GLU cc_start: 0.7133 (tt0) cc_final: 0.6808 (tt0) REVERT: d 7 VAL cc_start: 0.7364 (t) cc_final: 0.6854 (t) REVERT: e 67 SER cc_start: 0.8005 (m) cc_final: 0.7770 (p) REVERT: e 80 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7463 (ttpt) REVERT: f 92 LYS cc_start: 0.8146 (pttm) cc_final: 0.7882 (tttt) REVERT: g 19 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7930 (mttm) REVERT: g 51 LEU cc_start: 0.7846 (pt) cc_final: 0.7412 (mp) REVERT: g 61 GLN cc_start: 0.8418 (mt0) cc_final: 0.8107 (mt0) REVERT: g 64 THR cc_start: 0.7826 (m) cc_final: 0.7512 (p) REVERT: i 42 SER cc_start: 0.8298 (p) cc_final: 0.8094 (m) REVERT: j 32 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8105 (mtpt) REVERT: k 16 ARG cc_start: 0.6294 (mtm110) cc_final: 0.6003 (mtm110) REVERT: k 29 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7230 (mtpt) REVERT: k 74 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6503 (tttp) REVERT: n 34 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8026 (mtm180) REVERT: n 54 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7757 (mtpt) REVERT: n 120 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6642 (mt-10) REVERT: n 133 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.6074 (p0) REVERT: n 154 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7545 (ttpt) REVERT: n 453 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6017 (tp) REVERT: o 104 GLU cc_start: 0.6582 (mp0) cc_final: 0.6100 (mp0) REVERT: o 118 LYS cc_start: 0.5364 (mtpt) cc_final: 0.4922 (tptp) REVERT: o 124 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7104 (mtp85) REVERT: o 196 LEU cc_start: 0.2457 (OUTLIER) cc_final: 0.1946 (mm) REVERT: p 7 LYS cc_start: 0.6763 (ttpt) cc_final: 0.6474 (ttpt) REVERT: p 25 GLN cc_start: 0.7188 (mt0) cc_final: 0.6925 (tt0) REVERT: p 28 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6797 (ttmt) REVERT: p 29 LEU cc_start: 0.8249 (mp) cc_final: 0.7980 (mp) REVERT: q 210 GLU cc_start: 0.5284 (pt0) cc_final: 0.5079 (pt0) REVERT: q 351 GLU cc_start: 0.3581 (mt-10) cc_final: 0.1812 (mm-30) REVERT: q 383 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5618 (tp) REVERT: q 386 LYS cc_start: 0.5401 (OUTLIER) cc_final: 0.4967 (pttm) REVERT: q 452 LYS cc_start: 0.5743 (ttmm) cc_final: 0.5385 (tptm) REVERT: r 21 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: r 150 MET cc_start: 0.4045 (ptm) cc_final: 0.3736 (tmm) REVERT: s 5 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7214 (tttm) REVERT: s 7 GLN cc_start: 0.7294 (mm110) cc_final: 0.6862 (mt0) REVERT: t 48 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6614 (tttt) REVERT: t 97 LYS cc_start: 0.5562 (OUTLIER) cc_final: 0.4666 (mttm) REVERT: t 207 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7706 (mp) REVERT: t 267 PHE cc_start: 0.7099 (t80) cc_final: 0.6895 (t80) REVERT: u 104 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7166 (tm-30) REVERT: w 380 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6066 (mtpt) REVERT: w 711 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6566 (tttm) REVERT: w 815 LYS cc_start: 0.5884 (mmmt) cc_final: 0.5616 (mtmt) REVERT: y 1 MET cc_start: 0.4932 (OUTLIER) cc_final: 0.4579 (mtt) REVERT: y 4 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6440 (mtt90) REVERT: y 8 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: y 99 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: y 126 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6112 (mt-10) outliers start: 320 outliers final: 211 residues processed: 1229 average time/residue: 2.0535 time to fit residues: 3483.3191 Evaluate side-chains 1279 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1012 time to evaluate : 6.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 233 GLN Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 137 LYS Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 43 LEU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 364 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 122 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 21 GLU Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 293 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 391 THR Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 711 LYS Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 623 optimal weight: 8.9990 chunk 402 optimal weight: 9.9990 chunk 602 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 640 optimal weight: 9.9990 chunk 686 optimal weight: 5.9990 chunk 498 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 792 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 163 GLN H 183 HIS K 295 GLN L 114 GLN M 41 GLN O 55 HIS 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 b 26 GLN b 166 ASN b 323 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN g 3 GLN n 69 GLN q 230 ASN t 209 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 133419 Z= 0.324 Angle : 0.698 12.030 194286 Z= 0.356 Chirality : 0.042 0.292 24157 Planarity : 0.006 0.065 13679 Dihedral : 22.699 179.348 54103 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.62 % Favored : 96.37 % Rotamer: Outliers : 4.94 % Allowed : 17.28 % Favored : 77.78 % 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: 0.33 (0.09), residues: 7630 helix: 1.36 (0.09), residues: 3181 sheet: -0.23 (0.15), residues: 1003 loop : -0.69 (0.10), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP e 32 HIS 0.010 0.002 HIS C 311 PHE 0.034 0.002 PHE F 229 TYR 0.028 0.003 TYR S 41 ARG 0.011 0.001 ARG j 24 *********************** 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 1352 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1023 time to evaluate : 7.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.5992 (mttt) cc_final: 0.5494 (mtpm) REVERT: A 104 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6984 (mp) REVERT: B 34 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7414 (tppp) REVERT: B 74 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: B 318 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7359 (mttp) REVERT: C 272 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8261 (m) REVERT: C 319 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7102 (tttt) REVERT: C 338 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7353 (mmpt) REVERT: E 77 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6999 (mtp-110) REVERT: E 89 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7676 (m) REVERT: E 143 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5913 (mmmt) REVERT: E 148 GLU cc_start: 0.5920 (tp30) cc_final: 0.5149 (tp30) REVERT: F 55 TYR cc_start: 0.8366 (m-10) cc_final: 0.7654 (m-10) REVERT: G 65 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7920 (mt) REVERT: G 111 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.6121 (mttp) REVERT: G 208 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6487 (mm-30) REVERT: G 219 ASP cc_start: 0.6395 (m-30) cc_final: 0.6086 (m-30) REVERT: H 51 GLN cc_start: 0.7225 (mp-120) cc_final: 0.6952 (mp10) REVERT: H 54 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7792 (mmtp) REVERT: H 69 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7209 (tpt90) REVERT: H 91 ARG cc_start: 0.7341 (mtm110) cc_final: 0.6826 (mtp-110) REVERT: K 39 LYS cc_start: 0.4506 (mtmt) cc_final: 0.3988 (mtpm) REVERT: K 76 LYS cc_start: 0.5424 (OUTLIER) cc_final: 0.4872 (tppp) REVERT: K 133 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5380 (ptpp) REVERT: K 153 GLU cc_start: 0.4722 (mt-10) cc_final: 0.4367 (tt0) REVERT: L 52 ASP cc_start: 0.8356 (p0) cc_final: 0.7915 (p0) REVERT: L 106 GLN cc_start: 0.7865 (tp40) cc_final: 0.7558 (mm-40) REVERT: L 160 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.6177 (mt0) REVERT: M 82 SER cc_start: 0.8433 (t) cc_final: 0.8204 (m) REVERT: M 92 GLU cc_start: 0.7122 (mp0) cc_final: 0.6817 (mp0) REVERT: M 137 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5808 (mtpt) REVERT: N 11 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: N 192 LYS cc_start: 0.7659 (ptpp) cc_final: 0.6980 (pttp) REVERT: N 193 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6512 (ttt90) REVERT: P 23 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7392 (mpp-170) REVERT: P 75 GLU cc_start: 0.8247 (tt0) cc_final: 0.8005 (tt0) REVERT: P 140 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6909 (mt-10) REVERT: R 82 LYS cc_start: 0.8151 (mmmm) cc_final: 0.7683 (mppt) REVERT: S 60 SER cc_start: 0.7090 (t) cc_final: 0.6803 (p) REVERT: S 85 SER cc_start: 0.5743 (m) cc_final: 0.5498 (t) REVERT: S 110 MET cc_start: 0.8082 (mmm) cc_final: 0.7564 (mmm) REVERT: U 74 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6827 (tppp) REVERT: V 59 MET cc_start: 0.8340 (mmm) cc_final: 0.8032 (mmp) REVERT: V 109 MET cc_start: 0.7352 (mmp) cc_final: 0.7075 (mmp) REVERT: V 120 LYS cc_start: 0.7493 (ttpt) cc_final: 0.7247 (ttpp) REVERT: W 43 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.5095 (mt) REVERT: W 46 ASP cc_start: 0.4660 (OUTLIER) cc_final: 0.4337 (m-30) REVERT: W 56 ILE cc_start: 0.5918 (mm) cc_final: 0.5600 (mm) REVERT: W 85 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.2768 (t80) REVERT: W 109 VAL cc_start: 0.5478 (OUTLIER) cc_final: 0.5220 (p) REVERT: W 121 ARG cc_start: 0.5003 (mmp80) cc_final: 0.4726 (mmm160) REVERT: X 27 ARG cc_start: 0.6818 (mtt-85) cc_final: 0.6444 (mtp85) REVERT: X 77 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: Y 87 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7293 (ptpt) REVERT: Z 27 LYS cc_start: 0.7522 (mttt) cc_final: 0.6991 (tppp) REVERT: a 135 GLU cc_start: 0.7478 (tt0) cc_final: 0.7147 (tt0) REVERT: b 3 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4831 (mp) REVERT: b 38 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6480 (mtmm) REVERT: b 60 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6614 (tptp) REVERT: b 82 MET cc_start: 0.6027 (mtt) cc_final: 0.5278 (mmt) REVERT: b 88 LYS cc_start: 0.6082 (tttp) cc_final: 0.5813 (tttp) REVERT: b 106 GLU cc_start: 0.6258 (tt0) cc_final: 0.6050 (tt0) REVERT: b 135 ARG cc_start: 0.7310 (mtt180) cc_final: 0.7074 (mtt180) REVERT: b 141 LYS cc_start: 0.6918 (mtmt) cc_final: 0.6630 (mttt) REVERT: b 146 PRO cc_start: 0.6500 (Cg_exo) cc_final: 0.6103 (Cg_endo) REVERT: b 220 ASP cc_start: 0.6646 (t0) cc_final: 0.6139 (t0) REVERT: b 328 VAL cc_start: 0.5733 (m) cc_final: 0.5393 (p) REVERT: b 442 TYR cc_start: 0.7544 (m-80) cc_final: 0.7252 (m-80) REVERT: b 448 GLU cc_start: 0.5059 (pm20) cc_final: 0.4659 (pt0) REVERT: b 503 MET cc_start: 0.5930 (mtp) cc_final: 0.5719 (mtp) REVERT: b 504 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5782 (mt) REVERT: b 519 MET cc_start: 0.4922 (mmm) cc_final: 0.3922 (mmm) REVERT: c 16 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6457 (tt) REVERT: c 55 GLU cc_start: 0.7128 (tt0) cc_final: 0.6810 (tt0) REVERT: d 7 VAL cc_start: 0.7316 (t) cc_final: 0.6842 (t) REVERT: d 74 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7282 (ttm170) REVERT: e 67 SER cc_start: 0.8002 (m) cc_final: 0.7762 (p) REVERT: e 80 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7504 (ttpt) REVERT: f 92 LYS cc_start: 0.8164 (pttm) cc_final: 0.7882 (tttt) REVERT: g 19 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7933 (mttm) REVERT: g 51 LEU cc_start: 0.7856 (pt) cc_final: 0.7442 (mp) REVERT: g 61 GLN cc_start: 0.8408 (mt0) cc_final: 0.8097 (mt0) REVERT: g 64 THR cc_start: 0.7821 (m) cc_final: 0.7521 (p) REVERT: h 20 GLN cc_start: 0.8455 (tt0) cc_final: 0.8160 (tt0) REVERT: i 42 SER cc_start: 0.8316 (p) cc_final: 0.8107 (m) REVERT: j 32 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8086 (mtpt) REVERT: k 16 ARG cc_start: 0.6181 (mtm110) cc_final: 0.5841 (mtm110) REVERT: k 29 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7237 (mtpt) REVERT: k 74 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6522 (tttp) REVERT: n 34 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: n 54 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7654 (mtpp) REVERT: n 120 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6685 (mt-10) REVERT: n 133 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.6084 (p0) REVERT: n 154 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7521 (ttpt) REVERT: n 453 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6043 (tp) REVERT: o 104 GLU cc_start: 0.6640 (mp0) cc_final: 0.6166 (mp0) REVERT: o 118 LYS cc_start: 0.5302 (mtpt) cc_final: 0.4863 (tptp) REVERT: o 124 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7142 (mtp85) REVERT: p 7 LYS cc_start: 0.6769 (ttpt) cc_final: 0.6489 (ttpt) REVERT: p 25 GLN cc_start: 0.7235 (mt0) cc_final: 0.6970 (tt0) REVERT: p 28 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6803 (ttmt) REVERT: p 29 LEU cc_start: 0.8260 (mp) cc_final: 0.7990 (mp) REVERT: q 351 GLU cc_start: 0.3589 (mt-10) cc_final: 0.1775 (mm-30) REVERT: q 386 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.5114 (pttm) REVERT: q 452 LYS cc_start: 0.5741 (ttmm) cc_final: 0.5504 (tptm) REVERT: r 8 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6660 (mp0) REVERT: r 21 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: r 150 MET cc_start: 0.4104 (ptm) cc_final: 0.3871 (tmm) REVERT: s 5 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7210 (tttm) REVERT: s 7 GLN cc_start: 0.7304 (mm110) cc_final: 0.6881 (mt0) REVERT: t 48 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6659 (tttt) REVERT: t 97 LYS cc_start: 0.5478 (OUTLIER) cc_final: 0.4987 (ptpp) REVERT: t 207 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7701 (mp) REVERT: t 253 GLU cc_start: 0.4750 (OUTLIER) cc_final: 0.4536 (tp30) REVERT: u 104 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7166 (tm-30) REVERT: w 380 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.6053 (mtpt) REVERT: w 711 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6553 (tttm) REVERT: w 815 LYS cc_start: 0.5968 (mmmt) cc_final: 0.5683 (mtmt) REVERT: y 1 MET cc_start: 0.4980 (mtm) cc_final: 0.4627 (mtt) REVERT: y 4 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6452 (mtt90) REVERT: y 8 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: y 126 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6199 (mt-10) outliers start: 329 outliers final: 224 residues processed: 1234 average time/residue: 2.1118 time to fit residues: 3593.0486 Evaluate side-chains 1287 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1008 time to evaluate : 6.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 233 GLN Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 137 LYS Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 43 LEU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 167 THR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 504 ILE Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 15 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 364 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 122 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 21 GLU Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain r residue 216 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 253 GLU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 293 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 391 THR Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 711 LYS Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 33 ILE 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: 30.0000 chunk 881 optimal weight: 20.0000 chunk 939 optimal weight: 0.9990 chunk 565 optimal weight: 6.9990 chunk 409 optimal weight: 4.9990 chunk 737 optimal weight: 4.9990 chunk 288 optimal weight: 30.0000 chunk 848 optimal weight: 10.0000 chunk 888 optimal weight: 20.0000 chunk 936 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- 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 183 HIS L 114 GLN M 41 GLN ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 b 26 GLN b 166 ASN b 323 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN g 3 GLN n 69 GLN q 230 ASN r 244 GLN t 209 GLN t 291 GLN u 5 GLN u 110 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 133419 Z= 0.290 Angle : 0.664 11.855 194286 Z= 0.341 Chirality : 0.041 0.290 24157 Planarity : 0.005 0.064 13679 Dihedral : 22.689 179.482 54102 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.25 % Favored : 96.74 % Rotamer: Outliers : 4.68 % Allowed : 17.62 % Favored : 77.69 % 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: 0.37 (0.09), residues: 7630 helix: 1.42 (0.09), residues: 3176 sheet: -0.24 (0.15), residues: 1003 loop : -0.68 (0.10), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP q 234 HIS 0.010 0.001 HIS S 122 PHE 0.031 0.002 PHE F 229 TYR 0.033 0.002 TYR S 41 ARG 0.010 0.001 ARG b 168 *********************** 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 1331 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1019 time to evaluate : 6.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.5987 (mttt) cc_final: 0.5496 (mtpm) REVERT: A 104 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6971 (mp) REVERT: A 156 LYS cc_start: 0.5903 (ttmt) cc_final: 0.5697 (tttt) REVERT: B 34 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7410 (tppp) REVERT: B 74 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6982 (mm-30) REVERT: B 318 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7349 (mttp) REVERT: C 265 GLU cc_start: 0.6531 (mp0) cc_final: 0.6068 (mp0) REVERT: C 272 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (m) REVERT: C 319 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7100 (tttt) REVERT: C 338 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7355 (mmpt) REVERT: E 77 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7001 (mtp-110) REVERT: E 89 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7697 (m) REVERT: E 143 LYS cc_start: 0.6324 (OUTLIER) cc_final: 0.5911 (mmmt) REVERT: E 148 GLU cc_start: 0.5931 (tp30) cc_final: 0.5169 (tp30) REVERT: F 55 TYR cc_start: 0.8356 (m-10) cc_final: 0.7619 (m-10) REVERT: G 65 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7892 (mt) REVERT: G 111 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6159 (mttp) REVERT: G 208 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6488 (mm-30) REVERT: G 219 ASP cc_start: 0.6319 (m-30) cc_final: 0.6013 (m-30) REVERT: H 51 GLN cc_start: 0.7234 (mp-120) cc_final: 0.6956 (mp10) REVERT: H 69 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7186 (tpt90) REVERT: H 91 ARG cc_start: 0.7344 (mtm110) cc_final: 0.6828 (mtp-110) REVERT: K 39 LYS cc_start: 0.4535 (mtmt) cc_final: 0.4027 (mtpm) REVERT: K 76 LYS cc_start: 0.5449 (OUTLIER) cc_final: 0.4894 (tppp) REVERT: K 133 LYS cc_start: 0.5817 (OUTLIER) cc_final: 0.5295 (ptpp) REVERT: K 153 GLU cc_start: 0.4742 (mt-10) cc_final: 0.4391 (tt0) REVERT: L 52 ASP cc_start: 0.8355 (p0) cc_final: 0.7914 (p0) REVERT: L 106 GLN cc_start: 0.7818 (tp40) cc_final: 0.7562 (mm-40) REVERT: L 160 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.6175 (mt0) REVERT: M 82 SER cc_start: 0.8425 (t) cc_final: 0.8199 (m) REVERT: M 92 GLU cc_start: 0.7123 (mp0) cc_final: 0.6823 (mp0) REVERT: M 137 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5776 (mtpt) REVERT: N 11 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7136 (mm-40) REVERT: N 192 LYS cc_start: 0.7583 (ptpp) cc_final: 0.6990 (pttp) REVERT: N 193 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6565 (ttt90) REVERT: P 23 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7374 (mpp-170) REVERT: P 75 GLU cc_start: 0.8253 (tt0) cc_final: 0.8010 (tt0) REVERT: P 140 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6895 (mt-10) REVERT: R 82 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7687 (mppt) REVERT: S 60 SER cc_start: 0.7096 (t) cc_final: 0.6802 (p) REVERT: S 85 SER cc_start: 0.5686 (m) cc_final: 0.5443 (t) REVERT: S 110 MET cc_start: 0.8115 (mmm) cc_final: 0.7611 (mmm) REVERT: U 74 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6806 (tppp) REVERT: V 59 MET cc_start: 0.8319 (mmm) cc_final: 0.7987 (mmp) REVERT: V 109 MET cc_start: 0.7359 (mmp) cc_final: 0.7086 (mmp) REVERT: V 120 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7226 (ttpp) REVERT: W 43 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.5119 (mt) REVERT: W 46 ASP cc_start: 0.4654 (OUTLIER) cc_final: 0.4323 (m-30) REVERT: W 56 ILE cc_start: 0.5826 (mm) cc_final: 0.5599 (mm) REVERT: W 85 TYR cc_start: 0.4812 (OUTLIER) cc_final: 0.2737 (t80) REVERT: W 109 VAL cc_start: 0.5421 (OUTLIER) cc_final: 0.5167 (p) REVERT: W 121 ARG cc_start: 0.5003 (mmp80) cc_final: 0.4719 (mmm160) REVERT: X 27 ARG cc_start: 0.6788 (mtt-85) cc_final: 0.6423 (mtp85) REVERT: Y 87 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7292 (ptpt) REVERT: Z 27 LYS cc_start: 0.7517 (mttt) cc_final: 0.6978 (tppp) REVERT: a 135 GLU cc_start: 0.7472 (tt0) cc_final: 0.7146 (tt0) REVERT: b 3 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4886 (mp) REVERT: b 38 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6484 (mtmm) REVERT: b 60 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6590 (tptp) REVERT: b 82 MET cc_start: 0.6026 (mtt) cc_final: 0.5273 (mmt) REVERT: b 88 LYS cc_start: 0.6023 (tttp) cc_final: 0.5749 (tttp) REVERT: b 106 GLU cc_start: 0.6178 (tt0) cc_final: 0.5960 (tt0) REVERT: b 141 LYS cc_start: 0.6909 (mtmt) cc_final: 0.6619 (mttt) REVERT: b 146 PRO cc_start: 0.6496 (Cg_exo) cc_final: 0.6105 (Cg_endo) REVERT: b 220 ASP cc_start: 0.6644 (t0) cc_final: 0.6148 (t0) REVERT: b 328 VAL cc_start: 0.5730 (m) cc_final: 0.5388 (p) REVERT: b 442 TYR cc_start: 0.7504 (m-80) cc_final: 0.7229 (m-80) REVERT: b 448 GLU cc_start: 0.4985 (pm20) cc_final: 0.4551 (pt0) REVERT: b 503 MET cc_start: 0.6077 (mtp) cc_final: 0.5864 (mtp) REVERT: b 504 ILE cc_start: 0.6043 (OUTLIER) cc_final: 0.5757 (mt) REVERT: b 519 MET cc_start: 0.4915 (mmm) cc_final: 0.3915 (mmm) REVERT: c 16 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6306 (tt) REVERT: c 55 GLU cc_start: 0.7148 (tt0) cc_final: 0.6846 (tt0) REVERT: d 7 VAL cc_start: 0.7329 (t) cc_final: 0.6851 (t) REVERT: d 74 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7167 (ttm170) REVERT: e 67 SER cc_start: 0.8001 (m) cc_final: 0.7765 (p) REVERT: e 80 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7496 (ttpt) REVERT: f 92 LYS cc_start: 0.8160 (pttm) cc_final: 0.7878 (tttt) REVERT: g 19 LYS cc_start: 0.8182 (mmtm) cc_final: 0.7931 (mttm) REVERT: g 51 LEU cc_start: 0.7822 (pt) cc_final: 0.7455 (mp) REVERT: g 60 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7427 (tmt170) REVERT: g 61 GLN cc_start: 0.8412 (mt0) cc_final: 0.8092 (mt0) REVERT: g 64 THR cc_start: 0.7824 (m) cc_final: 0.7526 (p) REVERT: i 42 SER cc_start: 0.8319 (p) cc_final: 0.8112 (m) REVERT: j 32 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8093 (mtpt) REVERT: k 16 ARG cc_start: 0.6165 (mtm110) cc_final: 0.5827 (mtm110) REVERT: k 29 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7235 (mtpt) REVERT: k 74 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6511 (tttp) REVERT: n 34 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8038 (mtm180) REVERT: n 54 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7732 (mtpt) REVERT: n 120 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6656 (mt-10) REVERT: n 133 ASP cc_start: 0.6376 (OUTLIER) cc_final: 0.6062 (p0) REVERT: n 154 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7519 (ttpt) REVERT: n 453 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.5984 (tp) REVERT: o 104 GLU cc_start: 0.6642 (mp0) cc_final: 0.6169 (mp0) REVERT: o 118 LYS cc_start: 0.5276 (mtpt) cc_final: 0.4840 (tptp) REVERT: o 124 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7138 (mtp85) REVERT: p 7 LYS cc_start: 0.6760 (ttpt) cc_final: 0.6487 (ttpt) REVERT: p 25 GLN cc_start: 0.7228 (mt0) cc_final: 0.6962 (tt0) REVERT: p 28 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6777 (ttmt) REVERT: p 29 LEU cc_start: 0.8252 (mp) cc_final: 0.7981 (mp) REVERT: q 351 GLU cc_start: 0.3568 (mt-10) cc_final: 0.1812 (mm-30) REVERT: q 383 LEU cc_start: 0.5569 (tp) cc_final: 0.5365 (tp) REVERT: q 386 LYS cc_start: 0.5459 (OUTLIER) cc_final: 0.5054 (pttm) REVERT: q 452 LYS cc_start: 0.5741 (ttmm) cc_final: 0.5503 (tptm) REVERT: r 8 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6627 (mp0) REVERT: r 150 MET cc_start: 0.4104 (ptm) cc_final: 0.3791 (tmm) REVERT: s 5 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7214 (tttm) REVERT: s 7 GLN cc_start: 0.7299 (mm110) cc_final: 0.6877 (mt0) REVERT: t 48 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6669 (tttt) REVERT: t 97 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.4600 (mttm) REVERT: t 207 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7704 (mp) REVERT: t 253 GLU cc_start: 0.4717 (OUTLIER) cc_final: 0.4513 (tp30) REVERT: u 104 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7164 (tm-30) REVERT: w 380 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.6048 (mtpt) REVERT: w 711 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6553 (tttm) REVERT: w 815 LYS cc_start: 0.5954 (mmmt) cc_final: 0.5674 (mtmt) REVERT: y 1 MET cc_start: 0.4912 (mtm) cc_final: 0.4542 (mtt) REVERT: y 4 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6435 (mtt90) REVERT: y 8 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: y 126 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6206 (mt-10) outliers start: 312 outliers final: 223 residues processed: 1226 average time/residue: 2.1325 time to fit residues: 3597.6039 Evaluate side-chains 1289 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1012 time to evaluate : 6.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 233 GLN Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 137 LYS Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 43 LEU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 504 ILE Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 15 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 364 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 122 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 396 ILE Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain r residue 216 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 253 GLU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 293 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 391 THR Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 711 LYS Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 616 optimal weight: 6.9990 chunk 993 optimal weight: 5.9990 chunk 606 optimal weight: 6.9990 chunk 471 optimal weight: 20.0000 chunk 690 optimal weight: 0.0170 chunk 1042 optimal weight: 5.9990 chunk 959 optimal weight: 1.9990 chunk 829 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 640 optimal weight: 10.0000 chunk 508 optimal weight: 6.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- 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 183 HIS L 114 GLN M 41 GLN ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN 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 n 69 GLN q 230 ASN t 209 GLN t 291 GLN u 5 GLN u 110 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 133419 Z= 0.234 Angle : 0.616 11.819 194286 Z= 0.320 Chirality : 0.039 0.291 24157 Planarity : 0.005 0.060 13679 Dihedral : 22.666 179.357 54102 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 4.31 % Allowed : 18.15 % Favored : 77.54 % 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: 0.46 (0.09), residues: 7630 helix: 1.52 (0.09), residues: 3176 sheet: -0.23 (0.15), residues: 1014 loop : -0.64 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP q 234 HIS 0.010 0.001 HIS S 122 PHE 0.030 0.002 PHE B 67 TYR 0.032 0.002 TYR S 41 ARG 0.009 0.001 ARG b 144 ********************** 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 1302 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1015 time to evaluate : 6.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.6004 (mttt) cc_final: 0.5527 (mtpm) REVERT: A 104 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6884 (mp) REVERT: A 156 LYS cc_start: 0.5926 (ttmt) cc_final: 0.5712 (tttt) REVERT: B 34 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7402 (tppp) REVERT: B 74 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6966 (mm-30) REVERT: B 318 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7336 (mttp) REVERT: C 272 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 319 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7122 (tttt) REVERT: C 338 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7363 (mmpt) REVERT: E 77 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7199 (mtp-110) REVERT: E 89 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7678 (m) REVERT: E 143 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5916 (mmmt) REVERT: E 148 GLU cc_start: 0.5919 (tp30) cc_final: 0.5160 (tp30) REVERT: F 55 TYR cc_start: 0.8341 (m-10) cc_final: 0.7613 (m-10) REVERT: G 65 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7904 (mt) REVERT: G 111 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.6147 (mttp) REVERT: G 208 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6358 (mm-30) REVERT: H 51 GLN cc_start: 0.7240 (mp-120) cc_final: 0.6983 (mp10) REVERT: H 69 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7138 (tpt90) REVERT: H 91 ARG cc_start: 0.7340 (mtm110) cc_final: 0.6821 (mtp-110) REVERT: H 183 HIS cc_start: 0.6802 (t-90) cc_final: 0.6597 (t70) REVERT: K 39 LYS cc_start: 0.4525 (mtmt) cc_final: 0.4013 (mtpm) REVERT: K 76 LYS cc_start: 0.5451 (OUTLIER) cc_final: 0.4892 (tppp) REVERT: K 133 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.5330 (ptpp) REVERT: K 153 GLU cc_start: 0.4632 (mt-10) cc_final: 0.4272 (tt0) REVERT: L 52 ASP cc_start: 0.8367 (p0) cc_final: 0.7932 (p0) REVERT: L 136 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5811 (mp0) REVERT: L 160 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.6170 (mt0) REVERT: M 82 SER cc_start: 0.8414 (t) cc_final: 0.8194 (m) REVERT: M 92 GLU cc_start: 0.7122 (mp0) cc_final: 0.6823 (mp0) REVERT: M 137 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5756 (mtpt) REVERT: N 11 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7126 (mm-40) REVERT: N 192 LYS cc_start: 0.7516 (ptpp) cc_final: 0.6955 (pttp) REVERT: N 193 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6560 (ttt90) REVERT: P 23 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7542 (mpp-170) REVERT: P 75 GLU cc_start: 0.8264 (tt0) cc_final: 0.7928 (tt0) REVERT: P 140 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6876 (mt-10) REVERT: R 82 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7675 (mppt) REVERT: S 60 SER cc_start: 0.7095 (t) cc_final: 0.6810 (p) REVERT: S 85 SER cc_start: 0.5750 (m) cc_final: 0.5494 (t) REVERT: S 110 MET cc_start: 0.8124 (mmm) cc_final: 0.7615 (mmm) REVERT: U 74 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6805 (tppp) REVERT: V 59 MET cc_start: 0.8327 (mmm) cc_final: 0.7998 (mmp) REVERT: V 109 MET cc_start: 0.7436 (mmp) cc_final: 0.7157 (mmp) REVERT: V 120 LYS cc_start: 0.7378 (ttpt) cc_final: 0.7126 (ttpp) REVERT: W 46 ASP cc_start: 0.4520 (OUTLIER) cc_final: 0.4186 (m-30) REVERT: W 56 ILE cc_start: 0.5832 (mm) cc_final: 0.5565 (mm) REVERT: W 85 TYR cc_start: 0.4805 (OUTLIER) cc_final: 0.2732 (t80) REVERT: W 109 VAL cc_start: 0.5406 (OUTLIER) cc_final: 0.5147 (p) REVERT: W 121 ARG cc_start: 0.4996 (mmp80) cc_final: 0.4715 (mmm160) REVERT: X 27 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.6470 (mtp85) REVERT: X 77 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: Y 87 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7265 (ptpt) REVERT: Z 27 LYS cc_start: 0.7508 (mttt) cc_final: 0.6972 (tppp) REVERT: a 135 GLU cc_start: 0.7470 (tt0) cc_final: 0.7141 (tt0) REVERT: b 3 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.4842 (mp) REVERT: b 38 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6479 (mtmm) REVERT: b 60 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6572 (tptp) REVERT: b 82 MET cc_start: 0.6033 (mtt) cc_final: 0.5239 (mmt) REVERT: b 88 LYS cc_start: 0.5999 (tttp) cc_final: 0.5727 (tttp) REVERT: b 106 GLU cc_start: 0.6138 (tt0) cc_final: 0.5874 (tt0) REVERT: b 141 LYS cc_start: 0.6902 (mtmt) cc_final: 0.6617 (mttt) REVERT: b 146 PRO cc_start: 0.6507 (Cg_exo) cc_final: 0.6124 (Cg_endo) REVERT: b 220 ASP cc_start: 0.6621 (t0) cc_final: 0.6119 (t0) REVERT: b 328 VAL cc_start: 0.5674 (m) cc_final: 0.5331 (p) REVERT: b 442 TYR cc_start: 0.7500 (m-80) cc_final: 0.7229 (m-80) REVERT: b 448 GLU cc_start: 0.4978 (pm20) cc_final: 0.4545 (pt0) REVERT: b 503 MET cc_start: 0.6080 (mtp) cc_final: 0.5821 (mtp) REVERT: b 504 ILE cc_start: 0.6049 (OUTLIER) cc_final: 0.5753 (mt) REVERT: b 519 MET cc_start: 0.4836 (mmm) cc_final: 0.3836 (mmm) REVERT: c 16 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6255 (tt) REVERT: c 55 GLU cc_start: 0.7125 (tt0) cc_final: 0.6857 (tt0) REVERT: d 7 VAL cc_start: 0.7321 (t) cc_final: 0.6836 (t) REVERT: d 74 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7136 (ttm170) REVERT: e 67 SER cc_start: 0.8000 (m) cc_final: 0.7768 (p) REVERT: e 80 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7477 (ttpt) REVERT: f 92 LYS cc_start: 0.8150 (pttm) cc_final: 0.7886 (tttt) REVERT: g 19 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7928 (mttm) REVERT: g 51 LEU cc_start: 0.7829 (pt) cc_final: 0.7377 (mp) REVERT: g 60 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7385 (tmt170) REVERT: g 61 GLN cc_start: 0.8413 (mt0) cc_final: 0.8099 (mt0) REVERT: g 64 THR cc_start: 0.7824 (m) cc_final: 0.7528 (p) REVERT: j 32 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: k 16 ARG cc_start: 0.6192 (mtm110) cc_final: 0.5856 (mtm110) REVERT: k 29 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7214 (mtpt) REVERT: k 74 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6496 (tttp) REVERT: n 34 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8035 (mtm180) REVERT: n 54 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7743 (mtpt) REVERT: n 120 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6674 (mt-10) REVERT: n 133 ASP cc_start: 0.6419 (OUTLIER) cc_final: 0.6100 (p0) REVERT: n 193 LYS cc_start: 0.5562 (OUTLIER) cc_final: 0.4458 (tptt) REVERT: n 453 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.5982 (tp) REVERT: o 104 GLU cc_start: 0.6590 (mp0) cc_final: 0.6109 (mp0) REVERT: o 118 LYS cc_start: 0.5251 (mtpt) cc_final: 0.4852 (tptp) REVERT: o 124 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7075 (mtp85) REVERT: p 7 LYS cc_start: 0.6752 (ttpt) cc_final: 0.6480 (ttpt) REVERT: p 25 GLN cc_start: 0.7107 (mt0) cc_final: 0.6875 (tt0) REVERT: p 28 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6801 (ttmt) REVERT: p 29 LEU cc_start: 0.8244 (mp) cc_final: 0.7974 (mp) REVERT: q 351 GLU cc_start: 0.3566 (mt-10) cc_final: 0.1806 (mm-30) REVERT: q 383 LEU cc_start: 0.5669 (tp) cc_final: 0.5446 (tp) REVERT: q 386 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.5003 (pttm) REVERT: q 452 LYS cc_start: 0.5744 (ttmm) cc_final: 0.5378 (tptm) REVERT: r 8 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6594 (mp0) REVERT: r 150 MET cc_start: 0.4103 (ptm) cc_final: 0.3828 (tmm) REVERT: s 5 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7212 (tttm) REVERT: s 7 GLN cc_start: 0.7294 (mm110) cc_final: 0.6872 (mt0) REVERT: t 48 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6790 (tttt) REVERT: t 97 LYS cc_start: 0.5441 (OUTLIER) cc_final: 0.4577 (mttm) REVERT: t 207 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7713 (mp) REVERT: u 104 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7162 (tm-30) REVERT: w 380 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6044 (mtpt) REVERT: w 711 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6564 (tttm) REVERT: w 815 LYS cc_start: 0.5930 (mmmt) cc_final: 0.5652 (mtmt) REVERT: y 1 MET cc_start: 0.4886 (mtm) cc_final: 0.4398 (mtt) REVERT: y 4 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6422 (mtt90) REVERT: y 8 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6237 (mp0) outliers start: 287 outliers final: 214 residues processed: 1204 average time/residue: 2.1306 time to fit residues: 3536.8863 Evaluate side-chains 1275 residues out of total 6661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1008 time to evaluate : 6.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 233 GLN Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 137 LYS Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 85 TYR Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 195 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 167 THR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 201 THR Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 504 ILE Chi-restraints excluded: chain b residue 506 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain n residue 34 ARG Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 204 LYS Chi-restraints excluded: chain n residue 242 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 364 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 122 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 227 TYR Chi-restraints excluded: chain q residue 248 ARG Chi-restraints excluded: chain q residue 386 LYS Chi-restraints excluded: chain q residue 396 ILE Chi-restraints excluded: chain q residue 406 LEU Chi-restraints excluded: chain q residue 419 THR Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 151 ILE Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain r residue 216 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 207 LEU Chi-restraints excluded: chain t residue 239 LEU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain w residue 293 LEU Chi-restraints excluded: chain w residue 304 ILE Chi-restraints excluded: chain w residue 365 LEU Chi-restraints excluded: chain w residue 380 LYS Chi-restraints excluded: chain w residue 391 THR Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 711 LYS Chi-restraints excluded: chain w residue 724 LYS Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 100 ARG Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 659 optimal weight: 4.9990 chunk 883 optimal weight: 0.0060 chunk 254 optimal weight: 10.0000 chunk 765 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 30.0000 chunk 831 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 chunk 853 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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 ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN R 27 ASN R 34 GLN R 36 ASN S 122 HIS S 157 GLN 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 n 69 GLN q 230 ASN t 209 GLN t 291 GLN u 110 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.184405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.136840 restraints weight = 107920.974| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.58 r_work: 0.3145 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 133419 Z= 0.166 Angle : 0.542 11.635 194286 Z= 0.284 Chirality : 0.036 0.273 24157 Planarity : 0.004 0.058 13679 Dihedral : 22.525 179.055 54102 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.31 % Rotamer: Outliers : 3.63 % Allowed : 18.86 % Favored : 77.51 % 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: 0.73 (0.09), residues: 7630 helix: 1.78 (0.09), residues: 3175 sheet: -0.19 (0.15), residues: 1013 loop : -0.50 (0.10), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP q 234 HIS 0.008 0.001 HIS C 311 PHE 0.021 0.001 PHE B 67 TYR 0.030 0.002 TYR S 41 ARG 0.009 0.000 ARG b 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47672.03 seconds wall clock time: 823 minutes 32.35 seconds (49412.35 seconds total)